diff --git a/.aspell-api-exceptions.pws b/.aspell-api-exceptions.pws
new file mode 100644
index 0000000000000000000000000000000000000000..2f5c04dda5012ffb8eea710c86fc5a2bf661a38e
--- /dev/null
+++ b/.aspell-api-exceptions.pws
@@ -0,0 +1,703 @@
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diff --git a/.aspell.en.pws b/.aspell.en.pws
new file mode 100644
index 0000000000000000000000000000000000000000..d55156159364099eba8cb9d180d7bd8b5a01dd1c
--- /dev/null
+++ b/.aspell.en.pws
@@ -0,0 +1,568 @@
+personal_ws-1.1 en 0 utf-8
+Acetosalic
+ACETYLOXY
+ACETYLSALIC
+Acetylsalicylic
+ACETYLSALICYLIC
+ACETYLSALICYLICUM
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+url
+urlencoded
+urls
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+UTF
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+VAZALORE
+Vbase
+VBRC
+Vetinary
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+ViralZone
+VIRsiRNA
+vmh
+webpage
+whitespace
+WikiGenes
+Worfdb
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diff --git a/.gitignore b/.gitignore
index 086453b02d6c62843ccb976bbeac9ebf476e8ff1..3193dd9a22fbecf20f4ef209c5a3739c68d03a2d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,6 +16,7 @@ service/minerva-big/
#eclipse files
.classpath
.settings
+.externalToolBuilders
#maven build files
target/
@@ -28,3 +29,6 @@ debian/src/*.sql
#rpm build files
rpm/rpmbuildtemp/
+
+#local test
+web/src/test/java/lcsb/mapviewer/web/TestXXX.java
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9cc9e8425e1690a6ca7b625230ebcc513ce1a7f6..2d6c98f81d2b348d7e8238bd651b45b144ab543f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -589,3 +589,11 @@ test_postgres_14_compatibility:
<<: *test_database_definition
services:
- postgres:14
+
+changelog_spelling:
+ image: debian
+ stage: test
+ script:
+ - apt-get update
+ - apt-get install -y aspell aspell-en
+ - ./test_spelling.sh
diff --git a/CHANGELOG b/CHANGELOG
index 2c038263d1ed5a2c3c77cc77a7a0bb1004847d3c..0bc4cdd6dc60aa246c827d3616879d2e1b259cd0 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -13,9 +13,91 @@ minerva (16.3.0) unstable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 27 Jun 2022 15:00:00 +0200
+minerva (16.2.10) stable; urgency=medium
+ * Bug fix (API documentation): typos in API documentation corrected (#1806)
+ * Bug fix (API documentation): header in logout method change to keep
+ consistency with other methods (#1806)
+ * Bug fix (API documentation): missing information about genomeId added when
+ adding gene mapping (#1807)
+ * Bug fix: exporting map with data overlay coloring did not work (#1817)
+ * Bug fix: non-numeric character in pubmed id prevent publications from
+ being downloaded (#1802)
+ * Bug fix: line width was ignored when fetching information about advanced
+ data overlay (#1742)
+ * Bug fix: global xml namespace definition caused MINERVA to fail on
+ processing model notes (#1804)
+ * Bug fix: genetic data overlays from zip input did not contain proper info
+ about genome (#1815)
+ * Bug fix: overlay genetic data that contained multiple matches (for example
+ two different uniprot ID for the same gene) caused problem when visualizing
+ genome browser (#1815)
+ * Bug fix: when exporting elements the list of selected excluded/included
+ compartments was too long then the error was raised (#1798)
+ * Bug fix: when merged results in left panel contained different submap link
+ minerva crashed (#1764)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 25 Jan 2023 12:00:00 +0200
+
+minerva (16.2.9) stable; urgency=medium
+ * Bug fix (API documentation): authentication token is not needed (and
+ misleading) when accessing list of projects from guest account (#1775)
+ * Bug fix (API documentation): missing authentication token in logout
+ sample (#1775)
+ * Bug fix (API documentation): when starting downloading genome data the
+ response fields is empty and unnecessary (#1775)
+ * Bug fix (API documentation): information where genomeId can be found
+ added (#1775)
+ * Bug fix (API documentation): information where geneMappingId can be
+ found added (#1775)
+ * Bug fix (API documentation): when creating user use better user password
+ example (#1775)
+ * Bug fix (API documentation): when creating user list of parameters was
+ wrong (#1775)
+ * Bug fix (API documentation): remove unnecessary "-i" option in curl
+ examples (#1775)
+ * Bug fix: parsing GPML file with unknown ShapeType caused errors during
+ parsing (#1776)
+ * Bug fix: information about layers was not merged in merge API call (#1771)
+ * Bug fix: downloading model with limited list of reactions and elements
+ downloaded also text areas (#1770)
+ * Bug fix: when CellDesigner species contained notes in both Species and Gene
+ tags the notes were improperly parsed and could cause issues on export
+ (#1772, #1772)
+ * Bug fix: when the last cell in the last column of overlay data entered in
+ the upload dialog is empty there was an unexpected (#1743)
+ * Bug fix: disable delete plugin button when removing plugin (#1766)
+ * Bug fix: removing non existing overlay caused an error (#1791)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Sat, 22 Oct 2022 11:00:00 +0200
+
+minerva (16.2.8) stable; urgency=medium
+ * Bug fix: missing content-type header in REST API documentation caused
+ issues with converter API (#1745, #1754, #1759, #1755)
+ * Bug fix: MINERVA_AUTH token in REST API documentation was sometimes
+ missing and sometimes it was unnecessary (#1744)
+ * Bug fix: deprecated "semantic-zoom" changed to
+ "semantic-zoom-contains-multiple-layouts" in REST API documentation for
+ project upload (#1754)
+ * Bug fix: export to SBML did not work with empty complexes containing the
+ same structural state (#1757, #1756)
+ * Bug fix: updating user plugin data did not work (#1739)
+ * Bug fix: legend was not visualized properly for mix of defined and
+ undefined colors in overlay (#1749)
+ * Bug fix: misleading "undefined maps" removed from submaps tab (#1703)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 09 Sep 2022 10:00:00 +0200
+
+minerva (16.2.7) stable; urgency=medium
+ * Bug fix: when providing problematic input file in REST API converter the
+ status code should be 400 (BAD REQUEST) instead of 500
+ * Bug fix: default curl content type (application/x-www-form-urlencoded)
+ caused issues when using converter API (#1734)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Thu, 21 Jul 2022 11:00:00 +0200
+
minerva (16.2.6) stable; urgency=medium
- * Bug fix: partial update on defaultCenterX and defaultCenterY and defaultZoomLevel
- did not work
+ * Bug fix: partial update on defaultCenterX and defaultCenterY and
+ defaultZoomLevel did not work
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 7 Jul 2022 11:00:00 +0200
@@ -26,7 +108,7 @@ minerva (16.2.5) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 6 Jul 2022 16:00:00 +0200
minerva (16.2.4) stable; urgency=medium
- * Bug fix: rest api of uniprot.org changed
+ * Bug fix: rest API of UniProt changed
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 5 Jul 2022 14:00:00 +0200
@@ -35,7 +117,7 @@ minerva (16.2.3) stable; urgency=medium
annotators (#1722)
* Bug fix: modification residue id must start with a letter when exporting to
CellDesigner
- * Bug fix: expot to SBML did not work for cmaps that had two or more complexes
+ * Bug fix: export to SBML did not work for maps that had two or more complexes
with the same children that had modification residues (#1720)
* Bug fix: when providing invalid url in gene mapping proper error message is
shown (#1723)
@@ -54,7 +136,7 @@ minerva (16.2.2) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 20 Jun 2022 12:00:00 +0200
minerva (16.2.1) stable; urgency=medium
- * Bug fix: Kegg annotator stopped working after kegg moved to https
+ * Bug fix: Kegg annotator stopped working after Kegg moved to https
* Bug fix: General overlays were marked as editable even though they should
not be (#1706, #1702)
* Bug fix: searching for non existing chemical caused an error to be thrown
@@ -240,7 +322,7 @@ minerva (16.1.0) stable; urgency=medium
* Bug fix: help dialog is closed automatically after Add Project dialog is
closed (#1099)
* Bug fix: root url must be valid url pointing to minerva instance (#1689)
- * Bug fix: there were missing lines when exporting truncation/dissotiation
+ * Bug fix: there were missing lines when exporting truncation/dissociation
reaction to GPML (#1676)
* Bug fix: some SBML files were recognized as CellDesigner files (#1677)
* Bug fix: reaction middle was not highlighted (#1637)
@@ -390,8 +472,8 @@ minerva (16.0.0) stable; urgency=medium
* Small improvement: homomultimer information is provided in API (#1468)
* Small improvement: missing info about species for SBML parsing warning
(#1472)
- * Small improvement: information about dimer in sbgn is provided only once
- if the information is duplicated in sbgn data (#1358)
+ * Small improvement: information about dimer in SBGN is provided only once
+ if the information is duplicated in SBGN data (#1358)
* Small improvement: glyph quality is improved (#1458)
* Small improvement: search results are group by diagram (#1451)
* Small improvement: "Failed to fetch" errors are reported in a way that
@@ -421,7 +503,7 @@ minerva (16.0.0) stable; urgency=medium
caused issue (#1546)
* Bug fix: search results were limited to 10 elements
* Bug fix: Chrome autofill is disabled for "Search: " in admin panel tables
- * Bug fix: search tab becomes active when drug/chemical/mirna result are
+ * Bug fix: search tab becomes active when drug/chemical/MiRNA result are
available (#1491)
* Bug fix: arrows without a "process" box had an irregular empty space in
their lines (#1471)
@@ -434,7 +516,7 @@ minerva (16.0.0) stable; urgency=medium
* Bug fix: removing plugin that does not exist anymore does not raise an error
(#1289)
* Bug fix: md5 hash function of plugin was not computed properly
- * Bug fix: exported gpml for every compartment contained list of species name
+ * Bug fix: exported GPML for every compartment contained list of species name
in the comment section
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 29 Oct 2021 13:00:00 +0200
@@ -479,14 +561,14 @@ minerva (15.1.1) stable; urgency=medium
* Bug fix: zoom level change was not reflected in the url when submap was
opened (#1338)
* Bug fix: API call returning list of overlays returned for non existing
- project returned access denied status insted Not Found (#1370)
- * Bug fix: results for chembl targetting uniprot without gene name (for
+ project returned access denied status instead Not Found (#1370)
+ * Bug fix: results for chembl targetting UniProt without gene name (for
example P0C2L1) could crash caching (#1377)
* Bug fix: removing non-existing project results in warning not an error
message (#1367)
* Bug fix: opening map in google maps without background resulted in
unexpected error (#1416)
- * Bug fix: normal user could not update tos information (#1419)
+ * Bug fix: normal user could not update ToS information (#1419)
* Bug fix: and operator in SBGN-like view was not drawn (#1408)
* Bug fix: export of overlayed map as an image did not respect overlay colors
(#1417)
@@ -558,15 +640,15 @@ minerva (15.0.3) stable; urgency=medium
* Bug fix: when there is a problem with minerva deployment on tomcat proper
warning message is presented in admin panel (#1332)
* Bug fix: API call updating user preferences did not handle properly
- conflicts on new gui properties (#1326)
- * Bug fix: "bqbiol:hasTaxon" relation type is not supported by CellDedigner
+ conflicts on new GUI properties (#1326)
+ * Bug fix: "bqbiol:hasTaxon" relation type is not supported by CellDesigner
and is now transformed during export into something readable by
CellDesigner (#1281)
* Bug fix: concurrency issue that could happen rarely on first search of the
map and put the project into "unsearchable" state is fixed (#1333)
- * Bug fix: when edit project buton was clicked on project that was removed in
+ * Bug fix: when edit project button was clicked on project that was removed in
another tab there was an error thrown (#1343)
- * Bug fix: chebi and entrez annotations were incorrectly exported to GPML
+ * Bug fix: CHEBI and Entrez annotations were incorrectly exported to GPML
(#1349)
* Bug fix: exporting to GPML sometimes resulted in invalid modification point
end for catalysis (#1350)
@@ -597,11 +679,11 @@ minerva (15.0.2) stable; urgency=medium
not handled properly (#1281)
* Bug fix: "bqmodel:isInstanceOf", "bqmodel:hasInstance",
"bqbiol:hasProperty", "bqbiol:isPropertyOf" relation types are not
- supported by CellDedigner and are now transformed during export into
+ supported by CellDesigner and are now transformed during export into
something readable by CellDesigner (#1281)
* Bug fix: at random time points there was an issue with cached data (#1323)
* Bug fix: connection to DAPI timeouted sometimes which resulted in error
- when checking for all chemicals for specfific protein (#1324)
+ when checking for all chemicals for specific protein (#1324)
* Bug fix: complex/compartment with empty name was incorrectly exported to
CellDesigner (#1310)
@@ -680,7 +762,7 @@ minerva (15.0.0) stable; urgency=medium
* Small improvement: simple molecules in SBGN compliant view are drawn as
ellipses not circles (#796)
* Small improvement: uploaded map is automatically cached (#983)
- * Small improvement: molart updated to version 1.5.0: Ability to show
+ * Small improvement: MolArt updated to version 1.5.0: Ability to show
unobserved structure regions in the sequence view.
* Small improvement: list of genomes is automatically refreshed during genome
upload (#820)
@@ -717,7 +799,7 @@ minerva (15.0.0) stable; urgency=medium
* Bug fix: newt use incorrect attributes when exporting render information
that could not be parsed by minerva (#1127)
* Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
- * Bug fix: antisenseRNA shape is inferred from SBGN when antisenseRNA text is
+ * Bug fix: antisense RNA shape is inferred from SBGN when antisense RNA text is
present in glyph label (#1114)
* Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126)
* Bug fix: CellDesigner models where start and end point of reaction was the
@@ -766,9 +848,9 @@ minerva (14.0.13) stable; urgency=medium
minerva (14.0.12) stable; urgency=medium
* Bug fix: comments on submaps were not visible (#1230)
* Bug fix: removing comment from submap did not work
- * Bug fix: reaction name containing "<" character was exported inproperly to
+ * Bug fix: reaction name containing "<" character was exported improperly to
CellDesigner (#1227)
- * Bug fix: doi annotation was inproperly parsed from CellDesigner file and
+ * Bug fix: DOI annotation was improperly parsed from CellDesigner file and
resulted in not clickable link (#1231)
* Bug fix: when plugin data was too big 500 error was returned (#1232)
* Bug fix: removing plugin in admin panel removes it from server permanently
@@ -777,7 +859,7 @@ minerva (14.0.12) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 11 May 2020 17:00:00 +0200
minerva (14.0.11) stable; urgency=medium
- * Bug fix: complex with no border was inproperly imported from CellDesigner
+ * Bug fix: complex with no border was improperly imported from CellDesigner
(#1198)
* Bug fix: export to CellDesigner deal with CellDesigner issue that does not
allow compartment species alias to be shorter than 2 characters (#1204)
@@ -785,7 +867,7 @@ minerva (14.0.11) stable; urgency=medium
minerva (#1202)
* Bug fix: infinity value in kinetic parameter could not be parsed from
CellDesigner file minerva (#1203)
- * Bug fix: author list inproperly presented author data when some fields were
+ * Bug fix: author list improperly presented author data when some fields were
missing (#1201)
* Bug fix: refreshing minerva page with more than one plugin opened might
led to an error due to race condition (#1197)
@@ -801,7 +883,7 @@ minerva (14.0.10) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 16 Mar 2020 14:00:00 +0200
minerva (14.0.9) stable; urgency=medium
- * Bug fix: simultanous export to SBML of more than one file could result in
+ * Bug fix: simultaneous export to SBML of more than one file could result in
500 Internal Server Error (#1110)
* Bug fix: refresh data overlay did not hide data overlays that were removed
and selected (#1097)
@@ -832,7 +914,7 @@ minerva (14.0.9) stable; urgency=medium
minerva (14.0.8) stable; urgency=medium
* Bug fix: API didn't allow to upload plugins with local url (#1084,
regression 14.0.7)
- * Bug fix: upload of data overlay with two entries having different uniprot
+ * Bug fix: upload of data overlay with two entries having different UniProt
identifier but pointing to the same gene crashed (#1083)
* Bug fix: don't allow to remove plugin twice (#1081)
* Bug fix: upload of SBML file with very short reaction length could produce
@@ -866,13 +948,13 @@ minerva (14.0.6) stable; urgency=medium
* Bug fix: search by identifier didn't consider identifiers added by
annotators (#1047)
* Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not
- displayed at all (regresion 14.0.5, #1045)
+ displayed at all (regression 14.0.5, #1045)
* Bug fix: when there is a problem with database during removing project,
project removal doesn't hang (#1058)
* Bug fix: coloring of the reaction wasn't applied to center of reaction
(regression 14.0.0, #1057)
* Bug fix: genetic variant overlay improperly processed elements identified
- by miriam identifiers, like uniprot (#1059)
+ by miriam identifiers, like UniProt (#1059)
* Bug fix: invalid information was provided for genetic variants overlay when
map organism was defined (#1060)
@@ -881,7 +963,7 @@ minerva (14.0.6) stable; urgency=medium
minerva (14.0.5) stable; urgency=medium
* Bug fix: copy-paste of genetic-variant data overlay into Add overlay
content dialog could crash upload (#1040)
- * Bug fix: some annotators (like Cazy) were crashing on old installations
+ * Bug fix: some annotators (like CAZy) were crashing on old installations
(#1029)
* Bug fix: uploading a map that breaks postgres constraints hung upload of
the project (#1028)
@@ -891,7 +973,7 @@ minerva (14.0.5) stable; urgency=medium
* Bug fix: search for NADH drug resulted in drug with empty name (#1018)
* Bug fix: export to SBML didn't handle properly arrows (#1015)
* Bug fix: Font colour of text area was preserved in Empty view (#1014)
- * Bug fix: exported sbml file always contain model identifier (#1013)
+ * Bug fix: exported SBML file always contain model identifier (#1013)
* Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0,
#1012)
* Bug fix: after loading/removing too many plugins it was impossible to load
@@ -906,7 +988,7 @@ minerva (14.0.4) stable; urgency=high
due to problems with identifiers used by SBGN (#1006)
* Bug fix: upload of data overlay with conflicting overlay types caused error
(#998)
- * Bug fix: upload of sbml file with protein modifications inside complex
+ * Bug fix: upload of SBML file with protein modifications inside complex
crashed visualization (#966)
* Bug fix: list of overlays for admin and curator included also other people
overlays (regression 14.0.3, #1008)
@@ -918,7 +1000,7 @@ minerva (14.0.4) stable; urgency=high
minerva (14.0.3) stable; urgency=medium
* Bug fix: default zoom level on main map works even when x or y are
undefined (#993)
- * Bug fix: sbml parser had sometimes problems with combining layout and multi
+ * Bug fix: SBML parser had sometimes problems with combining layout and multi
packages (#966)
* Bug fix: parsing of CellDesigner files that contained substanceUnits could
crash the upload (#985)
@@ -954,7 +1036,7 @@ minerva (14.0.2) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 15 Oct 2019 11:00:00 +0200
minerva (14.0.1) stable; urgency=medium
- * Bug fix: maps that were annotated using old Biocompendium annotator could
+ * Bug fix: maps that were annotated using old BioCompendium annotator could
not load properly (#986)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 15 Oct 2019 9:00:00 +0200
@@ -1018,7 +1100,7 @@ minerva (14.0.0) stable; urgency=medium
(#936)
* Bug fix: work on FF Private Window mode could cause logout or raise an
error on when opening new tab with minerva (#892)
- * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
+ * Bug fix: fetching list of MiRNAs resulted sometimes in "Internal Server
Error" (#889)
* Bug fix: edit project dialog verifies organism id (#914)
* Bug fix: all colors in boolean reaction (from CellDesigner) are processed
@@ -1092,7 +1174,7 @@ minerva (13.1.1) stable; urgency=medium
inside compartment (#856)
* Bug fix: searching for some drugs in chembl didn't provide any results even
though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
- * Bug fix: user wasn't logged out in all tabs when the log out event appeard
+ * Bug fix: user wasn't logged out in all tabs when the log out event appeared
in only one of them (#847)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 2 Jul 2019 19:00:00 +0200
@@ -1133,7 +1215,7 @@ minerva (13.1.0) stable; urgency=medium
(#666)
* Small improvement: list of projects is auto refreshed every 5 seconds if at
least one of the project is uploading/removing (#610)
- * Small improvement: passwords to email account and ldap are not sent over
+ * Small improvement: passwords to email account and LDAP are not sent over
API (#732)
* Small improvement: reactant/product/modifier specific colors are parsed
properly from CellDesigner file (#597)
@@ -1142,7 +1224,7 @@ minerva (13.1.0) stable; urgency=medium
* Small improvement: Info tab provides information about model annotations
and submap tabs provide information about submaps annotations if applicable
(#591)
- * Small improvement: uploading sbml file should automatically discover a file
+ * Small improvement: uploading SBML file should automatically discover a file
type (#784)
* Small improvement: when plugin listeners crash the system notifies user
about problem with a plugin (#767)
@@ -1157,19 +1239,19 @@ minerva (13.1.0) stable; urgency=medium
SemanticZoomLevelTransparency (#801)
* Small improvement: export/import from SBML support z-index in LAYOUT
extension
- * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
+ * Bug fix: due to blocking of our requests from CTD base the autocomplete for
this database is disabled
* Bug fix: deprecated columns in data overlay are not visible to the end user
(#827)
* Bug fix: invalid color in data overlay provides proper feedback to the user
(#822)
* Bug fix: genetic variant overlay without name caused problems (#832)
- * Bug fix: tair locus identifiers were used improperly - instead of id the
+ * Bug fix: Tair locus identifiers were used improperly - instead of id the
name was used
* Bug fix: plugin tab header wasn't properly resized after adding plugins
that introduced second line for tab selection (#758)
* Bug fix: invisible layer shouldn't be shown on the map (#813)
- * Bug fix: list of availbale annotators is sorted alphabetically (#815)
+ * Bug fix: list of available annotators is sorted alphabetically (#815)
* Bug fix: redirect url from export panel is fixed (#819)
* Bug fix: allow to reupload the same file without closing add overlay dialog
(#833)
@@ -1193,8 +1275,8 @@ minerva (13.1.0) stable; urgency=medium
slightly separated from target phenotype (#664)
* Bug fix: order of genomes in admin panel doesn't change after refreshing
list of genomes (#761)
- * Bug fix: fixing situation when Molart started with variation overlay not
- having the aa change information
+ * Bug fix: fixing situation when MolArt started with variation overlay not
+ having the a change information
* Bug fix: plugin contect element width is adjusted when link to tabs are
wrapped in more than one line (#758)
* Bug fix: export to CellDesigner preserve font size (#798)
@@ -1246,7 +1328,7 @@ minerva (12.2.2) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 9 Apr 2019 17:00:00 +0200
minerva (12.2.1) stable; urgency=medium
- * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
+ * Bug fix: export of reaction colors in SBML is properly encoded (COPASI can
read colors properly) (#744)
* Bug fix: removing active plugin didn't switch plugin tab to the next loaded
plugin (#757)
@@ -1317,7 +1399,7 @@ minerva (12.2.0) stable; urgency=medium
email account is provided
* Small improvement: Plugin API allows to show/hide data overlays
* Bug fix: Icons were sometimes not properly loaded on Safari (#661)
- * Bug fix: migration scripts are compatibile with postgres 9.3 version that
+ * Bug fix: migration scripts are compatible with postgres 9.3 version that
is default on Ubuntu 14 (#762)
* Bug fix: update/remove button is disabled when user has no privileges for
managing overlays (#742)
@@ -1403,7 +1485,7 @@ minerva (12.1.6) stable; urgency=medium
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Jan 2019 16:00:00 +0200
minerva (12.1.5) stable; urgency=medium
- * Bug fix: Drugbank changed output format which crashed drug connector
+ * Bug fix: DrugBank changed output format which crashed drug connector
* Bug fix: word wrapping fixed in overlay table for long overlay names
in Firefox browser
@@ -1435,8 +1517,8 @@ minerva (12.1.3) stable; urgency=medium
minerva (12.1.2) stable; urgency=medium
* Bug fix: vmh annotations should be properly matching id entered in the input
- * Bug fix: opacity was not working when highliting objects in plugins
- * Bug fix: integer configurtion options (like SMTP_PORT) are properly
+ * Bug fix: opacity was not working when highlighting objects in plugins
+ * Bug fix: integer configuration options (like SMTP_PORT) are properly
validated before saving
* Bug fix: inside of reaction box wasn't properly aligned
* Bug fix: too long data overlay name disturbed size of the map div and
@@ -1470,7 +1552,7 @@ minerva (12.1.0) stable; urgency=medium
* Small improvement: plugins have to access information about active submap
* Feature: genome browser with gene variants
* Feature: support of all CellDesigner element modifications
- * Feature: ldap authentication
+ * Feature: LDAP authentication
* Feature: multicolored anchors for data overlays
* Feature: minerva is distributed using rpm packages
* Small improvement: annotations from RHEA are handled
@@ -1482,7 +1564,7 @@ minerva (12.1.0) stable; urgency=medium
weren't provided properly
* Bug fix: passwords in the configuration tab are hidden with '*'
* Bug fix: user has access to transparency level when creating custom semantic
- view (without this parametere functionality was very difficult to use)
+ view (without this parameter functionality was very difficult to use)
* Bug fix: loading invalid plugin doesn't render empty div anymore
* Bug fix: sorting of custom overlays was broken when description of overlay
was present
@@ -1495,7 +1577,7 @@ minerva (12.1.0) stable; urgency=medium
* Bug fix: double click on user add button disabled
* Bug fix: privileges are mirrored correctly across different popups
* Bug fix: plugin tab css fixed
- * Bug fix: uploading sbml file with no ids in glyphs returned error that
+ * Bug fix: uploading SBML file with no ids in glyphs returned error that
could not be easily understand
* Bug fix: ds_store files in subfolders crashed zip upload
* Bug fix: when creating new user default privileges were not filled
@@ -1564,7 +1646,7 @@ minerva (12.0.0) stable; urgency=medium
* Feature: plugin API
* Feature: all functionalities are provided via REST API
* Feature: visualization of two (or more) overlaying results (like drug
- target, mirna target) is highlighted with different icon
+ target, MiRNA target) is highlighted with different icon
* Small improvement: email for account request contain configurable text
* Small improvement: transparency level for data overlays is configurable
* Small improvement: CellDesigner reactions of Modifier type are acceptable
@@ -1585,7 +1667,7 @@ minerva (12.0.0) stable; urgency=medium
* Small improvement: Data overlays can submap column to differentiate between
maps
* Small improvement: search by chemical names is possible
- * Small improvement: auto complete functionality for drugs, mirnas and
+ * Small improvement: auto complete functionality for drugs, MiRNAs and
chemicals
* Small improvement: columns value and type are not mutually exclusive in
data overlays
@@ -1601,7 +1683,7 @@ minerva (12.0.0) stable; urgency=medium
* Small improvement: submap reference in publication list
* Small improvement: size of connection to database reduced to 90 (so default
connection pool to postgres is not completely filled with minerva)
- * Small improvement: visualization of sbml function improved (lambda
+ * Small improvement: visualization of SBML function improved (lambda
expression removed from the definition)
* Small improvement: handling of additional miriam types from BiGG ontology
* Small improvement: configuration options are grouped in categories
@@ -1681,17 +1763,17 @@ minerva (11.0.7) stable; urgency=medium
* Bug fix: there should be no problem with symlink when upgrading debian
package
* Bug fix: number of services changed API address to https: pmceurope
- (pubmed), uniprot, ensembl, hgnc, recon, ctd database
+ (pubmed), UniProt, Ensembl, HGNC, recon, CTD database
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Jan 2018 16:00:00 +0200
minerva (11.0.6) stable; urgency=medium
- * Bug fix: fix a bug when entering invalid mirna id
+ * Bug fix: fix a bug when entering invalid MiRNA id
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Dec 2017 16:00:00 +0200
minerva (11.0.5) stable; urgency=medium
- * Bug fix: fix on connection to drugbank database
+ * Bug fix: fix on connection to DrugBank database
* Bug fix: posttranslational modification data was sometimes unavailable
in search results panel
@@ -1710,7 +1792,7 @@ minerva (11.0.3) stable; urgency=medium
* Bug fix: links to invalid annotations were opening invalid web page
* Bug fix: service resolving miriam resources doesn't work over http
anymore
- * Bug fix: chebi annotator doesn't work over http anymore
+ * Bug fix: CHEBI annotator doesn't work over http anymore
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Oct 2017 13:50:00 +0200
@@ -1728,7 +1810,7 @@ minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
by the user login
- * Bug fix: sbgn import
+ * Bug fix: SBGN import
* Bug fix: mesh connector
* Rest API (documentation can be found here:
https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
@@ -1746,7 +1828,7 @@ minerva (10.0.5) stable; urgency=medium
* Bug fix: interacting drugs can be found for RNAs
* Bug fix: error handling improved on map upload
- * Bug fix: taxonomy ncbi server switched to https
+ * Bug fix: taxonomy NCBI server switched to https
* Overlay presents description field if possible
@@ -1774,7 +1856,7 @@ minerva (10.0.3) stable; urgency=medium
minerva (10.0.2) stable; urgency=medium
- * Bug fix: markers for mirna targets visibility
+ * Bug fix: markers for MiRNA targets visibility
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Sep 2016 10:01:16 +0200
@@ -1843,15 +1925,15 @@ minerva (6) stable; urgency=low
* Galaxy connector
* Miriam types report
* Advanced annotation options
- * Uniprot annotation module
+ * UniProt annotation module
* Customized validation of miriam annotations
* Recon annotation service
* Bug fix: Data autofill problem in user management
* Bug fix: User privileges for adding project
* Bug fix: Problem with some miriam entries in RDF format
* Bug fix: Reporting of drawing problems
- * Bug fix: Visualization of posttranslationa modification
- * Bug fix: Drugbank problem after update of Drugbank interface
+ * Bug fix: Visualization of posttranslational modification
+ * Bug fix: DrugBank problem after update of DrugBank interface
* Bug fix: Session scope fixed (browsing many maps at the same time)
* Bug fix: Asynchronous removing/adding maps
* Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file
@@ -1879,12 +1961,12 @@ minerva (5) stable; urgency=low
minerva (4) stable; urgency=low
* Export of the part of the map into CellDesigner file
- * Logo files managable via config webpage
+ * Logo files manageable via config webpage
* Import data from GO
* Custom overlay upload
* Additional structural information imported from annotation service
* Bug fix: Fonts and lines in hierarchical view
- * Bug fix: Visualization of residues in rna, antisense rna, proteins
+ * Bug fix: Visualization of residues in RNA, antisense RNA, proteins
* Bug fix: Problem with touching bubbles on touch interface
* Bug fix: Problem with special UTF-8 characters in CellDesigner file
* Bug fix: Problem with users and session expire
diff --git a/CellDesigner-plugin/.project b/CellDesigner-plugin/.project
index 7644e74c95ccb96514302b8fac71b10af8d5df71..5a8593cc67bc0f4a56843ed5043137b7b68fdcec 100644
--- a/CellDesigner-plugin/.project
+++ b/CellDesigner-plugin/.project
@@ -11,8 +11,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (12).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/annotation/.project b/annotation/.project
index 5dd65eed5eb071becf35fe19a7e9aaab629db307..cc8da93dfb1360118ff0a1e84298e27f0072081e 100644
--- a/annotation/.project
+++ b/annotation/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (3).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParserImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParserImpl.java
index 6ae3a6ba0480131109c5bb701b2e6811cdd68a0c..69012b6163542ff096c10681f0e6c47b2eabbcb7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParserImpl.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParserImpl.java
@@ -212,7 +212,7 @@ public class PubmedParserImpl extends CachableInterface implements PubmedParser
if (id == null) {
return null;
}
- return getPubmedArticleById(Integer.valueOf(id.trim()));
+ return getPubmedArticleById(Integer.valueOf(id.replaceAll("[^0-9.]", "").trim()));
}
/**
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorImpl.java
index 07b20b8a17d985153ed42120207f2d9ad39382ff..f7e7a33ac97e4fa897f31e7e1244e17a5385de41 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorImpl.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorImpl.java
@@ -46,7 +46,7 @@ public class EnsemblAnnotatorImpl extends ElementAnnotator implements EnsemblAnn
/**
* Version of the rest API that is supported by this annotator.
*/
- static final String SUPPORTED_VERSION = "15.1";
+ static final String SUPPORTED_VERSION = "15.3";
/**
* Url address of ensembl restful service.
@@ -128,7 +128,8 @@ public class EnsemblAnnotatorImpl extends ElementAnnotator implements EnsemblAnn
}
@Override
- public boolean annotateElement(final BioEntityProxy element, final MiriamData identifier, final AnnotatorData parameters)
+ public boolean annotateElement(final BioEntityProxy element, final MiriamData identifier,
+ final AnnotatorData parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.ENSEMBL)) {
String query = REST_SERVICE_URL + identifier.getResource() + URL_SUFFIX;
diff --git a/commons/.project b/commons/.project
index 2d0eff72f8eac2b33561e093d44e9ff86b84e90d..a26883597d46ac49b74ce855ae9b1c945e26ee8d 100644
--- a/commons/.project
+++ b/commons/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (1).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 30436f65e06122abcb38aed21043928fb5df813f..1a5b7a15675b5f829073b668362ee3c2882f499e 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -101,18 +101,27 @@ public final class XmlParser {
* @return node from nodes list with the tagName name, <b>null</b> if such node
* doesn't exist
*/
- public static Node getNode(final String tagName, final NodeList nodes) {
+ public static Node getNode(final String tagName, final NodeList nodes, final boolean ignoreNamespace) {
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase(tagName)) {
return node;
}
+ if (ignoreNamespace) {
+ if (node.getNodeName().toLowerCase().endsWith(":" + tagName.toLowerCase())) {
+ return node;
+ }
+ }
}
}
return null;
}
+ public static Node getNode(final String tagName, final NodeList nodes) {
+ return getNode(tagName, nodes, false);
+ }
+
/**
* Method returns the child node of xml 'parentNode' with 'tagName' name. If
* node could not be found then null is returned.
@@ -301,8 +310,8 @@ public final class XmlParser {
}
/**
- * This method transform color encoded in string (final CellDesigner format) into
- * Color.
+ * This method transform color encoded in string (final CellDesigner format)
+ * into Color.
*
* @param color
* string representing color
diff --git a/converter-CellDesigner/.project b/converter-CellDesigner/.project
index cf03151587cdb2953630e7b185b372732c08243e..bf1a13a878d0387dab56dd985e09c455750a7820 100644
--- a/converter-CellDesigner/.project
+++ b/converter-CellDesigner/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (5).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index c831e934e97a6e0224a3a118bafbf24162e431bd..e732d65f57e509eb6e3cf272a47bd67704691fe7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -445,11 +445,11 @@ public class RestAnnotationParser {
throw new InvalidArgumentException("Invalid notes node");
}
- Node htmlNode = XmlParser.getNode("html", node.getChildNodes());
+ Node htmlNode = XmlParser.getNode("html", node.getChildNodes(), true);
if (htmlNode == null) {
notes = XmlParser.nodeToString(node).trim();
} else {
- Node bodyNode = XmlParser.getNode("body", htmlNode.getChildNodes());
+ Node bodyNode = XmlParser.getNode("body", htmlNode.getChildNodes(), true);
if (bodyNode != null) {
notes = XmlParser.nodeToString(bodyNode).trim();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index cd1ec4aa44ea0f957c3430fee38600c30953cafc..f2343a619a997e887aebf3648ae7294657e5789f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -187,7 +187,7 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
setNotes(species.getNotes());
} else if (!string1.toLowerCase().contains(string2.toLowerCase())) {
// insert new information
- setNotes(string2 + getNotes());
+ setNotes(string2 + "\n" + getNotes());
}
}
@@ -597,7 +597,8 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
public void updateModelElementAfterLayoutAdded(final Species element) {
}
- protected StructuralState createStructuralState(final Species species, final String structuralState, final Double sourceAngle) {
+ protected StructuralState createStructuralState(final Species species, final String structuralState,
+ final Double sourceAngle) {
if (structuralState == null) {
return null;
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 40c94d91091354b33823f42e657c518a859c6b4d..91b9da293c501fa15498ff2961906258824156d4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -1044,4 +1044,13 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
assertNull(((Species) model2.getElementByElementId(protein2.getElementId())).getSubstanceUnits());
}
+ @Test
+ public void testNamespace() throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/problematic/namespace.xml")
+ .sizeAutoAdjust(false));
+ assertEquals("", model.getNotes());
+ }
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
index 959f74e50413a9aedf2d1f997fed50ad8bf4738a..6bbe527a54a7d16888ed0cc31ea5d57499d563d3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
@@ -182,6 +183,20 @@ public class SpeciesTest extends CellDesignerTestFunctions {
assertEquals(0, warningsCount);
}
+ @Test
+ public void testUpdateNotes() {
+ String notes1 = "XXX A";
+ String notes2 = "Notes B";
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes(notes1);
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes(notes2);
+ species.update(species2);
+ assertEquals(0, getWarnings().size());
+ assertNotEquals(notes1 + notes2, species.getNotes());
+ assertNotEquals(notes2 + notes1, species.getNotes());
+ }
+
@Test(expected = InvalidArgumentException.class)
public void testSetInvalidAmount() {
CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
diff --git a/converter-CellDesigner/testFiles/problematic/namespace.xml b/converter-CellDesigner/testFiles/problematic/namespace.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fe6a7035d60451dbea093c7281e93e46867af10a
--- /dev/null
+++ b/converter-CellDesigner/testFiles/problematic/namespace.xml
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:html="http://www.w3.org/1999/xhtml" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" level="2" version="4">
+ <model>
+ <notes>
+ <html:html>
+ <html:head>
+ <html:title />
+ </html:head>
+ <html:body />
+ </html:html>
+ </notes>
+ <annotation>
+ <celldesigner:extension>
+ <celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+ <celldesigner:modelDisplay sizeX="600" sizeY="400" />
+ <celldesigner:listOfCompartmentAliases />
+ <celldesigner:listOfComplexSpeciesAliases />
+ <celldesigner:listOfSpeciesAliases />
+ <celldesigner:listOfGroups />
+ <celldesigner:listOfProteins />
+ <celldesigner:listOfGenes />
+ <celldesigner:listOfRNAs />
+ <celldesigner:listOfAntisenseRNAs />
+ <celldesigner:listOfLayers />
+ <celldesigner:listOfBlockDiagrams />
+ </celldesigner:extension>
+ </annotation>
+ <listOfUnitDefinitions>
+ <unitDefinition metaid="substance" id="substance" name="substance">
+ <listOfUnits>
+ <unit metaid="CDMT00001" kind="mole" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition metaid="volume" id="volume" name="volume">
+ <listOfUnits>
+ <unit metaid="CDMT00002" kind="litre" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition metaid="area" id="area" name="area">
+ <listOfUnits>
+ <unit metaid="CDMT00003" kind="metre" exponent="2" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition metaid="length" id="length" name="length">
+ <listOfUnits>
+ <unit metaid="CDMT00004" kind="metre" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition metaid="time" id="time" name="time">
+ <listOfUnits>
+ <unit metaid="CDMT00005" kind="second" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment metaid="default" id="default" size="1" units="volume" />
+ </listOfCompartments>
+ </model>
+</sbml>
\ No newline at end of file
diff --git a/converter-SBGNML/.project b/converter-SBGNML/.project
index cee08a22554f452159725e87277b35fcc4639be8..339d4b3234ce97f358d444c1376d2ff74e3a74dd 100644
--- a/converter-SBGNML/.project
+++ b/converter-SBGNML/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (7).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/converter-graphics/.project b/converter-graphics/.project
index a0ccbe6c1b2791d99338688883a6465b946a257b..98b2440a4a066452a6a62999018c06507ebf7ccc 100644
--- a/converter-graphics/.project
+++ b/converter-graphics/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (6).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/LegendGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/LegendGenerator.java
index a8a566c09f89bd3e3b4003ada52d9cd6634936e4..8cb9369e1c61bcef2ef92a171bec4e6b95c39ac0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/LegendGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/LegendGenerator.java
@@ -172,7 +172,11 @@ public class LegendGenerator {
Font oldFont = graphics.getFont();
Set<Color> colorSet = new HashSet<>();
for (DataOverlayEntry entry : overlay.getEntries()) {
- colorSet.add(((GenericDataOverlayEntry) entry).getColor());
+ Color color = ((GenericDataOverlayEntry) entry).getColor();
+ if (color == null) {
+ color = colorExtractor.getSimpleColor();
+ }
+ colorSet.add(color);
}
List<Color> colors = new ArrayList<>(colorSet);
colors.sort(new Comparator<Color>() {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/LegendGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/LegendGeneratorTest.java
index 297cf345cb743d30d5ecebdc449bd169ae6f93b1..a866896e3033649db32bb5e939bdf61d0806b130 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/LegendGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/LegendGeneratorTest.java
@@ -69,6 +69,24 @@ public class LegendGeneratorTest extends GraphicsTestFunctions {
file.delete();
}
+ @Test
+ public void testGenericWithNullColor() throws IOException {
+ DataOverlay overlay = new DataOverlay();
+ GenericDataOverlayEntry entry = new GenericDataOverlayEntry();
+ entry.setColor(Color.YELLOW);
+ overlay.addEntry(entry);
+ entry = new GenericDataOverlayEntry();
+ entry.setColor(null);
+ entry.setElementId("re1");
+ overlay.addEntry(entry);
+ generator.savetToPng(overlay, extractor, "tmp.png");
+ File file = new File("tmp.png");
+ assertTrue(file.exists());
+ Mockito.verify(generator, times(1)).generateGenericLegendByColor(any(), any(), any());
+ // Desktop.getDesktop().open(file);
+ file.delete();
+ }
+
@Test
public void testGenetic() throws IOException {
DataOverlay overlay = new DataOverlay();
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
index 51873300ec19d791e123d2ea60757839c9f24513..1f10d6b1ec3840613b0ea585ccc4ef327d47cf7d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
@@ -66,10 +66,6 @@ public final class MultiPackageNamingUtils {
return feature.getIdPrefix() + getSpeciesTypeId(element).replace("minerva_species_type_", "");
}
- public static String getFeatureId(final Species element, final BioEntityFeature feature) {
- return getFeatureId(element, feature);
- }
-
public static boolean isFeatureId(final String featureTypeId, final BioEntityFeature feature) {
return featureTypeId.startsWith(feature.getIdPrefix());
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index 1ce0aecbe8b37f665cf6c0af8792148828265c70..dfca779a628a04ce66925f6427769e58745f53de 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -488,6 +488,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
multiDistinguisher += "\n" + element.getActivity();
multiDistinguisher += "\n" + element.getCharge();
multiDistinguisher += "\n" + element.getHomodimer();
+ if (element instanceof Complex) {
+ multiDistinguisher += "\n" + element.getElementId();
+ }
}
String result = element.getClass().getSimpleName() + "\n" + annotationNames + "\n" + element.getName() + "\n"
+ compartmentName + "\n"
diff --git a/converter-sbml/testFiles/cd_for_multi/equal_complexes_with_structural_state.xml b/converter-sbml/testFiles/cd_for_multi/equal_complexes_with_structural_state.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4bb3a99c2282847c176786a1a224d92acd518be4
--- /dev/null
+++ b/converter-sbml/testFiles/cd_for_multi/equal_complexes_with_structural_state.xml
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="Axonal_remodelling" id="Axonal_remodelling">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="6000" sizeY="2000"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:complexSpeciesAlias id="csa18" species="s12096">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="3391.3334686147173" y="453.18641774891717" w="130.0" h="50.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:structuralState angle="1.5707963267948966"/>
+<celldesigner:usualView>
+<celldesigner:boxSize width="130.0" height="50.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa24" species="s12096">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="4074.6971049783497" y="615.6409632034627" w="130.0" h="50.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:structuralState angle="1.5707963267948966"/>
+<celldesigner:usualView>
+<celldesigner:boxSize width="130.0" height="50.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases/>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00180" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00181" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00182" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00183" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00184" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s12096" id="s12096" name="filamentous actin" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+<celldesigner:name>filamentous actin</celldesigner:name>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="ADP"/>
+</celldesigner:listOfStructuralStates>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter/.project b/converter/.project
index 129ec9da5c64d938f92db650d7a107e1ecfb58fc..305714127019af79159400ec54675e21ef291964 100644
--- a/converter/.project
+++ b/converter/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (4).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index d45ef7e7a449fbfce1fa1ed92c60f44585db84f5..b32fd50e3cba1e864ad7dab3708b26c6cb86907c 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -31,6 +31,7 @@ import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -56,8 +57,7 @@ import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
public class ComplexZipConverter {
/**
- * Size of the buffer used for accessing single chunk of data from input
- * stream.
+ * Size of the buffer used for accessing single chunk of data from input stream.
*/
private static final int BUFFER_SIZE = 1024;
@@ -94,8 +94,8 @@ public class ComplexZipConverter {
* Creates complex {@link Model} that contains submaps.
*
* @param params
- * {@link ComplexZipConverterParams object} with information about
- * data from which result is going to be created
+ * {@link ComplexZipConverterParams object} with information about data
+ * from which result is going to be created
* @return complex {@link Model} created from input data
* @throws InvalidInputDataExecption
* thrown when there is a problem with accessing input data
@@ -258,8 +258,8 @@ public class ComplexZipConverter {
}
/**
- * This method validates if information about model and submodels in the
- * params are sufficient. If not then appropriate exception will be thrown.
+ * This method validates if information about model and submodels in the params
+ * are sufficient. If not then appropriate exception will be thrown.
*
* @param params
* parameters to validate
@@ -356,6 +356,18 @@ public class ComplexZipConverter {
ByteArrayInputStream baos = new ByteArrayInputStream(fileEntry.getFileContent());
try {
layout.addEntries(reader.readColorSchema(baos, parameters));
+
+ if (colorSchemaType == DataOverlayType.GENETIC_VARIANT) {
+ String genomeVersion = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_GENOME_VERSION);
+ ReferenceGenomeType genomeType = ReferenceGenomeType.UCSC;
+ if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_GENOME_TYPE) != null) {
+ genomeType = ReferenceGenomeType
+ .valueOf(parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_GENOME_TYPE));
+ }
+ layout.setGenomeType(genomeType);
+ layout.setGenomeVersion(genomeVersion);
+ }
+
} catch (final InvalidDataOverlayException e) {
throw new InvalidInputDataExecption("Data overlay is invalid", e);
}
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 9998423f73d13a2197ed4fdcfe58f88e5569c6d3..cf3e453212c83a87884d05544b8b2986b4cf621e 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -2126,6 +2126,17 @@ ServerConnector.getReactions = function (params) {
});
};
+/**
+ *
+ * @param {number} [params.modelId]
+ * @param {number[]} [params.ids]
+ * @param {number[]} [params.includedCompartmentIds]
+ * @param {number[]} [params.excludedCompartmentIds]
+ * @param {string[]} [params.columns]
+ * @param {string} [params.projectId]
+ * @param {string} [params.type]
+ * @returns {*}
+ */
ServerConnector.getAliases = function (params) {
var self = this;
var queryParams = {
@@ -2150,7 +2161,10 @@ ServerConnector.getAliases = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- if (filterParams.id.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY) {
+ if (filterParams.id.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY
+ || filterParams.excludedCompartmentIds.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY
+ || filterParams.includedCompartmentIds.length > self.MAX_NUMBER_OF_IDS_IN_GET_QUERY
+ ) {
return self.sendPostRequest(self.getAliasesUrl(queryParams), filterParams);
} else {
return self.sendGetRequest(self.getAliasesUrl(queryParams, filterParams));
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index ba42107154a7879db4ca909f674df77269c367c4..a827253a285ae1be316c0a5798f2bd6a3467dd15 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -225,8 +225,7 @@ AddOverlayDialog.prototype.getFileContent = function () {
var contentInput = $("[name='overlay-content']", self.getElement())[0];
if (contentInput.value !== undefined && contentInput.value !== null) {
- contentInput.value = contentInput.value.trim();
- if (contentInput.value !== "") {
+ if (contentInput.value.trim() !== "") {
self.setFileContent(contentInput.value);
}
}
diff --git a/frontend-js/src/main/js/gui/admin/PluginAdminPanel.js b/frontend-js/src/main/js/gui/admin/PluginAdminPanel.js
index d9a9f8c53fa8206358aa11373d99e93e85e4b64e..c813ae5c8fa8496c0f593af9fc7ab792284d920b 100644
--- a/frontend-js/src/main/js/gui/admin/PluginAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/PluginAdminPanel.js
@@ -89,6 +89,7 @@ PluginAdminPanel.prototype._createGui = function () {
input: false
}).then(function (param) {
if (param.status) {
+ $(button).prop('disabled', true);
return self.getServerConnector().removePlugin({hash: $(button).attr("data")}).catch(function (error) {
if (error instanceof NetworkError && error.statusCode === HttpStatus.NOT_FOUND) {
GuiConnector.warn("Plugin does not exist anymore");
@@ -96,6 +97,7 @@ PluginAdminPanel.prototype._createGui = function () {
throw error;
}
}).finally(function () {
+ $(button).prop('disabled', false);
return self.onRefreshClicked();
});
}
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 36bcad174e7394b7946e326e54f97833251616b9..454a86cbb4ba16be13ae9d397723c37d222fa1f4 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -601,14 +601,17 @@ GuiUtils.prototype.createSubMapLink = function (params) {
var result = Functions.createElement({type: "div", className: params.className});
if (params.mapId !== undefined) {
var button = document.createElement("button");
- var model = self.getMap().getSubmapById(params.mapId).getModel();
-
- button.innerHTML = model.getName();
- button.onclick = function () {
- return self.getMap().openSubmap(params.mapId);
- };
- result.appendChild(this.createLabel(params.label));
- result.appendChild(button);
+ var submap = self.getMap().getSubmapById(params.mapId);
+ if (submap !== null) {
+ var model = submap.getModel();
+
+ button.innerHTML = model.getName();
+ button.onclick = function () {
+ return self.getMap().openSubmap(params.mapId);
+ };
+ result.appendChild(this.createLabel(params.label));
+ result.appendChild(button);
+ }
}
return result;
};
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index a18c3f54815f1da5354eaf603c46204271391c78..7d7d028d03bd4c126a9c7f7683e9297de32cfc5c 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -9,6 +9,7 @@ var AddOverlayDialog = require('../AddOverlayDialog');
var Panel = require('../Panel');
var PanelControlElementType = require('../PanelControlElementType');
var ValidationError = require('../../ValidationError');
+var NetworkError = require('../../NetworkError');
var GuiConnector = require('../../GuiConnector');
// noinspection JSUnusedLocalSymbols
@@ -526,7 +527,15 @@ OverlayPanel.prototype.openEditOverlayDialog = function (overlay) {
GuiConnector.showProcessing("Removing");
return self.removeOverlay(overlay).then(function () {
$(windowSelf).dialog("close");
- }).catch(GuiConnector.alert).finally(function () {
+ }).catch(function (error) {
+ if (error instanceof NetworkError && error.statusCode === 404) {
+ GuiConnector.warn("Overlay has been already removed.");
+ $(windowSelf).dialog("close");
+ return self.refresh();
+ } else {
+ GuiConnector.alert(error);
+ }
+ }).finally(function () {
GuiConnector.hideProcessing();
});
}
diff --git a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
index 0888efa83975f935482f9401c16a57a17c0558b0..496c5d7e78f87d2ab4f3f3b316e4d6cc94926971 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
@@ -184,7 +184,7 @@ SubmapPanel.prototype.init = function () {
for (i = 0; i < types.length; i++) {
var type = types[i];
var tableName = type + " submaps";
- if (type === "UNKNOWN") {
+ if (type === "UNKNOWN" || type === undefined || type === null) {
tableName = ""
}
modelsByType[type].sort(function (modelA, modelB) {
diff --git a/frontend-js/src/main/js/map/data/GeneVariant.js b/frontend-js/src/main/js/map/data/GeneVariant.js
index b38277db7aea575b970ac4deac261623c04bdd86..d052b9894134767b61e39360a8b1e38793270241 100644
--- a/frontend-js/src/main/js/map/data/GeneVariant.js
+++ b/frontend-js/src/main/js/map/data/GeneVariant.js
@@ -1,30 +1,45 @@
"use strict";
+/**
+ * @typedef GeneVariantOptions
+ * @property {number} position
+ * @property {string} originalDna
+ * @property {string} modifiedDna
+ * @property {string} referenceGenomeType
+ * @property {string} referenceGenomeVersion
+ * @property {string} contig
+ * @property {string} [aminoAcidChange]
+ * @property {null|string} [allelFrequency]
+ * @property {null|string} [variantIdentifier]
+ */
+
/**
*
- * @param {Object} javaObject
- * @param {number} javaObject.position
- * @param {string} javaObject.originalDna
- * @param {string} javaObject.modifiedDna
- * @param {string} javaObject.referenceGenomeType
- * @param {string} javaObject.referenceGenomeVersion
- * @param {string} javaObject.contig
- * @param {string} [javaObject.aminoAcidChange]
- * @param {null|string} [javaObject.allelFrequency]
- * @param {null|string} [javaObject.variantIdentifier]
- *
+ * @param {GeneVariantOptions|GeneVariant} javaObject
* @constructor
- */
+ * */
function GeneVariant(javaObject) {
- this.setPosition(javaObject.position);
- this.setOriginalDna(javaObject.originalDna);
- this.setModifiedDna(javaObject.modifiedDna);
- this.setReferenceGenomeType(javaObject.referenceGenomeType);
- this.setReferenceGenomeVersion(javaObject.referenceGenomeVersion);
- this.setContig(javaObject.contig);
- this.setAllelFrequency(javaObject.allelFrequency);
- this.setVariantIdentifier(javaObject.variantIdentifier);
- this.setAminoAcidChange(javaObject.aminoAcidChange);
+ if (javaObject instanceof GeneVariant) {
+ this.setPosition(javaObject.getPosition());
+ this.setOriginalDna(javaObject.getOriginalDna());
+ this.setModifiedDna(javaObject.getModifiedDna());
+ this.setReferenceGenomeType(javaObject.getReferenceGenomeType());
+ this.setReferenceGenomeVersion(javaObject.getReferenceGenomeVersion());
+ this.setContig(javaObject.getContig());
+ this.setAllelFrequency(javaObject.getAllelFrequency());
+ this.setVariantIdentifier(javaObject.getVariantIdentifier());
+ this.setAminoAcidChange(javaObject.getAminoAcidChange());
+ } else {
+ this.setPosition(javaObject.position);
+ this.setOriginalDna(javaObject.originalDna);
+ this.setModifiedDna(javaObject.modifiedDna);
+ this.setReferenceGenomeType(javaObject.referenceGenomeType);
+ this.setReferenceGenomeVersion(javaObject.referenceGenomeVersion);
+ this.setContig(javaObject.contig);
+ this.setAllelFrequency(javaObject.allelFrequency);
+ this.setVariantIdentifier(javaObject.variantIdentifier);
+ this.setAminoAcidChange(javaObject.aminoAcidChange);
+ }
}
/**
@@ -109,7 +124,7 @@ GeneVariant.prototype.getContig = function () {
/**
*
- * @param {string} allelFrequency
+ * @param {string|number} allelFrequency
*/
GeneVariant.prototype.setAllelFrequency = function (allelFrequency) {
if (allelFrequency === null) {
diff --git a/frontend-js/src/main/js/map/data/LayoutAlias.js b/frontend-js/src/main/js/map/data/LayoutAlias.js
index f313a307967cec55f930fed581b16d10049f7a43..ea6b0fc4780dd888407b85797968933bd45b2e29 100644
--- a/frontend-js/src/main/js/map/data/LayoutAlias.js
+++ b/frontend-js/src/main/js/map/data/LayoutAlias.js
@@ -2,43 +2,63 @@
var GeneVariant = require('./GeneVariant');
+/**
+ * @typedef LayoutAliasOptions
+ * @property {number} idObject
+ * @property {number} [value]
+ * @property {{rgb:number}} [color]
+ * @property {number} modelId
+ * @property {string} [description]
+ * @property {number} [uniqueId]
+ * @property {string} [type=LayoutAlias.LIGHT]
+ * @property {Array} [geneVariations] */
+
/**
* Class representing alias visualized in a overlay.
*
- * @param {number} javaObject.idObject
- * @param {number} [javaObject.value]
- * @param {{rgb:number}} [javaObject.color]
- * @param {number} javaObject.modelId
- * @param {string} [javaObject.description]
- * @param {number} [javaObject.uniqueId]
- * @param {string} [javaObject.type=LayoutAlias.LIGHT]
- * @param {Array} [javaObject.geneVariations]
- */
+ * @param {LayoutAliasOptions|LayoutAlias} javaObject
+ * @constructor
+ * */
function LayoutAlias(javaObject) {
- this.setId(javaObject.idObject);
- this.setValue(javaObject.value);
- this.setColor(javaObject.color);
- this.setModelId(javaObject.modelId);
- this.setDescription(javaObject.description);
- this.setDataOverlayEntryId(javaObject.uniqueId);
- if (javaObject.type === undefined) {
- this.setType(LayoutAlias.LIGHT);
- } else if (javaObject.type === LayoutAlias.GENETIC_VARIANT) {
- if (javaObject.geneVariations !== undefined) {
- this.setType(LayoutAlias.GENETIC_VARIANT);
- } else {
- this.setType(LayoutAlias.LIGHT);
+ if (javaObject instanceof LayoutAlias) {
+ this.setId(javaObject.getId());
+ this.setValue(javaObject.getValue());
+ this.setColor(javaObject.getColor());
+ this.setModelId(javaObject.getModelId());
+ this.setDescription(javaObject.getDescription());
+ this.setDataOverlayEntryId(javaObject.getDataOverlayEntryId());
+ this.setType(javaObject.getType());
+
+ this.setGeneVariants([]);
+ for (var i = 0; i < javaObject.getGeneVariants().length; i++) {
+ this.addGeneVariant(new GeneVariant(javaObject.getGeneVariants()[i]));
}
- } else if (javaObject.type === LayoutAlias.GENERIC) {
- this.setType(LayoutAlias.GENERIC);
} else {
- throw new Error("Unknown type: " + javaObject.type);
- }
+ this.setId(javaObject.idObject);
+ this.setValue(javaObject.value);
+ this.setColor(javaObject.color);
+ this.setModelId(javaObject.modelId);
+ this.setDescription(javaObject.description);
+ this.setDataOverlayEntryId(javaObject.uniqueId);
+ if (javaObject.type === undefined) {
+ this.setType(LayoutAlias.LIGHT);
+ } else if (javaObject.type === LayoutAlias.GENETIC_VARIANT) {
+ if (javaObject.geneVariations !== undefined) {
+ this.setType(LayoutAlias.GENETIC_VARIANT);
+ } else {
+ this.setType(LayoutAlias.LIGHT);
+ }
+ } else if (javaObject.type === LayoutAlias.GENERIC) {
+ this.setType(LayoutAlias.GENERIC);
+ } else {
+ throw new Error("Unknown type: " + javaObject.type);
+ }
- this.setGeneVariants([]);
- if (javaObject.geneVariations !== undefined) {
- for (var i = 0; i < javaObject.geneVariations.length; i++) {
- this.addGeneVariant(new GeneVariant(javaObject.geneVariations[i]));
+ this.setGeneVariants([]);
+ if (javaObject.geneVariations !== undefined) {
+ for (var j = 0; j < javaObject.geneVariations.length; j++) {
+ this.addGeneVariant(new GeneVariant(javaObject.geneVariations[j]));
+ }
}
}
}
diff --git a/frontend-js/src/main/js/map/window/AliasInfoWindow.js b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
index d14c5ac9a24ad4ff259eeb1f20c091f414f7490e..e4c874f0e8afbbabe90df5fab507cea46adeded9 100644
--- a/frontend-js/src/main/js/map/window/AliasInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
@@ -450,7 +450,16 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
promises = [];
result.forEach(function (overlayEntries) {
if (overlayEntries !== undefined) {
- overlaysData = overlaysData.concat(overlayEntries);
+ //check if we have gene variants split into multiple groups
+ if (overlayEntries.length > 1 && overlayEntries[0].getType() === LayoutAlias.GENETIC_VARIANT) {
+ var tmpAlias = new LayoutAlias(overlayEntries[0]);
+ for (var i = 1; i < overlayEntries.length; i++) {
+ tmpAlias.setGeneVariants(tmpAlias.getGeneVariants().concat(overlayEntries[i].getGeneVariants()));
+ overlaysData.push(tmpAlias);
+ }
+ } else {
+ overlaysData = overlaysData.concat(overlayEntries);
+ }
}
});
return Promise.all(promises);
diff --git a/model-command/.project b/model-command/.project
index 9dbb4bccdca54896776ec561b100cd19e5790deb..76db27f2b567de901675394f1adc139045b9abdf 100644
--- a/model-command/.project
+++ b/model-command/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (8).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/AddElementPrefixCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/AddElementPrefixCommand.java
index 752aa47d3532df9135ef1432d24381f69a0a8460..8184b8a700d4837f6579ec85cbe123899f4c00b5 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/AddElementPrefixCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/AddElementPrefixCommand.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.commands;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -37,6 +38,9 @@ public class AddElementPrefixCommand extends ModelCommand {
reaction.setIdReaction(prefix + reaction.getElementId());
model.addReaction(reaction);
}
+ for (Layer layer : model.getLayers()) {
+ layer.setLayerId(prefix + layer.getLayerId());
+ }
}
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MergeCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MergeCommand.java
index e7a1e84e71672aa0e5f1dfc4aaa9eef385c5e11c..d40aaa69e4e148cee4879ed4b3cf1c6ad4bcb76e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MergeCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MergeCommand.java
@@ -40,6 +40,7 @@ public class MergeCommand extends NewModelCommand {
result.addElements(model.getElements());
result.addReactions(new ArrayList<>(model.getReactions()));
+ result.addLayers(model.getLayers());
mapHeight = Math.max(mapHeight, offsetY + model.getHeight() + MARGIN);
mapWidth = Math.max(mapWidth, offsetX + model.getWidth() + MARGIN);
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
index 96508b571b460834547b7758713085f34d499d27..e1755ce3db6240587209fff1558c03bdc4d1c764 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
@@ -3,6 +3,11 @@ package lcsb.mapviewer.commands;
import java.awt.geom.Line2D;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -24,6 +29,7 @@ public class MoveCommand extends ModelCommand {
* Delta x.
*/
private double dx;
+
/**
* Delta y.
*/
@@ -93,6 +99,27 @@ public class MoveCommand extends ModelCommand {
reaction.getLine().setLine(i, line.getX1() + dx, line.getY1() + dy, line.getX2() + dx, line.getY2() + dy);
}
}
+
+ for (Layer layer : model.getLayers()) {
+ for (LayerText text : layer.getTexts()) {
+ text.setX(text.getX() + dx);
+ text.setY(text.getY() + dy);
+ }
+ for (LayerRect rect : layer.getRectangles()) {
+ rect.setX(rect.getX() + dx);
+ rect.setY(rect.getY() + dy);
+ }
+ for (LayerOval oval : layer.getOvals()) {
+ oval.setX(oval.getX() + dx);
+ oval.setY(oval.getY() + dy);
+ }
+ for (PolylineData line : layer.getLines()) {
+ for (int i = 0; i < line.getLines().size(); i++) {
+ Line2D l = line.getLines().get(i);
+ line.setLine(i, l.getX1() + dx, l.getY1() + dy, l.getX2() + dx, l.getY2() + dy);
+ }
+ }
+ }
}
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
index 5c8dba38badd517a8ecac322cf6ddf441faa6f86..d70b50c701fba73ee93b5da8e1721aa7672c7fc6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -54,7 +54,8 @@ public class SubModelCommand extends NewModelCommand {
* @param polygon
* #polygon that limits the area for the new model
*/
- public SubModelCommand(final Model model, final Path2D polygon, final Set<Integer> elementIds, final Set<Integer> reactionIds) {
+ public SubModelCommand(final Model model, final Path2D polygon, final Set<Integer> elementIds,
+ final Set<Integer> reactionIds) {
super(model);
this.polygon = polygon;
this.elementIds = elementIds;
@@ -165,7 +166,7 @@ public class SubModelCommand extends NewModelCommand {
for (final Layer layer : result.getLayers()) {
List<LayerText> textToRemove = new ArrayList<>();
for (final LayerText text : layer.getTexts()) {
- if (!(polygon.intersects(text.getBorder()))) {
+ if (!(polygon.intersects(text.getBorder())) || elementIds.size() > 0 || reactionIds.size() > 0) {
textToRemove.add(text);
}
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/AddElementPrefixCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/AddElementPrefixCommandTest.java
index 9433ffaaaa1a5e7469cd7df18af12e12e2296a7d..e77efee4da9403c1f9826e585ebc7a85dd31de3d 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/AddElementPrefixCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/AddElementPrefixCommandTest.java
@@ -1,9 +1,11 @@
package lcsb.mapviewer.commands;
+import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import org.junit.Test;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.Model;
public class AddElementPrefixCommandTest extends CommandTestFunctions {
@@ -16,4 +18,14 @@ public class AddElementPrefixCommandTest extends CommandTestFunctions {
assertNotNull(model.getElementByElementId("pre" + id));
}
+ @Test
+ public void testPrefixLayer() throws CommandExecutionException {
+ Model model = super.createSimpleModel();
+ Layer layer = new Layer();
+ layer.setLayerId("x");
+ model.addLayer(layer);
+ new AddElementPrefixCommand(model, "pre").execute();
+ assertNotEquals("x", layer.getLayerId());
+ }
+
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/MoveCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/MoveCommandTest.java
index 309846d2bf93f1cd319b2003e2e769b00c83a9de..fa83087774b268ddeb184a9f4718fbe6425857ee 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/MoveCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/MoveCommandTest.java
@@ -5,11 +5,16 @@ import static org.junit.Assert.assertTrue;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
@@ -72,4 +77,66 @@ public class MoveCommandTest extends CommandTestFunctions {
assertEquals(new Point2D.Double(50, 40), state.getPosition());
}
+ @Test
+ public void testMoveLayerText() throws CommandExecutionException {
+ Model model = super.createSimpleModel();
+
+ Layer layer = new Layer();
+ LayerText text = new LayerText(new Rectangle2D.Double(10, 20, 30, 40), "xyz");
+ layer.addLayerText(text);
+ model.addLayer(layer);
+
+ new MoveCommand(model, 10, 20).execute();
+
+ assertEquals(20, text.getX(), Configuration.EPSILON);
+ assertEquals(40, text.getY(), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testMoveLayerRect() throws CommandExecutionException {
+ Model model = super.createSimpleModel();
+
+ Layer layer = new Layer();
+ LayerRect rect = new LayerRect(new Rectangle2D.Double(10, 20, 30, 40));
+ layer.addLayerRect(rect);
+ model.addLayer(layer);
+
+ new MoveCommand(model, 10, 20).execute();
+
+ assertEquals(20, rect.getX(), Configuration.EPSILON);
+ assertEquals(40, rect.getY(), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testMoveLayerOval() throws CommandExecutionException {
+ Model model = super.createSimpleModel();
+
+ Layer layer = new Layer();
+ LayerOval oval = new LayerOval();
+ oval.setX(10.0);
+ oval.setY(20.0);
+ layer.addLayerOval(oval);
+ model.addLayer(layer);
+
+ new MoveCommand(model, 10, 20).execute();
+
+ assertEquals(20, oval.getX(), Configuration.EPSILON);
+ assertEquals(40, oval.getY(), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testMoveLayerLine() throws CommandExecutionException {
+ Model model = super.createSimpleModel();
+
+ Layer layer = new Layer();
+ PolylineData line = new PolylineData(new Point2D.Double(10, 20), new Point2D.Double(30, 40));
+ layer.addLayerLine(line);
+ model.addLayer(layer);
+
+ new MoveCommand(model, 10, 20).execute();
+
+ assertEquals(0, new Point2D.Double(20, 40).distance(line.getStartPoint()), Configuration.EPSILON);
+ assertEquals(0, new Point2D.Double(40, 60).distance(line.getEndPoint()), Configuration.EPSILON);
+ }
+
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
index b96f428a94b66a7a1525cbf00a3b6d0fc056cb6f..4150cb89665bd91763b6489f68ed1b3ce1580e9b 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -4,6 +4,7 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import java.awt.geom.Path2D;
+import java.awt.geom.Rectangle2D;
import java.util.Arrays;
import java.util.HashSet;
@@ -11,6 +12,8 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -148,6 +151,31 @@ public class SubModelCommandTest extends CommandTestFunctions {
assertEquals(0, copy.getReactions().size());
}
+ @Test
+ public void testGetSubmodelWithElementIdsAndTextArea() throws Exception {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 1000);
+ polygon.lineTo(1000, 1000);
+ polygon.lineTo(1000, 0);
+ polygon.closePath();
+ model.getElementByElementId("sa2").setId(-2);
+
+ Layer layer = new Layer();
+ LayerText text = new LayerText(new Rectangle2D.Double(10, 10, 20, 20), "xy");
+ layer.addLayerText(text);
+ model.addLayer(layer);
+
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(Arrays.asList(-2)), new HashSet<>()).execute();
+
+ assertEquals(1, copy.getElements().size());
+ assertEquals(0, copy.getReactions().size());
+ assertEquals(1, copy.getLayers().size());
+ assertEquals(0, copy.getLayers().iterator().next().getTexts().size());
+ }
+
@Test
public void testGetSubmodelWithEmptyElementIds() throws Exception {
Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
diff --git a/model/.project b/model/.project
index aaaa0fce06cdb04fcc7a38db966e3d7a802e568f..44a99170d5a1d8c098ee5fc1f26b3028de600c4c 100644
--- a/model/.project
+++ b/model/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (2).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 934187f82a623151ad14f9cb85a89152405f5b39..7690ea3d5d77a176034128ff729f8939a2e409e6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -3463,7 +3463,7 @@ public enum MiriamType {
}, new Class<?>[] {}, "MIR:00000273",
new Class<?>[] {},
"massbank",
- "PB000166"),
+ "MSBNK-IPB_Halle-PB000166"),
MATHEMATICAL_MODELLING_ONTOLOGY("Mathematical Modelling Ontology",
"http://bioportal.bioontology.org/ontologies/MAMO",
@@ -6670,8 +6670,8 @@ public enum MiriamType {
private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
/**
- * When class from this list is marked as "require at least one annotation"
- * then annotation of this type is valid.
+ * When class from this list is marked as "require at least one annotation" then
+ * annotation of this type is valid.
*/
private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
@@ -6775,8 +6775,8 @@ public enum MiriamType {
* identifier in the format NAME:IDENTIFIER. Where NAME is the name
* from {@link MiriamType#commonName} and IDENTIFIER is resource
* identifier.
- * @return {@link MiriamData} representing generalIdentifier, when identifier
- * is invalid InvalidArgumentException is thrown
+ * @return {@link MiriamData} representing generalIdentifier, when identifier is
+ * invalid InvalidArgumentException is thrown
*/
public static MiriamData getMiriamDataFromIdentifier(final String generalIdentifier) {
int index = generalIdentifier.indexOf(":");
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
index 03619c01582a599651288c0933dd296fd9c9a545..0eeff2c1ee6062c55f2f075b384d4ca0138efc32 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.layout.graphics;
import java.awt.Color;
+import java.awt.geom.Rectangle2D;
import java.io.Serializable;
import javax.persistence.Column;
@@ -103,6 +104,13 @@ public class LayerRect implements Serializable, Drawable {
height = layerRect.getHeight();
}
+ public LayerRect(final Rectangle2D rect) {
+ x = rect.getX();
+ y = rect.getY();
+ width = rect.getWidth();
+ height = rect.getHeight();
+ }
+
/**
* Prepares a copy of the object.
*
@@ -260,10 +268,12 @@ public class LayerRect implements Serializable, Drawable {
return width * height;
}
+ @Override
public Color getBorderColor() {
return borderColor;
}
+ @Override
public void setBorderColor(final Color borderColor) {
this.borderColor = borderColor;
}
diff --git a/pathvisio/.project b/pathvisio/.project
index 03de699bdd6e159ef0855b7312363a55bc669abf..d68188f8af21a94b27220f3577020e3b37604f87 100644
--- a/pathvisio/.project
+++ b/pathvisio/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder.launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
index be478b490aeed102e684fc2345a12ab06c8fdca0..c3262b837b30ab0a5bf13625e6d23103b9af4650 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
@@ -249,8 +249,8 @@ public class ModelContructor {
}
/**
- * This function adds {@link Complex} to model from graph. ComplexName is set
- * as groupId from GPML
+ * This function adds {@link Complex} to model from graph. ComplexName is set as
+ * groupId from GPML
*
* @param groups
* list of groups
@@ -303,6 +303,7 @@ public class ModelContructor {
* ...
*/
protected void addElement(final Model model, final Graph graph, final Data data) {
+
for (final DataNode dataNode : graph.getDataNodes()) {
Species species = createSpecies(dataNode);
species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReferences()));
@@ -338,7 +339,7 @@ public class ModelContructor {
} else {
if (!shape.isCompartment()) {
- if (shape.getShape().equals(GpmlShape.OVAL)) {
+ if (Objects.equals(shape.getShape(), GpmlShape.OVAL)) {
LayerOval oval = createOval(shape);
data.layer.addLayerOval(oval);
} else if (shape.getComments().size() > 0 || shape.getTextLabel() != null) {
@@ -1242,8 +1243,7 @@ public class ModelContructor {
}
/**
- * Tries to find a name to assign to complexes if complexes don't contain
- * them.
+ * Tries to find a name to assign to complexes if complexes don't contain them.
*
* @param model
* model where complexes are placed
@@ -1314,8 +1314,8 @@ public class ModelContructor {
}
/**
- * Tries to find a name to assign to compartments if compartments don't
- * contain them.
+ * Tries to find a name to assign to compartments if compartments don't contain
+ * them.
*
* @param model
* model where compartments are placed
@@ -1365,8 +1365,8 @@ public class ModelContructor {
}
/**
- * By default gpml doesn't offer information about compartments structure.
- * This function fixes assignments to compartment and compartment aliases.
+ * By default gpml doesn't offer information about compartments structure. This
+ * function fixes assignments to compartment and compartment aliases.
*
* @param model
* model where assignments are fixed.
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 0bfed93e4100eece5dabb7ff96db13fdced30858..43314e18d3ba4dafcac70bbc99238b5f269a5a60 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -262,6 +262,13 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, getWarnings().size());
}
+ @Test
+ public void testUnknownElementType() throws Exception {
+ String fileName = "testFiles/complex/unknown_element.gpml";
+ new GPMLToModel().getModel(fileName);
+ assertEquals(1, getWarnings().size());
+ }
+
@Test
public void testComplexName() throws Exception {
String fileName = "testFiles/complex/complex_with_name.gpml";
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/ShapeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/ShapeParserTest.java
index 071e64f9b365872437751f3f23f2672f1260835c..10fb112f723a1497705d4bb7a5542e4b24aa255e 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/ShapeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/ShapeParserTest.java
@@ -118,6 +118,15 @@ public class ShapeParserTest extends WikipathwaysTestFunctions {
assertEquals(0, getWarnings().size());
}
+ @Test
+ public void testParseUnknown() throws Exception {
+ Element node = fileToNode("testFiles/elements/unknown.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(1, getWarnings().size());
+ }
+
@Test
public void testParsePent() throws Exception {
Element node = fileToNode("testFiles/elements/pent.xml");
diff --git a/pathvisio/testFiles/complex/unknown_element.gpml b/pathvisio/testFiles/complex/unknown_element.gpml
new file mode 100644
index 0000000000000000000000000000000000000000..57ea5983c95db00e73a9f2d565bc7d517f813177
--- /dev/null
+++ b/pathvisio/testFiles/complex/unknown_element.gpml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Insulin Signaling" Last-Modified="10/17/2013" Organism="Homo sapiens">
+ <Graphics BoardWidth="769.3333333333334" BoardHeight="710.0" />
+ <Shape TextLabel="eee" GraphId="c42d9">
+ <Comment>oval</Comment>
+ <BiopaxRef>d35</BiopaxRef>
+ <Graphics CenterX="668.25" CenterY="636.25" Width="353.5" Height="123.5" ZOrder="16384" FontSize="10" Valign="Middle" ShapeType="unknown-type" Rotation="0.0" />
+ </Shape>
+ <Biopax>
+ </Biopax>
+</Pathway>
+
diff --git a/pathvisio/testFiles/elements/unknown.xml b/pathvisio/testFiles/elements/unknown.xml
new file mode 100644
index 0000000000000000000000000000000000000000..04dfe4a9ec14beb3e9f424109943f3587d63630e
--- /dev/null
+++ b/pathvisio/testFiles/elements/unknown.xml
@@ -0,0 +1,5 @@
+ <Shape TextLabel="eee" GraphId="c42d9">
+ <Comment>oval</Comment>
+ <BiopaxRef>d35</BiopaxRef>
+ <Graphics CenterX="668.25" CenterY="636.25" Width="353.5" Height="123.5" ZOrder="16384" FontSize="10" Valign="Middle" ShapeType="unknown-type" Rotation="0.0" />
+ </Shape>
diff --git a/persist/.project b/persist/.project
index c76dcb2aefa82b83fd6ecb778b2001f2f790c783..6988b02d15c133024d99338879f5734516594fb0 100644
--- a/persist/.project
+++ b/persist/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (9).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/rest-api/.project b/rest-api/.project
index a4d854734795cb0c96fbba9960acd8b0cc90d759..fc78f7be58cd8140b065e18ab8de6a529224fa10 100644
--- a/rest-api/.project
+++ b/rest-api/.project
@@ -21,8 +21,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (10).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
index 15b6edf1280b61f156199492d5f25378f1247c4d..606fd8ab2c38a3a7f200bb6b4359934893cb881c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertController.java
@@ -60,13 +60,19 @@ public class ConvertController extends BaseController {
this.modelConverters = modelConverters;
}
- @PostMapping(value = "/{fromFormat}:{toFormat:.+}", produces = MediaType.APPLICATION_XML_VALUE)
+ @PostMapping(value = "/{fromFormat}:{toFormat:.+}",
+ consumes = {
+ MediaType.APPLICATION_XML_VALUE,
+ MediaType.APPLICATION_OCTET_STREAM_VALUE,
+ MediaType.TEXT_PLAIN_VALUE
+ },
+ produces = MediaType.APPLICATION_XML_VALUE)
public byte[] convertInput(final @PathVariable(value = "fromFormat") String fromFormat,
final @PathVariable(value = "toFormat") String toFormat,
- final @RequestBody byte[] body)
- throws IOException, QueryException, SBMLException,
+ final @RequestBody byte[] body) throws IOException, QueryException, SBMLException,
InvalidInputDataExecption, InconsistentModelException, ConverterException {
- ConverterParams params = createConvertParams(body);
+
+ ConverterParams params = new ConverterParams().inputStream(new ByteArrayInputStream(body));
MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
Model original;
try {
@@ -78,6 +84,8 @@ public class ConvertController extends BaseController {
}
}
original.setNotes(notes.toString());
+ } catch (final InvalidInputDataExecption | ConverterException e) {
+ throw new QueryException("Problem with input file", e);
} finally {
MinervaLoggerAppender.unregisterLogEventStorage(appender);
}
@@ -101,14 +109,19 @@ public class ConvertController extends BaseController {
return model;
}
- @PostMapping(value = "/image/{fromFormat}:{toFormat:.+}")
+ @PostMapping(value = "/image/{fromFormat}:{toFormat:.+}",
+ consumes = {
+ MediaType.APPLICATION_XML_VALUE,
+ MediaType.APPLICATION_OCTET_STREAM_VALUE,
+ MediaType.TEXT_PLAIN_VALUE
+ })
public @ResponseBody ResponseEntity<byte[]> convertInputToImage(
final @PathVariable(value = "fromFormat") String fromFormat,
final @PathVariable(value = "toFormat") String toFormat,
final @RequestBody byte[] body) throws QueryException, IOException, DrawingException {
Model original = null;
try {
- original = getModelParserByNameOrClass(fromFormat).createModel(createConvertParams(body));
+ original = getModelParserByNameOrClass(fromFormat).createModel(new ConverterParams().inputStream(new ByteArrayInputStream(body)));
} catch (final InvalidInputDataExecption | ConverterException e) {
throw new QueryException("Problem with input file", e);
}
@@ -172,7 +185,11 @@ public class ConvertController extends BaseController {
}
- @PostMapping(value = "/merge/{fromFormat}:{toFormat}")
+ @PostMapping(value = "/merge/{fromFormat}:{toFormat}",
+ consumes = {
+ MediaType.APPLICATION_OCTET_STREAM_VALUE,
+ MediaType.TEXT_PLAIN_VALUE
+ })
public @ResponseBody ResponseEntity<byte[]> mergeFilesToFile(
final @PathVariable(value = "fromFormat") String fromFormat,
final @PathVariable(value = "toFormat") String toFormat,
@@ -255,12 +272,6 @@ public class ConvertController extends BaseController {
return result;
}
- private ConverterParams createConvertParams(final byte[] input) {
- InputStream is = new ByteArrayInputStream(input);
-
- return new ConverterParams().inputStream(is);
- }
-
private Converter getModelParserByNameOrClass(final String id) throws QueryException {
try {
return getModelParserByName(id);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
index 2791e86191abc4a43f2f776da083c7de121d4329..78c0261ca8c8b711c89e3a2de4d565362d11fa1e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
@@ -72,7 +72,7 @@ public class FileController extends BaseController {
}
@PreAuthorize("@fileService.getOwnerByFileId(#id)?.login == authentication.name")
- @PostMapping(value = "/{id}:uploadContent")
+ @PostMapping(value = "/{id}:uploadContent", consumes = { MediaType.APPLICATION_OCTET_STREAM_VALUE })
public UploadedFileEntry uploadContent(final @PathVariable(value = "id") Integer id, final @RequestBody byte[] data)
throws QueryException {
UploadedFileEntry fileEntry = fileService.getById(id);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/DirectoryNameGenerator.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/DirectoryNameGenerator.java
new file mode 100644
index 0000000000000000000000000000000000000000..6945611975e77a3c3cceea97524720011fd012c0
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/DirectoryNameGenerator.java
@@ -0,0 +1,25 @@
+package lcsb.mapviewer.api.projects;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import lcsb.mapviewer.common.Md5;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+
+@Service
+public class DirectoryNameGenerator implements IDirectoryNameGenerator {
+
+ private IProjectService projectService;
+
+ @Autowired
+ public DirectoryNameGenerator(final IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ @Override
+ public String projectIdToDirectoryName(final String projectId) {
+ long id = projectService.getNextId();
+ return Md5.compute(projectId + "-" + id);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/IDirectoryNameGenerator.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/IDirectoryNameGenerator.java
new file mode 100644
index 0000000000000000000000000000000000000000..5c9ef3a36ba74112bb41e331c899ecf21d1f49f1
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/IDirectoryNameGenerator.java
@@ -0,0 +1,6 @@
+package lcsb.mapviewer.api.projects;
+
+public interface IDirectoryNameGenerator {
+ String projectIdToDirectoryName(final String projectId);
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index 7070811b4698af462796af34be0f85649812f122..23fe21ddd8e4a9a100f32feeca2ea71db62437c3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -56,7 +56,6 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.api.OperationNotAllowedException;
import lcsb.mapviewer.api.minervanet.MinervaNetController;
-import lcsb.mapviewer.common.Md5;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.Converter;
@@ -103,6 +102,7 @@ public class ProjectController extends BaseController {
private ServletContext context;
private MinervaNetController minervaNetController;
private IProjectService projectService;
+ private IDirectoryNameGenerator directoryNameGenerator;
private IConfigurationService configurationService;
private IModelService modelService;
private IElementService elementService;
@@ -116,10 +116,14 @@ public class ProjectController extends BaseController {
private List<Converter> modelConverters;
@Autowired
- public ProjectController(final ServletContext context, final IUserService userService, final IProjectService projectService,
- final IMeshService meshService, final List<Converter> modelConverters, final IFileService fileService, final IElementService elementService,
- final IReactionService reactionService, final IModelService modelService, final IConfigurationService configurationService,
- final IProjectBackgroundService projectBackgroundService, final MinervaNetController minervaNetController) {
+ public ProjectController(final ServletContext context, final IUserService userService,
+ final IProjectService projectService,
+ final IMeshService meshService, final List<Converter> modelConverters, final IFileService fileService,
+ final IElementService elementService,
+ final IReactionService reactionService, final IModelService modelService,
+ final IConfigurationService configurationService,
+ final IProjectBackgroundService projectBackgroundService, final MinervaNetController minervaNetController,
+ final IDirectoryNameGenerator directoryNameGenerator) {
this.context = context;
this.userService = userService;
this.projectService = projectService;
@@ -132,6 +136,7 @@ public class ProjectController extends BaseController {
this.configurationService = configurationService;
this.projectBackgroundService = projectBackgroundService;
this.minervaNetController = minervaNetController;
+ this.directoryNameGenerator = directoryNameGenerator;
}
@PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
@@ -533,7 +538,8 @@ public class ProjectController extends BaseController {
final Authentication authentication,
final @RequestParam Map<String, Object> body,
final @Size(max = 255) @Pattern(regexp = "^[a-z0-9A-Z\\-_]+$",
- message = "projectId can contain only alphanumeric characters and -_") @PathVariable(value = "projectId") String projectId)
+ message = "projectId can contain only alphanumeric characters and -_")
+ @PathVariable(value = "projectId") String projectId)
throws IOException, QueryException, SecurityException {
fixFormUrlEncodedBody(body);
if (Objects.equals(body.get("zip-entries"), "")) {
@@ -642,8 +648,7 @@ public class ProjectController extends BaseController {
}
protected String computePathForProject(final String projectId, final String path) {
- long id = projectService.getNextId();
- return path + "/../map_images/" + Md5.compute(projectId + "-" + id) + "/";
+ return path + "/../map_images/" + directoryNameGenerator.projectIdToDirectoryName(projectId) + "/";
}
@PreAuthorize("hasAuthority('IS_ADMIN')"
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
index 41c4aa8425ae438d297d08f8d7ea61c0c7a9a931..855237c155cb6fe578d49e75c2ef2eb8e2574046 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -75,7 +75,6 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.overlay.DataOverlay;
import lcsb.mapviewer.model.overlay.DataOverlayEntry;
import lcsb.mapviewer.model.overlay.InvalidDataOverlayException;
import lcsb.mapviewer.model.user.User;
@@ -440,9 +439,8 @@ public class ModelController extends BaseController {
// Color with overlays
for (final Integer overlayId : overlayIdsList) {
- DataOverlay overlay = dataOverlayService.getDataOverlayById(projectId, overlayId);
+ Set<DataOverlayEntry> schemas = dataOverlayService.getDataOverlayEntriesById(projectId, overlayId);
- Set<DataOverlayEntry> schemas = overlay.getEntries();
new ColorModelCommand(part, schemas, userService.getColorExtractorForUser(user)).execute();
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java
index 0be25c64e64a9763e0b3d5d390d69adec39e3771..289b2067995b215fad89145fd6de8c265a0142e3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayEntryDTOSerializer.java
@@ -101,7 +101,8 @@ public class OverlayEntryDTOSerializer extends JsonSerializer<OverlayEntryDTO> {
"description",
"type",
"geneVariations",
- "uniqueId");
+ "uniqueId",
+ "width");
}
private void writeField(final JsonGenerator gen, final String field, final Object value, final PropertyFilter filter) throws IOException {
diff --git a/service/.project b/service/.project
index ec5afbcdc1c391a84415795af66de4941722f8d2..ba2b83aa611bce5c683cfb1ce886d97d3cf16200 100644
--- a/service/.project
+++ b/service/.project
@@ -16,8 +16,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (11).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java b/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java
index a0e639c28e176c772d6885c63329c0bed4010d68..e4475473940695c92f458d01ed6a106e37ab5eaf 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java
@@ -9,6 +9,7 @@ import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
@@ -261,13 +262,13 @@ public class DataOverlayService implements IDataOverlayService {
}
/**
- * {@link DataOverlayEntry} sometimes contains merged value from few rows.
- * This method split single {@link DataOverlayEntry} object to simple flat
- * objects that can be serialized in a simple tab separated file.
+ * {@link DataOverlayEntry} sometimes contains merged value from few rows. This
+ * method split single {@link DataOverlayEntry} object to simple flat objects
+ * that can be serialized in a simple tab separated file.
*
* @param originalSchema
- * original {@link DataOverlayEntry} object that we want to split
- * into flat objects
+ * original {@link DataOverlayEntry} object that we want to split into
+ * flat objects
* @return {@link List} of flat schema objects obtained from input
*/
private List<DataOverlayEntry> splitColorSchema(final DataOverlayEntry originalSchema) {
@@ -372,8 +373,8 @@ public class DataOverlayService implements IDataOverlayService {
}
/**
- * Returns String representing data of {@link GeneVariantDataOverlayEntry}
- * that should appear in a given {@link ColorSchemaColumn}.
+ * Returns String representing data of {@link GeneVariantDataOverlayEntry} that
+ * should appear in a given {@link ColorSchemaColumn}.
*
* @param schema
* object for which data will be returned
@@ -592,4 +593,16 @@ public class DataOverlayService implements IDataOverlayService {
}
}
+ @Override
+ public Set<DataOverlayEntry> getDataOverlayEntriesById(final String projectId, final Integer overlayId) throws ObjectNotFoundException {
+ Set<DataOverlayEntry> result = getDataOverlayById(projectId, overlayId).getEntries();
+ Hibernate.initialize(result);
+ for (DataOverlayEntry dataOverlayEntry : result) {
+ Hibernate.initialize(dataOverlayEntry.getTypes());
+ Hibernate.initialize(dataOverlayEntry.getMiriamData());
+ Hibernate.initialize(dataOverlayEntry.getCompartments());
+ }
+ return result;
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/PluginService.java b/service/src/main/java/lcsb/mapviewer/services/impl/PluginService.java
index 91a30a5943b49df9a93843be26af0c6898c8edd2..ae10e42858fd9265a2de7409d31396cbe5304fda 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/PluginService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/PluginService.java
@@ -80,7 +80,7 @@ public class PluginService implements IPluginService {
@Override
public void update(final PluginDataEntry entry) {
- pluginDataEntryDao.add(entry);
+ pluginDataEntryDao.update(entry);
}
@Override
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/PublicationService.java b/service/src/main/java/lcsb/mapviewer/services/impl/PublicationService.java
index a33c3b08f5ec40ae1f4c9be0b25781d6b41203ad..20d8f7a8938c0fe7c28ad99f8ee68a7bd29457ed 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/PublicationService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/PublicationService.java
@@ -41,7 +41,7 @@ public class PublicationService implements IPublicationService {
for (final String id : missingIds) {
try {
Article article = pubmedParser.getPubmedArticleById(id);
- if (article != null) {
+ if (article != null && id.equals(article.getPubmedId())) {
articleDao.add(article);
}
} catch (final PubmedSearchException e) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataOverlayService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataOverlayService.java
index e1d7490320316be2235074ce268acdde49f9a419..1160199429516bb02dd0b7b4e67bfe6d7c56a895 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataOverlayService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataOverlayService.java
@@ -5,6 +5,7 @@ import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
+import java.util.Set;
import java.util.concurrent.ExecutionException;
import lcsb.mapviewer.commands.ColorExtractor;
@@ -38,11 +39,11 @@ public interface IDataOverlayService {
private User user;
/**
- * Input stream with coloring information data in the stream should
- * correspond to a file that can be parsed by
- * {@link lcsb.mapviewer.services.utils.ColorSchemaXlsxReader
- * ColorSchemaReader} . This is a copy of original input stream, so we can
- * read this input stream multiple times.
+ * Input stream with coloring information data in the stream should correspond
+ * to a file that can be parsed by
+ * {@link lcsb.mapviewer.services.utils.ColorSchemaXlsxReader ColorSchemaReader}
+ * . This is a copy of original input stream, so we can read this input stream
+ * multiple times.
*/
private ByteArrayOutputStream colorInputStreamCopy;
@@ -169,10 +170,11 @@ public interface IDataOverlayService {
void waitForJobQueueToEmpty() throws InterruptedException, ExecutionException;
-
void add(final DataOverlay overlay);
FileEntry getDataOverlayFileById(final String projectId, final Integer overlayId) throws ObjectNotFoundException;
byte[] generateLegend(String projectId, Integer overlayId, ColorExtractor colorExtractor) throws ObjectNotFoundException, IOException;
+
+ Set<DataOverlayEntry> getDataOverlayEntriesById(String projectId, Integer overlayId) throws ObjectNotFoundException;
}
diff --git a/test_spelling.sh b/test_spelling.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5ecbd2f27d8c91b53a0860fb04ec99cc815d88f8
--- /dev/null
+++ b/test_spelling.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+result=0
+
+while read filename
+do
+ html=''
+ case $filename in *.html)
+ html=" --mode html ";;
+ esac
+ lines=`cat $filename | aspell $html --lang=en --encoding=utf-8 --add-extra-dicts=./.aspell.en.pws --add-extra-dicts=./.aspell-api-exceptions.pws list|wc -l`
+ if [ $lines -ne 0 ]
+ then
+ echo "[$filename] Unknown words:"
+ echo
+ cat $filename | aspell --lang=en $html --encoding=utf-8 --add-extra-dicts=./.aspell.en.pws --add-extra-dicts=./.aspell-api-exceptions.pws list |sort |uniq
+ result=1
+ fi
+done <<< "$(ls web/target/generated-docs/*.html CHANGELOG -c1)"
+
+exit $result
diff --git a/web/.project b/web/.project
index 0897627f36b8100d9a710728adbbec63f6411634..fc438eb8ab84b68d91263d67ef2b69ca18fed173 100644
--- a/web/.project
+++ b/web/.project
@@ -21,8 +21,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/net.sf.eclipsecs.core.CheckstyleBuilder (13).launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
diff --git a/web/src/main/asciidoc/genomics.adoc b/web/src/main/asciidoc/genomics.adoc
index a265d559e15ffd583cf0d22c6cb456f6d76cf510..881c63c77c0c34fe162250ba15f7eb628fe68925 100644
--- a/web/src/main/asciidoc/genomics.adoc
+++ b/web/src/main/asciidoc/genomics.adoc
@@ -64,9 +64,6 @@ include::{snippets}/genomics/download_genome/curl-request.adoc[]
=== Request Parameters
include::{snippets}/genomics/download_genome/request-parameters.adoc[]
-=== Response Fields
-include::{snippets}/genomics/download_genome/response-fields.adoc[]
-
== Get information about specific downloaded genome
=== CURL sample
@@ -105,9 +102,6 @@ include::{snippets}/genomics/delete_genome_information/path-parameters.adoc[]
=== Path Parameters
include::{snippets}/genomics/add_gene_mapping/path-parameters.adoc[]
-=== Response Fields
-include::{snippets}/genomics/add_gene_mapping/response-fields.adoc[]
-
=== CURL sample
include::{snippets}/genomics/add_gene_mapping/curl-request.adoc[]
diff --git a/web/src/main/asciidoc/index.adoc b/web/src/main/asciidoc/index.adoc
index ee56886b186ef75271330782698c27730fdc48bb..b5eb4d5e4ed806a989e53d46b6d9c6a72781d830 100644
--- a/web/src/main/asciidoc/index.adoc
+++ b/web/src/main/asciidoc/index.adoc
@@ -17,7 +17,7 @@ For API calls that require authentication MINERVA_AUTH_TOKEN obtained during log
== QuickStart guide
Here is sample example that shows information about all projects accessible by guest account (anonymous user):
-include::{snippets}/projects/project_data/list/curl-request.adoc[]
+include::{snippets}/projects/project_data/list_guest/curl-request.adoc[]
If we are interested in the API calls that require more privileges than anonymous user we need to login first:
diff --git a/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java b/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java
index dfbd94d4b23f3d1f3ce62107a145f40d0a98b734..b1f7095eddf13633e96c71d77e23f03a62169e54 100644
--- a/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java
+++ b/web/src/test/java/lcsb/mapviewer/web/AllIntegrationTests.java
@@ -9,6 +9,7 @@ import lcsb.mapviewer.web.bean.utils.StartupBeanTest;
@RunWith(Suite.class)
@SuiteClasses({ ConfigurationControllerIntegrationTest.class,
ChemicalControllerIntegrationTest.class,
+ CommandFormatterTest.class,
CommentControllerIntegrationTest.class,
ConvertControllerIntegrationTest.class,
DrugControllerIntegrationTest.class,
@@ -24,6 +25,7 @@ import lcsb.mapviewer.web.bean.utils.StartupBeanTest;
ParameterControllerIntegrationTest.class,
PluginControllerIntegrationTest.class,
ProjectControllerIntegrationTest.class,
+ ProjectControllerIntegrationForDocsTest.class,
PublicationsControllerIntegrationTest.class,
ReactionControllerIntegrationTest.class,
SpringSecurityGeneralIntegrationTest.class,
diff --git a/web/src/test/java/lcsb/mapviewer/web/CommandFormatterTest.java b/web/src/test/java/lcsb/mapviewer/web/CommandFormatterTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c14fa665a8bc585d05401ac1903c7e859041ae0e
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/web/CommandFormatterTest.java
@@ -0,0 +1,46 @@
+package lcsb.mapviewer.web;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Arrays;
+
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.http.MediaType;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+import lcsb.mapviewer.web.utils.CommandFormatterWithReplacingPostFilenameHeader;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+public class CommandFormatterTest extends ControllerIntegrationTest {
+
+ @Test
+ public void testExtractDefaultContentTypeContentType() throws Exception {
+ CommandFormatterWithReplacingPostFilenameHeader commandFormatter = new CommandFormatterWithReplacingPostFilenameHeader(" ");
+ String contentType = commandFormatter.getContentType(Arrays.asList(" "));
+ assertEquals(MediaType.APPLICATION_OCTET_STREAM_VALUE, contentType);
+ }
+
+ @Test
+ public void testExtractCustomContentType() throws Exception {
+ CommandFormatterWithReplacingPostFilenameHeader commandFormatter = new CommandFormatterWithReplacingPostFilenameHeader(" ");
+ String contentType = commandFormatter.getContentType(Arrays.asList(" ", "-H \"Content-Type: text/plain\""));
+ assertEquals("text/plain", contentType);
+ }
+
+ @Test
+ public void testExtractCustomContentTypeSingleQuote() throws Exception {
+ CommandFormatterWithReplacingPostFilenameHeader commandFormatter = new CommandFormatterWithReplacingPostFilenameHeader(" ");
+ String contentType = commandFormatter.getContentType(Arrays.asList(" ", "-H 'Content-Type: text/plain'"));
+ assertEquals("text/plain", contentType);
+ }
+
+ @Test
+ public void testExtractCustomContentTypeWithCharset() throws Exception {
+ CommandFormatterWithReplacingPostFilenameHeader commandFormatter = new CommandFormatterWithReplacingPostFilenameHeader(" ");
+ String contentType = commandFormatter.getContentType(Arrays.asList(" ", "-H 'Content-Type: text/html; charset=utf-8'"));
+ assertTrue(contentType.contains("charset=utf-8"));
+ }
+
+}
diff --git a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
index 176d3c651664de0a825f5f33372714d07b69cf24..9d28d3f46ea35c993a93ccc96482bf9c5286ff30 100644
--- a/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/CommentControllerIntegrationTest.java
@@ -672,7 +672,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -717,7 +717,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
public void testAddElementCommentAsAnonymous() throws Exception {
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -748,7 +748,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -789,7 +789,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -815,7 +815,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -844,7 +844,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -871,7 +871,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -892,7 +892,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -919,7 +919,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -941,7 +941,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("modelId", map.getId() + ""))));
@@ -1024,7 +1024,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
private String createContentBody(final String type, final String value) throws IOException, UnsupportedEncodingException {
List<BasicNameValuePair> params = new ArrayList<>(Arrays.asList(
new BasicNameValuePair("email", "a@a.lu"),
- new BasicNameValuePair("content", "tes content"),
+ new BasicNameValuePair("content", "test content"),
new BasicNameValuePair("pinned", "true"),
new BasicNameValuePair("coordinates", "10,2"),
new BasicNameValuePair("modelId", map.getId() + "")));
diff --git a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
index 101b715b8e6e12e0eedb43382de6551c7092b32d..80b5ad1d833ffac55b91fd7ed2d6d9a9ffb93962 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ControllerIntegrationTest.java
@@ -194,12 +194,12 @@ public abstract class ControllerIntegrationTest extends TestUtils {
}
/**
- * This method can be used to work around the fact that MockMvc cannot
- * retrieve cookies from Spring Security. The Reason for that is that MockMvc
- * calls the controller directly and (partially?) bypasses Spring.
+ * This method can be used to work around the fact that MockMvc cannot retrieve
+ * cookies from Spring Security. The Reason for that is that MockMvc calls the
+ * controller directly and (partially?) bypasses Spring.
* <p>
- * This method creates a mocked session that can be used in a request as
- * opposed to the token.
+ * This method creates a mocked session that can be used in a request as opposed
+ * to the token.
* </p>
* <p>
* FIXME: Find a better solution, that does not violate the spirit of
@@ -366,13 +366,13 @@ public abstract class ControllerIntegrationTest extends TestUtils {
+ "</lambda></math>");
map.addFunction(sbmlFunction);
- SbmlParameter sbmlParameter = new SbmlParameter("param1");
- sbmlParameter.setName("ppp");
+ SbmlParameter sbmlParameter = new SbmlParameter("parameter1");
+ sbmlParameter.setName("D coefficient");
sbmlParameter.setValue(1.2);
map.addParameter(sbmlParameter);
SbmlUnit sbmlUnit = new SbmlUnit("u1");
- sbmlUnit.setName("uuu");
+ sbmlUnit.setName("Weight");
map.addUnit(sbmlUnit);
Compartment comp = createCompartment();
@@ -382,6 +382,7 @@ public abstract class ControllerIntegrationTest extends TestUtils {
reaction.setZ(2);
reaction.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 0)));
reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "28725475"));
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "123,"));
SbmlKinetics kinetics = new SbmlKinetics();
kinetics.setDefinition("<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><lambda>\n"
+ "<bvar>\n"
@@ -444,7 +445,7 @@ public abstract class ControllerIntegrationTest extends TestUtils {
ProjectBackground background = new ProjectBackground("Normal");
int id = 0;
for (final ModelData model : project.getModels()) {
- ProjectBackgroundImageLayer layer = new ProjectBackgroundImageLayer(model, "dir_" + (id++));
+ ProjectBackgroundImageLayer layer = new ProjectBackgroundImageLayer(model, "directory_" + (id++));
background.addProjectBackgroundImageLayer(layer);
}
background.setDefaultOverlay(true);
@@ -483,7 +484,8 @@ public abstract class ControllerIntegrationTest extends TestUtils {
return element;
}
- private void assignCoordinates(final double x, final double y, final double width, final double height, final Element protein) {
+ private void assignCoordinates(final double x, final double y, final double width, final double height,
+ final Element protein) {
protein.setX(x);
protein.setY(y);
protein.setZ(z++);
@@ -585,7 +587,8 @@ public abstract class ControllerIntegrationTest extends TestUtils {
return createOverlay(project, admin, content, DataOverlayType.GENERIC);
}
- protected DataOverlay createOverlay(final Project project, final User admin, final String content, final DataOverlayType type)
+ protected DataOverlay createOverlay(final Project project, final User admin, final String content,
+ final DataOverlayType type)
throws Exception {
UploadedFileEntry file = new UploadedFileEntry();
file.setFileContent(content.getBytes());
@@ -668,4 +671,9 @@ public abstract class ControllerIntegrationTest extends TestUtils {
.description("target element that we are searching for in format TYPE:ID")
.optional());
}
+
+ protected PathParametersSnippet projectPathParameters() {
+ return pathParameters(parameterWithName("projectId").description("project identifier"));
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java
index 0a703d35f65b0cd616f71542ab61bbbc1d508bf1..54618a6497af371dce41dffbded9462a6ba12181 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ConvertControllerIntegrationTest.java
@@ -11,17 +11,22 @@ import static org.springframework.restdocs.request.RequestDocumentation.paramete
import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+import java.awt.geom.Rectangle2D;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
import org.apache.commons.io.FileUtils;
import org.junit.Test;
@@ -38,7 +43,10 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Element;
@RunWith(SpringJUnit4ClassRunner.class)
@@ -51,7 +59,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
public void testConvertInvalidFile() throws Exception {
String body = "invalid content";
RequestBuilder request = post("/api/convert/image/SBGN-ML:svg")
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .contentType(MediaType.TEXT_PLAIN_VALUE)
.content(body);
mockMvc.perform(request)
@@ -79,7 +87,7 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
public void testConvertInvalidMapFormat() throws Exception {
String body = "invalid content";
RequestBuilder request = post("/api/convert/image/unknown:svg")
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .contentType(MediaType.TEXT_PLAIN_VALUE)
.content(body);
mockMvc.perform(request)
@@ -155,8 +163,8 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8);
RequestBuilder request = post("/api/convert/{inputFormat}:{outputFormat}", "CellDesigner_SBML", "GPML")
.header("post-filename", "input_file.xml")
- .content(content.getBytes("UTF-8"))
- .characterEncoding("UTF-8");
+ .contentType(MediaType.TEXT_PLAIN_VALUE)
+ .content(content);
mockMvc.perform(request)
.andDo(document("converter/format_conversion",
@@ -428,4 +436,89 @@ public class ConvertControllerIntegrationTest extends ControllerIntegrationTest
assertTrue(inputs.size() > 0);
}
+ @Test
+ public void testInvalidGpml2Sbml() throws Exception {
+ String content = "blah";
+
+ RequestBuilder request = post("/api/convert/{inputFormat}:{outputFormat}", "GPML", "SBML")
+ .header("post-filename", "input_file.xml")
+ .content(content.getBytes("UTF-8"))
+ .characterEncoding("UTF-8");
+ mockMvc.perform(request)
+ .andExpect(status().isBadRequest());
+ }
+
+ @Test
+ public void testInvalidGpml2Svg() throws Exception {
+ String content = "blah";
+
+ RequestBuilder request = post("/api/convert/image/{inputFormat}:{outputFormat}", "GPML", "svg")
+ .header("post-filename", "input_file.xml")
+ .content(content.getBytes("UTF-8"))
+ .characterEncoding("UTF-8");
+ mockMvc.perform(request)
+ .andExpect(status().isBadRequest());
+ }
+
+ @Test
+ public void convertCellDesignerToGpmlUsingUrlEncoded() throws Exception {
+ File file = new File("src/test/resources/convert/cd-sample.xml");
+ String content = FileUtils.readFileToString(file, StandardCharsets.UTF_8);
+ content = URLEncoder.encode(content, "UTF-8");
+ RequestBuilder request = post("/api/convert/{inputFormat}:{outputFormat}", "CellDesigner_SBML", "GPML")
+ .header("post-filename", "input_file.xml")
+ .content(content.getBytes("UTF-8"))
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .characterEncoding("UTF-8");
+
+ mockMvc.perform(request)
+ .andExpect(status().isUnsupportedMediaType());
+ }
+
+ @Test
+ public void testMergeCellDesignerWithTextArea() throws Exception {
+ Model model = new ModelFullIndexed(null);
+ Layer layer = new Layer();
+ LayerText text = new LayerText(new Rectangle2D.Double(10, 20, 30, 40), "test text");
+ model.addLayer(layer);
+ layer.addLayerText(text);
+ model.setWidth(300);
+ model.setHeight(400);
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.model2String(model);
+
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ try (ZipOutputStream zos = new ZipOutputStream(baos)) {
+ ZipEntry entry = new ZipEntry("maps/map.xml");
+
+ zos.putNextEntry(entry);
+ zos.write(xml.getBytes());
+ zos.closeEntry();
+ } catch (IOException ioe) {
+ ioe.printStackTrace();
+ }
+
+ byte[] body = baos.toByteArray();
+ RequestBuilder request = post("/api/convert/merge/{inputFormat}:{outputFormat}", "CellDesigner_SBML",
+ "CellDesigner_SBML")
+ .header("post-filename", "maps.zip")
+ .content(body);
+
+ byte[] content = mockMvc.perform(request)
+ .andDo(document("converter/merge_maps",
+ pathParameters(
+ parameterWithName("inputFormat")
+ .description("input format, available options: " + getModelInputConverters()),
+ parameterWithName("outputFormat")
+ .description("output format, available options: " + getModelOutputConverters()))))
+ .andExpect(status().is2xxSuccessful())
+ .andReturn().getResponse().getContentAsByteArray();
+
+ Model outputMap = parser.createModel(new ConverterParams().inputStream(new ByteArrayInputStream(content)));
+
+ assertEquals(1, outputMap.getLayers().size());
+ assertEquals(1, outputMap.getLayers().iterator().next().getTexts().size());
+
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java b/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java
index 984d0be04199d94527772cd05f9143fa79e6c0cd..8841c35648e60602da1304f4a7a178c8dbf8ebc2 100644
--- a/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java
+++ b/web/src/test/java/lcsb/mapviewer/web/EndPointsInputValidationTests.java
@@ -43,7 +43,7 @@ public class EndPointsInputValidationTests extends ControllerIntegrationTest {
private static String[] testValues = { " ", "-1", "0", "empty", "admin", "1.00,2.00", "17.00", "1" };
private static List<HttpStatus> validResponses = Arrays.asList(HttpStatus.OK, HttpStatus.BAD_REQUEST,
- HttpStatus.NOT_FOUND, HttpStatus.FORBIDDEN, HttpStatus.UNAVAILABLE_FOR_LEGAL_REASONS);
+ HttpStatus.NOT_FOUND, HttpStatus.FORBIDDEN, HttpStatus.UNAVAILABLE_FOR_LEGAL_REASONS, HttpStatus.UNSUPPORTED_MEDIA_TYPE);
@Autowired
private RequestMappingHandlerMapping requestMappingHandlerMapping;
diff --git a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
index b139f65f101f4fc47f317fc078c8ab9bc22c87cf..fd8e1413177da84c515d7f0873db1ac123b611a2 100644
--- a/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/FileControllerIntegrationTest.java
@@ -83,12 +83,11 @@ public class FileControllerIntegrationTest extends ControllerIntegrationTest {
.get("id")
.getAsString();
- body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
-
- new BasicNameValuePair("data", "test_content"))));
+ body = "test_content\nhello world";
request = post("/api/files/{fileId}:uploadContent", fileId)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .contentType(MediaType.APPLICATION_OCTET_STREAM_VALUE)
+ .header("post-filename", "input_file.txt")
.content(body)
.session(session);
@@ -96,13 +95,13 @@ public class FileControllerIntegrationTest extends ControllerIntegrationTest {
.andDo(document("file/upload_content",
pathParameters(parameterWithName("fileId")
.description("file id")),
- requestParameters(
- parameterWithName("data")
- .description("content to append")),
+ requestParameters(),
responseFields(fileResponseFields())))
.andExpect(status().is2xxSuccessful());
- assertNotNull(fileService.getById(Integer.valueOf(fileId)));
+ UploadedFileEntry file = fileService.getById(Integer.valueOf(fileId));
+ assertNotNull(file);
+ assertEquals(body, new String(file.getFileContent()));
}
@Test
diff --git a/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java
index 43717a34696934599e98e81e7075d60dff0198ad..5d985272ab110d6f585e5538e513ad46ed0780e6 100644
--- a/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java
@@ -75,7 +75,8 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
@After
public void tearDown() throws Exception {
referenceGenomeConnector.waitForDownloadsToFinish();
- ReferenceGenome referenceGenome = referenceGenomeService.getReferenceGenomeViewByParams(ebolaId, ReferenceGenomeType.UCSC, "eboVir3");
+ ReferenceGenome referenceGenome = referenceGenomeService.getReferenceGenomeViewByParams(ebolaId,
+ ReferenceGenomeType.UCSC, "eboVir3");
if (referenceGenome != null) {
referenceGenomeService.removeGenome(referenceGenome);
}
@@ -212,7 +213,8 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
.andDo(document("genomics/download_genome",
requestParameters(
parameterWithName("organismId").description("organism taxonomy id"),
- parameterWithName("type").description("genome type, acceptable values: " + snippets.getOptionsAsString(ReferenceGenomeType.class)),
+ parameterWithName("type").description(
+ "genome type, acceptable values: " + snippets.getOptionsAsString(ReferenceGenomeType.class)),
parameterWithName("version").description("genome version"),
parameterWithName("url").description("url address from where the file should be downloaded")),
responseFields()))
@@ -243,7 +245,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
genome.setType(ReferenceGenomeType.UCSC);
genome.setVersion("eboVir3");
ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
- mapping.setName("xy");
+ mapping.setName("custom-gene-mapping");
mapping.setSourceUrl("https://minerva-dev.lcsb.uni.lu/tmp/refGene.bb");
genome.addReferenceGenomeGeneMapping(mapping);
@@ -307,7 +309,8 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
.description("download progress")
.type(JsonFieldType.NUMBER),
fieldWithPath("geneMapping[].idObject")
- .ignored(),
+ .description("id of the gene mapping")
+ .type(JsonFieldType.NUMBER),
fieldWithPath("idObject")
.description("unique id of genome in minerva")
.type(JsonFieldType.NUMBER),
@@ -352,7 +355,8 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
mockMvc.perform(request)
.andDo(document("genomics/delete_genome_information",
pathParameters(
- parameterWithName("genomeId").description("genome id")),
+ parameterWithName("genomeId")
+ .description("genome id (genomeId is retrieved as idObject described above in 6.3)")),
responseFields()))
.andExpect(status().is2xxSuccessful());
@@ -398,7 +402,7 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
mockMvc.perform(request)
.andDo(document("genomics/add_gene_mapping",
pathParameters(
- parameterWithName("genomeId").description("genome id")),
+ parameterWithName("genomeId").description("genome id (genomeId is retrieved as idObject described above in 6.3)")),
requestParameters(parameterWithName("name").description("name of the gene-genome mapping"),
parameterWithName("url").description("url where file with mapping is located")),
responseFields()))
@@ -425,8 +429,10 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
mockMvc.perform(request)
.andDo(document("genomics/delete_gene_mapping",
pathParameters(
- parameterWithName("genomeId").description("genome id"),
- parameterWithName("geneMappingId").description("gene genome mapping id"))))
+ parameterWithName("genomeId")
+ .description("genome id (genomeId is retrieved as idObject described above in 6.3)"),
+ parameterWithName("geneMappingId")
+ .description("gene genome mapping id (geneMapping[].objectId described in 6.3)"))))
.andExpect(status().is2xxSuccessful());
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
index a6badf6ddfb46196510448c7aa38b164bf80e572..998f231085c328b53b77ca4b6358f50359313ed4 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java
@@ -218,7 +218,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
.type("int")
.optional(),
subsectionWithPath("[].other")
- .description("list of oher properties")
+ .description("list of other properties")
.type("object")
.optional());
}
@@ -282,7 +282,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
.type(JsonFieldType.OBJECT)
.optional(),
subsectionWithPath("[].other")
- .description("list of oher properties")
+ .description("list of other properties")
.type(JsonFieldType.OBJECT)
.optional()));
fields.addAll(reactionNodeFields("[].reactants[]"));
@@ -636,7 +636,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
mapPathParameters(),
responseFields(
fieldWithPath("[]")
- .description("list of all full search queries that could be used for quering the map")
+ .description("list of all full search queries that could be used for querying the map")
.type("array<string>"))))
.andExpect(status().is2xxSuccessful());
}
@@ -655,7 +655,7 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
.type("number"),
fieldWithPath("defaultZoomLevel").description("default zoom level used in frontend visualization")
.type("number"),
- fieldWithPath("minZoom").description("minimum zoom level availbale for the map").type("number"),
+ fieldWithPath("minZoom").description("minimum zoom level available for the map").type("number"),
fieldWithPath("maxZoom").description("maximum zoom level available for the map").type("number"),
fieldWithPath("authors").description("list of authors").type("array<Author>"),
fieldWithPath("references").description("list of references").type("array<Reference>"),
@@ -856,6 +856,25 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
.andExpect(status().is2xxSuccessful());
}
+ @Test
+ public void testDownloadModelWithOverlay() throws Exception {
+ MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ ModelData submap = getSubmap();
+ User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+ DataOverlay overlay = createOverlay(project, admin, "name\tvalue\nGSTA4\t1");
+
+ RequestBuilder request = get("/api/projects/{projectId}/models/{mapId}:downloadModel?"
+ + "handlerClass={handlerClass}"
+ + "&overlayIds={overlayId}", TEST_PROJECT, submap.getId(),
+ CellDesignerXmlParser.class.getCanonicalName(),
+ overlay.getId())
+ .session(session);
+
+ mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful());
+ }
+
@Test
public void testDownloadSubmapModelWithPost() throws Exception {
ModelData submap = getSubmap();
diff --git a/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java
index fd595ba6dd62f5c3b742524407831e74888b33f9..18eed126aa33a26842516925e1325146926d57e0 100644
--- a/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/MiRnaControllerIntegrationTest.java
@@ -18,7 +18,6 @@ import org.springframework.test.web.servlet.RequestBuilder;
@RunWith(SpringJUnit4ClassRunner.class)
public class MiRnaControllerIntegrationTest extends ControllerIntegrationTest {
-
@Before
public void setup() {
}
@@ -72,7 +71,7 @@ public class MiRnaControllerIntegrationTest extends ControllerIntegrationTest {
getProjectPathParameters(),
responseFields(
fieldWithPath("[]")
- .description("list of suggested mirna queries")
+ .description("list of suggested miRNA queries")
.type("array<string>"))))
.andExpect(status().is2xxSuccessful())
.andReturn().getResponse().getContentAsString();
@@ -92,7 +91,7 @@ public class MiRnaControllerIntegrationTest extends ControllerIntegrationTest {
private ResponseFieldsSnippet listOfMiRnaFields() {
return responseFields(
subsectionWithPath("[].id")
- .description("identifier of the mirna")
+ .description("identifier of the miRNA")
.type("object"),
fieldWithPath("[].name")
.description("name")
diff --git a/web/src/test/java/lcsb/mapviewer/web/NumericDirectoryNameGeneratorConfiguration.java b/web/src/test/java/lcsb/mapviewer/web/NumericDirectoryNameGeneratorConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..f4894f40e1c52c9dac01be122eae7b54dc8aa528
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/web/NumericDirectoryNameGeneratorConfiguration.java
@@ -0,0 +1,34 @@
+package lcsb.mapviewer.web;
+
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+
+import lcsb.mapviewer.api.projects.IDirectoryNameGenerator;
+import lcsb.mapviewer.common.Md5;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+
+@Profile("NumericDirectoryNameGeneratorProfile")
+@Configuration
+public class NumericDirectoryNameGeneratorConfiguration {
+
+ @Autowired
+ private IProjectService projectService;
+
+ @Bean
+ @Primary
+ public IDirectoryNameGenerator directoryNameGenerator() throws Exception {
+ IDirectoryNameGenerator mock = Mockito.mock(IDirectoryNameGenerator.class);
+
+ Mockito.when(mock.projectIdToDirectoryName(Mockito.anyString())).thenAnswer(projectId -> {
+ long id = projectService.getNextId();
+ return Md5.compute(projectId + "-" + id).replaceAll("[a-z]", "0");
+ });
+
+ return mock;
+ }
+
+}
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 1ee23b297ffd747577db30fe3b22729f8e200237..e261c654fea3ece0f237683ec215caef4efa13b9 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -437,6 +437,28 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
.andReturn().getResponse().getContentAsString();
}
+ @Test
+ public void testGetReactionForOverlayWithWidth() throws Exception {
+ String reactionId = reaction.getElementId();
+ DataOverlay overlay = createOverlay(project, user, "element_identifier\tvalue\tline_width\n" + reactionId + "\t1\t6");
+
+ MockHttpSession session = createSession(TEST_USER_LOGIN, TEST_USER_PASSWORD);
+
+ RequestBuilder request = get(
+ "/api/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bioEntities/reactions/{reactionId}/",
+ TEST_PROJECT, overlay.getId(), map.getId(), reaction.getId())
+ .session(session);
+
+ String json = mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful())
+ .andReturn().getResponse().getContentAsString();
+ List<Map<String, Object>> objects = objectMapper.readValue(json, new TypeReference<List<Map<String, Object>>>() {
+ });
+ Map<?, ?> content = (Map<?, ?>) objects.get(0).get("overlayContent");
+ assertTrue(content.containsKey("width"));
+
+ }
+
private PathParametersSnippet getOverlayReactionPathParameters() {
return getOverlayMapPathParameters().and(parameterWithName("reactionId").description("reaction identifier"));
}
@@ -578,10 +600,11 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("content", "element_identifier\tvalue\n\t-1"),
new BasicNameValuePair("name", "overlay name"),
- new BasicNameValuePair("description", "overlay name"),
- new BasicNameValuePair("filename", "overlay name"),
+ new BasicNameValuePair("description", "overlay description"),
+ new BasicNameValuePair("filename", "source.txt"),
new BasicNameValuePair("googleLicenseConsent", "false"),
new BasicNameValuePair("type", "GENERIC"))));
+ logger.debug(body);
RequestBuilder request = post("/api/projects/{projectId}/overlays/", TEST_PROJECT)
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
@@ -1333,7 +1356,7 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
.description("identifier")
.type(JsonFieldType.NUMBER),
fieldWithPath("publicOverlay")
- .description("is the data overlay publicaly available to all users")
+ .description("is the data overlay publicly available to all users")
.type(JsonFieldType.BOOLEAN),
fieldWithPath("googleLicenseConsent")
.description("did creator accepted license required by Google Maps API")
diff --git a/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
index b1f45c22adc1a7c46d839d32416498fa5cdf1dbc..1f5352d5813971b05bea3183aab1ed13115d8907 100644
--- a/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/PluginControllerIntegrationTest.java
@@ -132,7 +132,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
.description("version"),
parameterWithName("isDefault")
.optional()
- .description("should be opened automatically whem map is browsed"),
+ .description("should be opened automatically when map is browsed"),
parameterWithName("isPublic")
.description("should the plugin be visible by all users"),
parameterWithName("url")
@@ -171,7 +171,7 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
.description("md5 checksum of the source file")
.type("string"),
fieldWithPath("isDefault")
- .description("should be opened automatically whem map is browsed")
+ .description("should be opened automatically when map is browsed")
.type("boolean"),
fieldWithPath("isPublic")
.description("should be visible on plugin list to all users")
@@ -325,6 +325,46 @@ public class PluginControllerIntegrationTest extends ControllerIntegrationTest {
assertEquals("xxx", result);
}
+ @Test
+ public void updateUserPluginData() throws Exception {
+ MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_LOGIN);
+
+ String body = "value=xxx";
+ Plugin plugin = createPlugin();
+
+ RequestBuilder request = post("/api/plugins/{hash}/data/users/{key}/", plugin.getHash(), "my_key")
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .session(session)
+ .content(body);
+
+ mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful());
+
+ body = "value=xxx2";
+ request = post("/api/plugins/{hash}/data/users/{key}/", plugin.getHash(), "my_key")
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .session(session)
+ .content(body);
+
+ mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful());
+
+ request = get("/api/plugins/{hash}/data/users/{key}/", plugin.getHash(), "my_key")
+ .session(session);
+
+ String response = mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful())
+ .andReturn().getResponse().getContentAsString();
+
+ String result = new JsonParser()
+ .parse(response)
+ .getAsJsonObject()
+ .get("value")
+ .getAsString();
+
+ assertEquals("xxx2", result);
+ }
+
@Test
public void removeGlobalPluginData() throws Exception {
Plugin plugin = createPlugin();
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..ac5f1eeccedcb7efa59ca1776c7849e22e870922
--- /dev/null
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationForDocsTest.java
@@ -0,0 +1,262 @@
+package lcsb.mapviewer.web;
+
+import static org.junit.Assert.assertEquals;
+import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
+import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.post;
+import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
+import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
+
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.message.BasicNameValuePair;
+import org.apache.http.util.EntityUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.restdocs.request.ParameterDescriptor;
+import org.springframework.restdocs.request.RequestParametersSnippet;
+import org.springframework.test.context.ActiveProfiles;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.RequestBuilder;
+
+import lcsb.mapviewer.converter.zip.ZipEntryFileDeserializer;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.graphics.MapCanvasType;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ActiveProfiles("NumericDirectoryNameGeneratorProfile")
+public class ProjectControllerIntegrationForDocsTest extends ControllerIntegrationTest {
+
+ private static final String CURATOR_PASSWORD = "curator_pass";
+ private static final String CURATOR_LOGIN = "curator_user";
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IProjectService projectService;
+
+ @Autowired
+ private ProjectSnippets snippets;
+
+ private User curator;
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Before
+ public void setup() {
+ curator = createCurator(CURATOR_LOGIN, CURATOR_PASSWORD);
+ configurationService.setConfigurationValue(ConfigurationElementType.MINERVA_ROOT, "https://pdmap.uni.lu/minerva/");
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ removeProject(TEST_PROJECT);
+ removeUser(curator);
+ configurationService.setConfigurationValue(ConfigurationElementType.MINERVA_ROOT, "");
+ }
+
+ @Test
+ public void addComplexProjectAsCurator() throws Exception {
+ User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+ try {
+ UploadedFileEntry fileEntry = createFile(
+ Files.readAllBytes(Paths.get("./src/test/resources/complex_model_with_submaps.zip")), admin);
+
+ String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("projectId", TEST_PROJECT),
+ new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+ new BasicNameValuePair("name", "Project name"),
+ new BasicNameValuePair("version", "0.0.1"),
+ new BasicNameValuePair("notify-email", "minerva@uni.lu"),
+ new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+ new BasicNameValuePair("parser",
+ "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"),
+
+ new BasicNameValuePair("zip-entries[0][_type]", "MAP"),
+ new BasicNameValuePair("zip-entries[0][_filename]", "main.xml"),
+ new BasicNameValuePair("zip-entries[0][_data][root]", "true"),
+ new BasicNameValuePair("zip-entries[0][_data][name]", "main"),
+ new BasicNameValuePair("zip-entries[0][_data][type][id]", "UNKNOWN"),
+
+ new BasicNameValuePair("zip-entries[1][_type]", "MAP"),
+ new BasicNameValuePair("zip-entries[1][_filename]", "submaps/mapping.xml"),
+ new BasicNameValuePair("zip-entries[1][_data][root]", "false"),
+ new BasicNameValuePair("zip-entries[1][_data][name]", "mapping"),
+ new BasicNameValuePair("zip-entries[1][_data][type][id]", "UNKNOWN"),
+
+ new BasicNameValuePair("zip-entries[2][_type]", "MAP"),
+ new BasicNameValuePair("zip-entries[2][_filename]", "submaps/s1.xml"),
+ new BasicNameValuePair("zip-entries[2][_data][root]", "false"),
+ new BasicNameValuePair("zip-entries[2][_data][name]", "s1"),
+ new BasicNameValuePair("zip-entries[2][_data][type][id]", "UNKNOWN"),
+
+ new BasicNameValuePair("zip-entries[3][_type]", "MAP"),
+ new BasicNameValuePair("zip-entries[3][_filename]", "submaps/s2.xml"),
+ new BasicNameValuePair("zip-entries[3][_data][root]", "false"),
+ new BasicNameValuePair("zip-entries[3][_data][name]", "s2"),
+ new BasicNameValuePair("zip-entries[3][_data][type][id]", "UNKNOWN"),
+
+ new BasicNameValuePair("zip-entries[4][_type]", "MAP"),
+ new BasicNameValuePair("zip-entries[4][_filename]", "submaps/s3.xml"),
+ new BasicNameValuePair("zip-entries[4][_data][root]", "false"),
+ new BasicNameValuePair("zip-entries[4][_data][name]", "s3"),
+ new BasicNameValuePair("zip-entries[4][_data][type][id]", "UNKNOWN")
+
+ )));
+
+ RequestBuilder request = post("/api/projects/{projectId}/", TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
+
+ mockMvc.perform(request).andExpect(status().is2xxSuccessful())
+ .andDo(document("projects/project_data/create_zip",
+ projectPathParameters(),
+ createProjectRequestSnippet(),
+
+ snippets.getProjectSnippet()));
+
+ } finally {
+ waitForProjectToFinishLoading(TEST_PROJECT);
+ Project project = projectService.getProjectByProjectId(TEST_PROJECT);
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ }
+ }
+
+ @Test
+ public void addProjectAsCurator() throws Exception {
+ User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+ try {
+ UploadedFileEntry fileEntry = createFile(
+ new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
+ admin);
+
+ String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("projectId", TEST_PROJECT),
+ new BasicNameValuePair("name", "New Disease Map"),
+ new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+ new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+ new BasicNameValuePair("cache", "false"),
+ new BasicNameValuePair("description", "this is my awesome project"),
+ new BasicNameValuePair("notify-email", "notify.me@uni.lu"),
+ new BasicNameValuePair("disease", "D010300"),
+ new BasicNameValuePair("organism", "9606"),
+ new BasicNameValuePair("sbgn", "false"),
+ new BasicNameValuePair("version", "0.0.1"),
+ new BasicNameValuePair("annotate", "false"),
+ new BasicNameValuePair("verify-annotations", "false"),
+ new BasicNameValuePair("parser", "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
+
+ RequestBuilder request = post("/api/projects/{projectId}/", TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
+
+ mockMvc.perform(request).andExpect(status().is2xxSuccessful())
+ .andDo(document("projects/project_data/create_simple",
+ projectPathParameters(),
+ createProjectRequestSnippet(),
+ snippets.getProjectSnippet()));
+
+ } finally {
+ waitForProjectToFinishLoading(TEST_PROJECT);
+ }
+ }
+
+ private RequestParametersSnippet createProjectRequestSnippet() {
+ return requestParameters(
+ parameterWithName("projectId")
+ .description("project identifier"),
+ parameterWithName("file-id")
+ .description("identifier of the file that should be used to create project"),
+ parameterWithName("parser")
+ .description("class of the parser that should be used for parsing the file. Available options: "
+ + snippets.getParsers()),
+ parameterWithName("cache")
+ .description("should the data from external sources be cached after project was created")
+ .optional(),
+ parameterWithName("description")
+ .description("description of the project")
+ .optional(),
+ parameterWithName("notify-email")
+ .description("email address that should be when something change in the project")
+ .optional(),
+ parameterWithName("disease")
+ .description("disease associated with the project (final MESH id)")
+ .optional(),
+ parameterWithName("name")
+ .description("name of the project")
+ .optional(),
+ parameterWithName("organism")
+ .description("organism associated with the project (final TAXONOMY id)")
+ .optional(),
+ parameterWithName("sbgn")
+ .description("should the map be visualized in sbgn-like way")
+ .optional(),
+ parameterWithName("semantic-zooming-contains-multiple-overlays")
+ .description("display each semantic zoom level in separate overlay")
+ .optional(),
+ parameterWithName("version")
+ .description("version of the project")
+ .optional(),
+ parameterWithName("mapCanvasType")
+ .description("type of map canvas engine to be used when visualizing map. Available options: "
+ + snippets.getOptionsAsString(MapCanvasType.class))
+ .optional(),
+ parameterWithName("annotate")
+ .description("should the project be automatically annotated")
+ .optional(),
+ parameterWithName("verify-annotations")
+ .description("should the annotations be verified")
+ .optional(),
+ parameterWithName("zip-entries")
+ .description(
+ "array of parameters describing each file in the zipped input file, file-index is number starting from 0")
+ .optional()
+
+ )
+ .and(createArrayParameters("zip-entries[{number}][_filename]", "name of the file"))
+ .and(createArrayParameters("zip-entries[{number}][_type]",
+ "type of the file. Possible values: "
+ + snippets.getOptionsAsString(ZipEntryFileDeserializer.ZipEntryFileType.class)))
+ .and(createArrayParameters("zip-entries[{number}][_data][name]", "name of the map/name of the overlay"))
+ .and(createArrayParameters("zip-entries[{number}][_data][mapping]",
+ "for submaps - is this map a mapping file (true/false)"))
+ .and(createArrayParameters("zip-entries[{number}][_data][root]",
+ "for submaps - is this map a root map (true/false)"))
+ .and(createArrayParameters("zip-entries[{number}][_data][type][id]",
+ "for submaps defines type of the connection. Possible values: "
+ + snippets.getOptionsAsString(SubmodelType.class)))
+ .and(createArrayParameters("zip-entries[{number}][_data][description]",
+ "for overlays - description of the overlay"));
+ }
+
+ private List<ParameterDescriptor> createArrayParameters(final String name, final String description) {
+ List<ParameterDescriptor> result = new ArrayList<>();
+ result.add(parameterWithName(name).description(description).optional());
+ for (int i = 0; i < 10; i++) {
+ result.add(parameterWithName(name.replace("{number}", i + "")).description(description).optional().ignored());
+ }
+ return result;
+ }
+
+}
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
index 05f0ec5ac43031ac89950ed861cc0504258f7d0f..8d65f84bbb5314b557a0a9e6f00188ca66b9b5ab 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.web;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
@@ -14,16 +15,17 @@ import static org.springframework.restdocs.payload.PayloadDocumentation.requestF
import static org.springframework.restdocs.payload.PayloadDocumentation.responseFields;
import static org.springframework.restdocs.payload.PayloadDocumentation.subsectionWithPath;
import static org.springframework.restdocs.request.RequestDocumentation.parameterWithName;
-import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
import static org.springframework.restdocs.request.RequestDocumentation.requestParameters;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
import java.io.File;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
import java.nio.file.Files;
import java.nio.file.Paths;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Map;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.message.BasicNameValuePair;
@@ -37,9 +39,7 @@ import org.springframework.http.MediaType;
import org.springframework.mock.web.MockHttpSession;
import org.springframework.restdocs.payload.FieldDescriptor;
import org.springframework.restdocs.payload.JsonFieldType;
-import org.springframework.restdocs.request.ParameterDescriptor;
import org.springframework.restdocs.request.PathParametersSnippet;
-import org.springframework.restdocs.request.RequestParametersSnippet;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.test.web.servlet.RequestBuilder;
@@ -47,7 +47,6 @@ import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.JsonParser;
-import lcsb.mapviewer.converter.zip.ZipEntryFileDeserializer;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
@@ -55,7 +54,6 @@ import lcsb.mapviewer.model.graphics.MapCanvasType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundStatus;
-import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.security.Privilege;
import lcsb.mapviewer.model.security.PrivilegeType;
import lcsb.mapviewer.model.user.ConfigurationElementType;
@@ -117,6 +115,11 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = get("/api/projects/")
.session(session);
+
+ Project project = projectService.getProjectByProjectId(BUILT_IN_PROJECT);
+ project.setDirectory(project.getDirectory().replaceAll("[a-z]", "0"));
+ projectService.updateProject(project);
+
String response = mockMvc.perform(request)
.andExpect(status().is2xxSuccessful())
.andDo(document("projects/project_data/list",
@@ -170,6 +173,29 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
assertEquals("curator should see only limited list of projects", 1, projects);
}
+ @Test
+ public void testGetLimitedProjectsAsGuest() throws Exception {
+ Project project2 = new Project(TEST_PROJECT_2);
+ project2.setOwner(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
+ projectService.add(project2);
+
+ RequestBuilder request = get("/api/projects/");
+
+ String response = mockMvc.perform(request)
+ .andDo(document("projects/project_data/list_guest",
+ responseFields(
+ subsectionWithPath("[]")
+ .description("list of projects").type(JsonFieldType.ARRAY))))
+ .andExpect(status().is2xxSuccessful())
+ .andReturn().getResponse().getContentAsString();
+
+ int projects = new JsonParser()
+ .parse(response)
+ .getAsJsonArray().size();
+
+ assertEquals("guest should see only limited list of projects", 1, projects);
+ }
+
@Test
public void testUserPrivilegesChangeDuringActiveSession() throws Exception {
MockHttpSession session = createSession(CURATOR_LOGIN, CURATOR_PASSWORD);
@@ -208,7 +234,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
.description("log entry column that should be used for sorting (default: id)").optional(),
parameterWithName("sortOrder").description("log entry sort order (asc, desc)").optional(),
parameterWithName("level").description("level of log entry (warning, error)").optional(),
- parameterWithName("length").description("number of log entres we want to obtain").optional(),
+ parameterWithName("length").description("number of log entries we want to obtain").optional(),
parameterWithName("search").description("search query used for filtering").optional()),
projectPathParameters(),
responseFields(
@@ -576,232 +602,6 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
mockMvc.perform(request).andExpect(status().isBadRequest());
}
- @Test
- public void addProjectAsCurator() throws Exception {
- User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
- try {
- UploadedFileEntry fileEntry = createFile(
- new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
- admin);
-
- String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
- new BasicNameValuePair("projectId", TEST_PROJECT),
- new BasicNameValuePair("name", "New Disease Map"),
- new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
- new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
- new BasicNameValuePair("cache", "false"),
- new BasicNameValuePair("description", "this is my awesome project"),
- new BasicNameValuePair("notify-email", "notify.me@uni.lu"),
- new BasicNameValuePair("disease", "D010300"),
- new BasicNameValuePair("organism", "9606"),
- new BasicNameValuePair("sbgn", "false"),
- new BasicNameValuePair("version", "0.0.1"),
- new BasicNameValuePair("annotate", "false"),
- new BasicNameValuePair("verify-annotations", "false"),
- new BasicNameValuePair("parser", "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
-
- RequestBuilder request = post("/api/projects/{projectId}/", TEST_PROJECT)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .content(body)
- .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
-
- mockMvc.perform(request).andExpect(status().is2xxSuccessful())
- .andDo(document("projects/project_data/create_simple",
- projectPathParameters(),
- createProjectRequestSnippet(),
- snippets.getProjectSnippet()));
-
- } finally {
- waitForProjectToFinishLoading(TEST_PROJECT);
- }
- }
-
- @Test
- public void addProjectWithEmptyZipEntries() throws Exception {
- User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
- try {
- UploadedFileEntry fileEntry = createFile(
- new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
- admin);
-
- String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
- new BasicNameValuePair("projectId", TEST_PROJECT),
- new BasicNameValuePair("name", "New Disease Map"),
- new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
- new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
- new BasicNameValuePair("cache", "false"),
- new BasicNameValuePair("description", "this is my awesome project"),
- new BasicNameValuePair("notify-email", "notify.me@uni.lu"),
- new BasicNameValuePair("disease", "D010300"),
- new BasicNameValuePair("organism", "9606"),
- new BasicNameValuePair("sbgn", "false"),
- new BasicNameValuePair("version", "0.0.1"),
- new BasicNameValuePair("annotate", "false"),
- new BasicNameValuePair("verify-annotations", "false"),
- new BasicNameValuePair("zip-entries", ""),
- new BasicNameValuePair("parser", "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
-
- RequestBuilder request = post("/api/projects/{projectId}/", TEST_PROJECT)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .content(body)
- .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
-
- mockMvc.perform(request).andExpect(status().is2xxSuccessful())
- .andDo(document("projects/project_data/create_simple",
- projectPathParameters(),
- createProjectRequestSnippet(),
- snippets.getProjectSnippet()));
-
- } finally {
- waitForProjectToFinishLoading(TEST_PROJECT);
- }
- }
-
- @Test
- public void addComplexProjectAsCurator() throws Exception {
- User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
- try {
- UploadedFileEntry fileEntry = createFile(
- Files.readAllBytes(Paths.get("./src/test/resources/complex_model_with_submaps.zip")), admin);
-
- String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
- new BasicNameValuePair("projectId", TEST_PROJECT),
- new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
- new BasicNameValuePair("name", "Project name"),
- new BasicNameValuePair("version", "0.0.1"),
- new BasicNameValuePair("notify-email", "minerva@uni.lu"),
- new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
- new BasicNameValuePair("parser",
- "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"),
-
- new BasicNameValuePair("zip-entries[0][_type]", "MAP"),
- new BasicNameValuePair("zip-entries[0][_filename]", "main.xml"),
- new BasicNameValuePair("zip-entries[0][_data][root]", "true"),
- new BasicNameValuePair("zip-entries[0][_data][name]", "main"),
- new BasicNameValuePair("zip-entries[0][_data][type][id]", "UNKNOWN"),
-
- new BasicNameValuePair("zip-entries[1][_type]", "MAP"),
- new BasicNameValuePair("zip-entries[1][_filename]", "submaps/mapping.xml"),
- new BasicNameValuePair("zip-entries[1][_data][root]", "false"),
- new BasicNameValuePair("zip-entries[1][_data][name]", "mapping"),
- new BasicNameValuePair("zip-entries[1][_data][type][id]", "UNKNOWN"),
-
- new BasicNameValuePair("zip-entries[2][_type]", "MAP"),
- new BasicNameValuePair("zip-entries[2][_filename]", "submaps/s1.xml"),
- new BasicNameValuePair("zip-entries[2][_data][root]", "false"),
- new BasicNameValuePair("zip-entries[2][_data][name]", "s1"),
- new BasicNameValuePair("zip-entries[2][_data][type][id]", "UNKNOWN"),
-
- new BasicNameValuePair("zip-entries[3][_type]", "MAP"),
- new BasicNameValuePair("zip-entries[3][_filename]", "submaps/s2.xml"),
- new BasicNameValuePair("zip-entries[3][_data][root]", "false"),
- new BasicNameValuePair("zip-entries[3][_data][name]", "s2"),
- new BasicNameValuePair("zip-entries[3][_data][type][id]", "UNKNOWN"),
-
- new BasicNameValuePair("zip-entries[4][_type]", "MAP"),
- new BasicNameValuePair("zip-entries[4][_filename]", "submaps/s3.xml"),
- new BasicNameValuePair("zip-entries[4][_data][root]", "false"),
- new BasicNameValuePair("zip-entries[4][_data][name]", "s3"),
- new BasicNameValuePair("zip-entries[4][_data][type][id]", "UNKNOWN")
-
- )));
-
- RequestBuilder request = post("/api/projects/{projectId}/", TEST_PROJECT)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .content(body)
- .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
-
- mockMvc.perform(request).andExpect(status().is2xxSuccessful())
- .andDo(document("projects/project_data/create_zip",
- projectPathParameters(),
- createProjectRequestSnippet(),
-
- snippets.getProjectSnippet()));
-
- } finally {
- waitForProjectToFinishLoading(TEST_PROJECT);
- Project project = projectService.getProjectByProjectId(TEST_PROJECT);
- assertEquals(ProjectStatus.DONE, project.getStatus());
- }
- }
-
- private RequestParametersSnippet createProjectRequestSnippet() {
- return requestParameters(
- parameterWithName("projectId")
- .description("project identifier"),
- parameterWithName("file-id")
- .description("identifier of the file that should be used to create project"),
- parameterWithName("parser")
- .description("class of the parser that should be used for parsing the file. Available options: "
- + snippets.getParsers()),
- parameterWithName("cache")
- .description("should the data from external sources be cached after project was created")
- .optional(),
- parameterWithName("description")
- .description("description of the project")
- .optional(),
- parameterWithName("notify-email")
- .description("email address that should be when something change in the project")
- .optional(),
- parameterWithName("disease")
- .description("disease associated with the project (final MESH id)")
- .optional(),
- parameterWithName("name")
- .description("name of the project")
- .optional(),
- parameterWithName("organism")
- .description("organism associated with the project (final TAXONOMY id)")
- .optional(),
- parameterWithName("sbgn")
- .description("should the map be visualized in sbgn-like way")
- .optional(),
- parameterWithName("semantic-zoom")
- .description("should custom semantic zooming be enabled")
- .optional(),
- parameterWithName("version")
- .description("version of the project")
- .optional(),
- parameterWithName("mapCanvasType")
- .description("type of map canvas engine to be used when visualizing map. Available options: "
- + snippets.getOptionsAsString(MapCanvasType.class))
- .optional(),
- parameterWithName("annotate")
- .description("should the project be automatically annotated")
- .optional(),
- parameterWithName("verify-annotations")
- .description("should the annotations be verified")
- .optional(),
- parameterWithName("zip-entries")
- .description(
- "array of parameters describing each file in the zipped input file, file-index is number starting from 0")
- .optional()
-
- )
- .and(createArrayParameters("zip-entries[{number}][_filename]", "name of the file"))
- .and(createArrayParameters("zip-entries[{number}][_type]",
- "type of the file. Possible values: "
- + snippets.getOptionsAsString(ZipEntryFileDeserializer.ZipEntryFileType.class)))
- .and(createArrayParameters("zip-entries[{number}][_data][name]", "name of the map/name of the overlay"))
- .and(createArrayParameters("zip-entries[{number}][_data][mapping]",
- "for submaps - is this map a mapping file (true/false)"))
- .and(createArrayParameters("zip-entries[{number}][_data][root]",
- "for submaps - is this map a root map (true/false)"))
- .and(createArrayParameters("zip-entries[{number}][_data][type][id]",
- "for submaps defines type of the connection. Possible values: "
- + snippets.getOptionsAsString(SubmodelType.class)))
- .and(createArrayParameters("zip-entries[{number}][_data][description]",
- "for overlays - description of the overlay"));
- }
-
- private List<ParameterDescriptor> createArrayParameters(final String name, final String description) {
- List<ParameterDescriptor> result = new ArrayList<>();
- result.add(parameterWithName(name).description(description).optional());
- for (int i = 0; i < 10; i++) {
- result.add(parameterWithName(name.replace("{number}", i + "")).description(description).optional().ignored());
- }
- return result;
- }
-
@Test
public void addInvalidProject() throws Exception {
User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
@@ -899,34 +699,9 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
public void removeProjectWithUsedFile() throws Exception {
User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
try {
- UploadedFileEntry fileEntry = createFile(
- new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
- admin);
-
- String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
- new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
- new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
- new BasicNameValuePair("name", "Project name"),
- new BasicNameValuePair("version", "0.0.1"),
- new BasicNameValuePair("notify-email", "minerva@uni.lu"),
- new BasicNameValuePair("parser",
- "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
+ createFullProject(admin);
- RequestBuilder request = post("/api/projects/" + TEST_PROJECT)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .content(body)
- .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
- mockMvc.perform(request).andExpect(status().is2xxSuccessful());
-
- request = post("/api/projects/" + TEST_PROJECT_2)
- .contentType(MediaType.APPLICATION_FORM_URLENCODED)
- .content(body)
- .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
- mockMvc.perform(request).andExpect(status().is2xxSuccessful());
-
- waitForProjectToFinishLoading(TEST_PROJECT_2);
-
- request = delete("/api/projects/{projectId}/", TEST_PROJECT_2)
+ RequestBuilder request = delete("/api/projects/{projectId}/", TEST_PROJECT_2)
.session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
mockMvc.perform(request).andExpect(status().is2xxSuccessful())
@@ -939,6 +714,40 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
}
}
+ private void createFullProject(final User admin)
+ throws UnsupportedEncodingException, IOException, Exception, InterruptedException {
+ UploadedFileEntry fileEntry = createFile(
+ new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
+ admin);
+
+ String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+ new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+ new BasicNameValuePair("name", "Project name"),
+ new BasicNameValuePair("version", "0.0.1"),
+ new BasicNameValuePair("notify-email", "minerva@uni.lu"),
+ new BasicNameValuePair("parser",
+ "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
+
+ RequestBuilder request = post("/api/projects/" + TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
+ mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+
+ request = post("/api/projects/" + TEST_PROJECT_2)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD));
+ mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+
+ waitForProjectToFinishLoading(TEST_PROJECT_2);
+
+ Project project = projectService.getProjectByProjectId(TEST_PROJECT_2);
+ project.setDirectory(project.getDirectory().replaceAll("[a-z]", "0"));
+ projectService.updateProject(project);
+ }
+
@Test
public void addComplexProjectWithInvalidOverlayName() throws Exception {
User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
@@ -1062,6 +871,29 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
responseFields().andWithPrefix("[].", getBackgroundFields())));
}
+ private List<FieldDescriptor> getUpdateBackgroundFields() {
+ return Arrays.asList(
+ fieldWithPath("id")
+ .type(JsonFieldType.NUMBER)
+ .description("identifier"),
+ fieldWithPath("name")
+ .type(JsonFieldType.STRING)
+ .description("name"),
+ fieldWithPath("description")
+ .type(JsonFieldType.STRING)
+ .description("description"),
+ fieldWithPath("creator")
+ .type(JsonFieldType.STRING)
+ .description("who created background"),
+ fieldWithPath("order")
+ .type(JsonFieldType.NUMBER)
+ .description("order used when listing all backgrounds"),
+ fieldWithPath("defaultOverlay")
+ .type(JsonFieldType.BOOLEAN)
+ .description(
+ "should the background be used as default (at most one per project should be marked with true)"));
+ }
+
private List<FieldDescriptor> getBackgroundFields() {
return Arrays.asList(
fieldWithPath("id")
@@ -1128,6 +960,8 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
Project project = createAndPersistProject(TEST_PROJECT);
ProjectBackground background = new ProjectBackground("weird_title");
background.setId(project.getProjectBackgrounds().get(0).getId());
+ background.setCreator(userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
+ background.setDescription("new description");
ObjectMapper mapper = new ObjectMapper();
mapper.addMixIn(ProjectBackground.class, ProjectBackgroundUpdateMixIn.class);
@@ -1142,6 +976,7 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
.andExpect(status().is2xxSuccessful())
.andDo(document("projects/project_backgrounds/update_background",
backgroundPathParameters(),
+ requestFields(getUpdateBackgroundFields()),
responseFields(getBackgroundFields())))
.andReturn().getResponse().getContentAsString();
@@ -1194,10 +1029,6 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
assertEquals(backgrounds.size() - 1, backgroundCount);
}
- private PathParametersSnippet projectPathParameters() {
- return pathParameters(parameterWithName("projectId").description("project identifier"));
- }
-
private PathParametersSnippet backgroundPathParameters() {
return projectPathParameters().and(parameterWithName("backgroundId").description("background identifier"));
}
@@ -1446,4 +1277,56 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
.andExpect(status().is2xxSuccessful());
}
+ @Test
+ public void addComplexProjectWithGenomicLayout() throws Exception {
+ User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+ MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ UploadedFileEntry fileEntry = createFile(
+ Files.readAllBytes(Paths.get("./src/test/resources/complex_model_with_genomic_layout.zip")), admin);
+ try {
+ String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+ new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+ new BasicNameValuePair("parser", "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"),
+
+ new BasicNameValuePair("zip-entries[0][_type]", "MAP"),
+ new BasicNameValuePair("zip-entries[0][_filename]", "main.xml"),
+ new BasicNameValuePair("zip-entries[0][_data][root]", "true"),
+ new BasicNameValuePair("zip-entries[0][_data][name]", "s1"),
+ new BasicNameValuePair("zip-entries[0][_data][type][id]", "UNKNOWN"),
+ new BasicNameValuePair("zip-entries[0][_data][type][name]", "Unknown"),
+
+ new BasicNameValuePair("zip-entries[1][_type]", "OVERLAY"),
+ new BasicNameValuePair("zip-entries[1][_filename]", "layouts/goodSchema.txt"),
+ new BasicNameValuePair("zip-entries[1][_data][name]", "test-o")
+
+ )));
+
+ RequestBuilder request = post("/api/projects/" + TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(session);
+
+ mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+ waitForProjectToFinishLoading(TEST_PROJECT);
+
+ RequestBuilder overlayRequest = get("/api/projects/{projectId}/overlays/", TEST_PROJECT)
+ .session(session);
+
+ String json = mockMvc.perform(overlayRequest)
+ .andExpect(status().is2xxSuccessful())
+ .andReturn().getResponse().getContentAsString();
+ List<Map<String, Object>> overlays = objectMapper.readValue(json, new TypeReference<List<Map<String, Object>>>() {
+ });
+
+ logger.debug(json);
+
+ assertNotNull(overlays.get(0).get("genomeType"));
+ assertNotNull(overlays.get(0).get("genomeVersion"));
+ } finally {
+ waitForProjectToFinishLoading(TEST_PROJECT);
+ }
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
index 2a18af22f3d8b678310c1f44ff1359d54ef846a0..26e391ceb1985edb6b4e40ba4c2b9f38f7d0987e 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerAnonymousIntegrationTest.java
@@ -15,6 +15,8 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
import java.util.Map;
+import javax.servlet.http.Cookie;
+
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
@@ -36,7 +38,6 @@ public class UserControllerAnonymousIntegrationTest extends ControllerIntegratio
@Autowired
private IUserService userService;
-
@Before
public void setup() {
}
@@ -153,13 +154,13 @@ public class UserControllerAnonymousIntegrationTest extends ControllerIntegratio
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
RequestBuilder request = post("/api/doLogout")
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .cookie(new Cookie(Configuration.AUTH_TOKEN, "xxxxxxxx"))
.session(session);
mockMvc.perform(request)
.andDo(document("authentication/logout",
- responseFields(
- fieldWithPath("status")
- .description("status message"))))
+ responseFields(fieldWithPath("status").description("status message"))))
.andExpect(status().is2xxSuccessful());
}
@@ -173,7 +174,6 @@ public class UserControllerAnonymousIntegrationTest extends ControllerIntegratio
Map<String, Object> result = objectMapper.readValue(content, new TypeReference<Map<String, Object>>() {
});
- logger.debug(result);
assertNotNull(result.get("preferences"));
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
index ababc861cf25ad503a3ff5d7b263e74b10e776c4..c06163b510596263606000bb769b6100cb56cc9b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/UserControllerIntegrationTest.java
@@ -24,6 +24,7 @@ import java.util.Calendar;
import java.util.Collections;
import java.util.List;
import java.util.Map;
+import java.util.UUID;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.client.entity.UrlEncodedFormEntity;
@@ -51,7 +52,6 @@ import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
import lcsb.mapviewer.api.users.UserController;
import lcsb.mapviewer.api.users.UserController.UserPrivilegesDTO;
@@ -92,7 +92,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
private static final String TEST_USER_PASSWORD = "test_pass";
private static final String TEST_USER_LOGIN = "test_user";
- private static final String TEST_LOGIN = "xyz";
+ private static final String TEST_LOGIN = "test_login";
private User user;
@@ -114,9 +114,6 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
@Autowired
private UserController userController;
- @Autowired
- private ModelAnnotator modelAnnotator;
-
@Before
public void setup() throws Exception {
user = createUser(TEST_USER_LOGIN, TEST_USER_PASSWORD);
@@ -194,7 +191,8 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
mockMvc.perform(request)
.andExpect(status().is2xxSuccessful());
- assertEquals("Privilege wasn't revoked", 0, userService.getUserByLogin(TEST_USER_LOGIN, true).getPrivileges().size());
+ assertEquals("Privilege wasn't revoked", 0,
+ userService.getUserByLogin(TEST_USER_LOGIN, true).getPrivileges().size());
}
@Test
@@ -420,8 +418,8 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
- new BasicNameValuePair("name", "FirstName"),
- new BasicNameValuePair("password", "FirstName"))));
+ new BasicNameValuePair("name", "Name"),
+ new BasicNameValuePair("password", "Password"))));
RequestBuilder grantRequest = post("/api/users/{login}", TEST_LOGIN)
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
@@ -431,7 +429,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
mockMvc.perform(grantRequest)
.andDo(document("user/create_user",
userPathParameters(),
- requestParameters(getUserRequestFieldsWithoutLogin()),
+ requestParameters(addUserRequestFields()),
responseFields(getUserResponseFields())))
.andExpect(status().is2xxSuccessful());
@@ -465,7 +463,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("name", "FirstName"),
- new BasicNameValuePair("password", "FirstName"),
+ new BasicNameValuePair("password", "UserPassword"),
new BasicNameValuePair("defaultPrivileges", "true"))));
RequestBuilder grantRequest = post("/api/users/" + TEST_LOGIN)
@@ -499,7 +497,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("name", "FirstName"),
- new BasicNameValuePair("password", "FirstName"),
+ new BasicNameValuePair("password", "UserPassword"),
new BasicNameValuePair("defaultPrivileges", "true"))));
RequestBuilder grantRequest = post("/api/users/" + TEST_LOGIN)
@@ -693,15 +691,13 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
@Test
public void resetPassword() throws Exception {
configureServerForResetPasswordRequest();
-
- RequestBuilder request = post("/api/users/" + TEST_USER_LOGIN + ":requestResetPassword");
-
- mockMvc.perform(request)
- .andExpect(status().is2xxSuccessful());
-
String newPassword = "pass2";
- ResetPasswordToken token = userService.getPasswordTokens(TEST_USER_LOGIN).get(0);
+ Calendar expires = Calendar.getInstance();
+ expires.add(Calendar.DAY_OF_MONTH, 1);
+ ResetPasswordToken token = new ResetPasswordToken(user, UUID.randomUUID().toString().replaceAll("[a-z]", "0"),
+ expires);
+ userService.add(token);
String content = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
new BasicNameValuePair("token", token.getToken()),
@@ -719,7 +715,7 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
.description("new password"),
parameterWithName("token")
.optional()
- .description("reset poassowrd token obtained using email"))))
+ .description("reset password token obtained using email"))))
.andExpect(status().is2xxSuccessful());
createSession(TEST_USER_LOGIN, newPassword);
@@ -808,7 +804,8 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
user.setEmail("test@test.xyz");
userService.updateUser(user);
- configurationService.setConfigurationValue(ConfigurationElementType.MINERVA_ROOT, "https://minerva-dev.lcsb.uni.lu/minerva/");
+ configurationService.setConfigurationValue(ConfigurationElementType.MINERVA_ROOT,
+ "https://minerva-dev.lcsb.uni.lu/minerva/");
}
@Test
@@ -850,11 +847,11 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
.optional()
.type(JsonFieldType.STRING),
fieldWithPath("connectedToLdap")
- .description("is user account connected to ldap")
+ .description("is user account connected to LDAP")
.optional()
.type(JsonFieldType.BOOLEAN),
fieldWithPath("ldapAccountAvailable")
- .description("does is account exist in ldap")
+ .description("does the account exist in LDAP")
.optional()
.type(JsonFieldType.BOOLEAN),
fieldWithPath("email")
@@ -918,6 +915,24 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
return result;
}
+ private List<ParameterDescriptor> addUserRequestFields() {
+ return Arrays.asList(
+ parameterWithName("name")
+ .optional()
+ .description("first name"),
+ parameterWithName("surname")
+ .optional()
+ .description("last name"),
+ parameterWithName("password")
+ .description("user password"),
+ parameterWithName("email")
+ .optional()
+ .description("email address"),
+ parameterWithName("defaultPrivileges")
+ .optional()
+ .description("should the default privileges be added to the user after user creation"));
+ }
+
private List<ParameterDescriptor> getUserRequestFieldsWithoutLogin() {
return Arrays.asList(
parameterWithName("password")
@@ -925,10 +940,10 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
.description("user password"),
parameterWithName("connectedToLdap")
.optional()
- .description("is user account connected to ldap"),
+ .description("is user account connected to LDAP"),
parameterWithName("ldapAccountAvailable")
.optional()
- .description("does is account exist in ldap"),
+ .description("does is account exist in LDAP"),
parameterWithName("email")
.optional()
.description("email address"),
@@ -994,7 +1009,8 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
uniprotAnnotator.addAnnotatorParameter(new AnnotatorOutputParameter(MiriamType.UNIPROT));
uniprotAnnotator.addAnnotatorParameter(new AnnotatorOutputParameter(MiriamType.EC));
uniprotAnnotator.addAnnotatorParameter(new AnnotatorOutputParameter(MiriamType.ENTREZ));
- uniprotAnnotator.addAnnotatorParameter(new AnnotatorConfigParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "XXX"));
+ uniprotAnnotator
+ .addAnnotatorParameter(new AnnotatorConfigParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "XXX"));
preferences.addClassAnnotator(new UserClassAnnotators(Gene.class, Arrays.asList(uniprotAnnotator)));
RequestBuilder request = patch("/api/users/{login}:updatePreferences", TEST_USER_LOGIN)
@@ -1024,8 +1040,10 @@ public class UserControllerIntegrationTest extends ControllerIntegrationTest {
UserAnnotationSchema preferences = new UserAnnotationSchema();
UserPreferencesDTO data = new UserPreferencesDTO(preferences);
- preferences.addClassRequiredAnnotations(new UserClassRequiredAnnotations(Protein.class, Arrays.asList(MiriamType.HGNC, MiriamType.HGNC_SYMBOL)));
- preferences.addClassRequiredAnnotations(new UserClassRequiredAnnotations(SimpleMolecule.class, Arrays.asList(MiriamType.CHEBI)));
+ preferences.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(Protein.class, Arrays.asList(MiriamType.HGNC, MiriamType.HGNC_SYMBOL)));
+ preferences.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(SimpleMolecule.class, Arrays.asList(MiriamType.CHEBI)));
preferences.getClassRequiredAnnotators().get(1).setRequireAtLeastOneAnnotation(false);
RequestBuilder request = patch("/api/users/{login}:updatePreferences", TEST_USER_LOGIN)
diff --git a/web/src/test/java/lcsb/mapviewer/web/serialization/ProjectBackgroundUpdateMixIn.java b/web/src/test/java/lcsb/mapviewer/web/serialization/ProjectBackgroundUpdateMixIn.java
index 51c649c3405edfb4d9b06ced01b7c2263ebad2e2..dcab549d802fefad027dd01096292dcaeb3b8228 100644
--- a/web/src/test/java/lcsb/mapviewer/web/serialization/ProjectBackgroundUpdateMixIn.java
+++ b/web/src/test/java/lcsb/mapviewer/web/serialization/ProjectBackgroundUpdateMixIn.java
@@ -3,10 +3,13 @@ package lcsb.mapviewer.web.serialization;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundImageLayer;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundStatus;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.modelutils.serializer.model.user.UserAsLoginSerializer;
public abstract class ProjectBackgroundUpdateMixIn {
@JsonIgnore
@@ -26,7 +29,10 @@ public abstract class ProjectBackgroundUpdateMixIn {
@JsonIgnore
public abstract double getProgress();
-
+
@JsonIgnore
public abstract List<ProjectBackgroundImageLayer> getProjectBackgroundImageLayer();
+
+ @JsonSerialize(using = UserAsLoginSerializer.class)
+ public abstract User getCreator();
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/utils/CommandFormatterWithReplacingPostFilenameHeader.java b/web/src/test/java/lcsb/mapviewer/web/utils/CommandFormatterWithReplacingPostFilenameHeader.java
index 608e42fdd17351e5089f551dc58d842d1564df91..b42b9465db3d4735d39ef7221928fbfc202ea16c 100644
--- a/web/src/test/java/lcsb/mapviewer/web/utils/CommandFormatterWithReplacingPostFilenameHeader.java
+++ b/web/src/test/java/lcsb/mapviewer/web/utils/CommandFormatterWithReplacingPostFilenameHeader.java
@@ -2,6 +2,8 @@ package lcsb.mapviewer.web.utils;
import java.util.List;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.restdocs.cli.CommandFormatter;
import org.springframework.util.CollectionUtils;
@@ -14,11 +16,20 @@ import lcsb.mapviewer.common.Configuration;
* reference @filename. The filename is taken from header "post-filename" which
* will be removed from the curl sample.
*
+ * <p>
+ * It is also a workaround the issue that restdocs ignores fact that curl by
+ * default uses application/x-www-form-urlencoded content-type if no content
+ * type is provided.
+ * </p>
+ *
+ *
* @author Piotr Gawron
*
*/
public class CommandFormatterWithReplacingPostFilenameHeader implements CommandFormatter {
+ protected static Logger logger = LogManager.getLogger();
+
private String separator;
/**
@@ -41,14 +52,14 @@ public class CommandFormatterWithReplacingPostFilenameHeader implements CommandF
@Override
public String format(final List<String> elements) {
if (CollectionUtils.isEmpty(elements)) {
- return "";
- }
- String contentFileName = null;
- for (final String element : elements) {
- if (element.startsWith("-H 'post-filename:")) {
- contentFileName = element.replace("-H 'post-filename: ", "").replace("'", "");
+ if (session) {
+ return String.format(this.separator) + "--cookie \"" + Configuration.AUTH_TOKEN + "=xxxxxxxx\"";
}
+ return "";
}
+ String contentFileName = getContentFileName(elements);
+ String contentType = getContentType(elements);
+
if (session) {
elements.add("--cookie \"" + Configuration.AUTH_TOKEN + "=xxxxxxxx\"");
}
@@ -58,14 +69,42 @@ public class CommandFormatterWithReplacingPostFilenameHeader implements CommandF
if (element.startsWith("-d") && contentFileName != null) {
element = "--data-binary @" + contentFileName;
}
- if (!element.startsWith("-H 'post-filename:")) {
+ if (!element.startsWith("-H 'post-filename:")
+ && !element.toLowerCase().startsWith("-h 'content-type:")) {
result.append(String.format(this.separator));
result.append(element);
}
}
+ if (contentType != null && !contentType.isEmpty()) {
+ result.append(String.format(this.separator));
+ result.append("-H 'Content-Type: " + contentType + "'");
+ }
return result.toString();
}
+ public String getContentType(final List<String> elements) {
+ String contentType = "application/octet-stream";
+ for (String orgString : elements) {
+ String string = orgString.replaceAll("\\s+", "")
+ .replaceAll("'", "")
+ .replaceAll("\"", "");
+ if (string.toLowerCase().startsWith("-hcontent-type:")) {
+ return string.split(":")[1];
+ }
+ }
+ return contentType;
+ }
+
+ private String getContentFileName(final List<String> elements) {
+ String contentFileName = null;
+ for (final String element : elements) {
+ if (element.startsWith("-H 'post-filename:")) {
+ contentFileName = element.replace("-H 'post-filename: ", "").replace("'", "");
+ }
+ }
+ return contentFileName;
+ }
+
public void setSessionAvailable(final boolean session) {
this.session = session;
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/utils/CustomCurlRequestSnippet.java b/web/src/test/java/lcsb/mapviewer/web/utils/CustomCurlRequestSnippet.java
index 3c37f8e3e963d06d5720b3a02564f54c81df4a25..0766e3a0054f08696859796e94923fb65d6fa49d 100644
--- a/web/src/test/java/lcsb/mapviewer/web/utils/CustomCurlRequestSnippet.java
+++ b/web/src/test/java/lcsb/mapviewer/web/utils/CustomCurlRequestSnippet.java
@@ -2,6 +2,8 @@ package lcsb.mapviewer.web.utils;
import java.util.Map;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.restdocs.cli.CommandFormatter;
import org.springframework.restdocs.cli.CurlRequestSnippet;
import org.springframework.restdocs.operation.Operation;
@@ -17,6 +19,8 @@ import org.springframework.restdocs.operation.Operation;
*/
public class CustomCurlRequestSnippet extends CurlRequestSnippet {
+ protected static Logger logger = LogManager.getLogger();
+
private final CommandFormatter commandFormatter;
public CustomCurlRequestSnippet(final CommandFormatter commandFormatter) {
@@ -35,11 +39,19 @@ public class CustomCurlRequestSnippet extends CurlRequestSnippet {
boolean session = false;
if (obj instanceof org.springframework.mock.web.MockHttpServletRequest) {
session = (((org.springframework.mock.web.MockHttpServletRequest) obj).getSession() != null);
+ if (session) {
+ session = !((org.springframework.mock.web.MockHttpServletRequest) obj).getSession().isNew();
+ }
}
if (commandFormatter instanceof CommandFormatterWithReplacingPostFilenameHeader) {
((CommandFormatterWithReplacingPostFilenameHeader) commandFormatter).setSessionAvailable(session);
}
- return super.createModel(operation);
+ Map<String, Object> result = super.createModel(operation);
+
+ String options = (String) result.get("options");
+ // get rid of writeIncludeHeadersInOutputOption
+ result.put("options", options.replace("-i ", ""));
+ return result;
}
}
diff --git a/web/src/test/resources/complex_model_with_genomic_layout.zip b/web/src/test/resources/complex_model_with_genomic_layout.zip
new file mode 100644
index 0000000000000000000000000000000000000000..b8df8b8a9ac8bca2b9428088ad125f76fd83cc48
Binary files /dev/null and b/web/src/test/resources/complex_model_with_genomic_layout.zip differ