diff --git a/.aspell.en.pws b/.aspell.en.pws
new file mode 100644
index 0000000000000000000000000000000000000000..aa5a11179b9ef369a6666638c1ff44a613f151f1
--- /dev/null
+++ b/.aspell.en.pws
@@ -0,0 +1,482 @@
+personal_ws-1.1 en 0 utf-8
+Aceview
+Affymetrix
+AFTOL
+allel
+Allergome
+AmoebaDB
+Analyte
+antisense
+AntWeb
+APD
+AphidBase
+api
+ArachnoServer
+ARITOX
+ArrayExpress
+arXiv
+AspGD
+ATCC
+AutDB
+AUTH
+autocomplete
+autofill
+BackgroundColor
+BacMap
+BBD
+bcrypt
+BDGP
+BeetleBase
+BEVASIRANIB
+Bgee
+BiGG
+BindingDB
+bioassay
+BioCarta
+BioCatalogue
+BioCompendium
+BioCyc
+bioEntities
+BioEntity
+BioGRID
+BioNumbers
+biopax
+BioPortal
+BioProject
+BioSample
+BioSystems
+Biotransformation
+BitterDB
+BOM
+boolean
+BorderColor
+bqbiol
+bqmodel
+BugBase
+BYKdb
+capslock
+cardinality
+CATH
+CAZy
+CellDesigner
+CGSC
+CharProt
+charset
+CHEBI
+checkboxes
+chembl
+ChemDB
+ChemIDplus
+CLDB
+ClinicalTrials
+ClinVar
+compartmentRef
+Compulyeast
+Concurent
+config
+Conoserver
+contect
+contentType
+coords
+COPASI
+Coriell
+CORS
+CORUM
+cron
+CryptoDB
+CSA
+css
+CTD
+ctdbase
+CutDB
+CVE
+DailyMed
+DAPI
+DARC
+DataBase
+dataset
+datasets
+DATF
+dbconfig
+DBD
+dbEST
+DBG
+dbProbe
+dbSNP
+debian
+defaultCenterX
+defaultCenterY
+defaultZoomLevel
+Degradome
+DEPOD
+dialogs
+Dictybase
+DisProt
+DMET
+DOI
+DOMMINO
+DORLIMOMAB
+DPV
+DragonDB
+DRSC
+DrugBank
+ds
+EchoBASE
+EcoGene
+EcoliWiki
+eggNOG
+elementIdentifier
+ENA
+Ensembl
+Entrez
+enviPath
+Environ
+EPD
+ExAC
+Expt
+FlyBase
+FMA
+FooDB
+frontend
+FuncBase
+FungiDB
+GABI
+Gawron
+GC
+Genatlas
+GeneCards
+GeneDB
+GeneFarm
+geneMappingId
+GeneTree
+genomeId
+genomic
+GenPept
+getWriter
+GiardiaDB
+GLIDA
+Glycan
+GlycoEpitope
+GlycomeDB
+glyphs
+Golm
+GPCR
+GPCRDB
+GPML
+Gramene
+graphicalObject
+GreenGenes
+GRSDB
+GWAS
+GXA
+HAMAP
+hasInstance
+hasProperty
+hasTaxon
+HCVDB
+heterodimer
+HGMD
+HGNC
+Hikari
+HLA
+HOGENOM
+HOMD
+Homeodomain
+HomoloGene
+homomultimer
+HOVERGEN
+HPA
+HPRD
+HSSP
+html
+http
+https
+hungs
+ICD
+ICEberg
+IMEx
+IMGT
+InChI
+InChIKey
+includedCompartmentIds
+InfoWindow
+IntAct
+Intron
+Introns
+InvDb
+IRD
+iRefWeb
+isDerivedFrom
+ISFinder
+isInstanceOf
+isPropertyOf
+ISSN
+IUPHAR
+javascript
+JAX
+JCGGDB
+jpg
+JS
+json
+JSTOR
+JWS
+Kegg
+KEGG
+KiSAO
+KNApSAcK
+LayerText
+layouted
+LDAP
+leprae
+ligand
+LigandBox
+LIGM
+LINCS
+lineWidth
+LipidBank
+logrotate
+MACiE
+MaizeGDB
+mapId
+marinum
+MassBank
+MatrixDB
+md
+MedlinePlus
+MEROPS
+MetaboLights
+Metabolome
+Metagenome
+Metainformation
+MetaNetX
+Metazoa
+METLIN
+MGED
+MicrosporidiaDB
+MimoDB
+minerva
+MIPModDB
+mirEX
+miriam
+MiRNA
+MiRNAs
+miRNEST
+mirtarbase
+misalign
+misaligning
+MMRRC
+ModelDB
+MolArt
+Molbase
+multimer
+multimers
+MycoBank
+MycoBrowser
+NADH
+NameBank
+NAPP
+NARCIS
+NASC
+NCBI
+NCI
+NCIm
+NCIt
+NeuroLex
+NeuroMorpho
+NeuronDB
+NEXTDB
+nextProt
+NIAEST
+NITE
+NONCODE
+NORINE
+NucleaRDB
+occursIn
+OMA
+OMIA
+openjdk
+OpenLayers
+OPM
+ORCID
+OriDB
+Orphanet
+OrthoDB
+Oryza
+Oryzabase
+overlayed
+PaleoDB
+parseable
+PATO
+PaxDb
+Pazar
+pdf
+PDR
+PeptideAtlas
+Peroxibase
+PharmGKB
+phenome
+phentoype
+phenotypes
+PhosphoPoint
+Phosphoprotein
+PhosphoSite
+PhylomeDB
+Phytozome
+PINA
+Piotr
+PiroplasmaDB
+PIRSF
+PlasmoDB
+PMC
+pmceurope
+PMP
+png
+Pocketome
+PolBase
+PomBase
+postgres
+postgresql
+posttranslational
+PredictProtein
+Probeset
+ProDom
+ProGlycProt
+projectId
+PROSITE
+ProtClustDB
+ProteinCard
+Proteome
+ProteomicsDB
+Protists
+ProtoNet
+PSCDB
+Pseudomonas
+PubChem
+pubmed
+px
+qTL
+QTL
+RDF
+reactionId
+reactionIdentifier
+reactome
+REBASE
+removeAllListeners
+reportable
+repositioned
+RESID
+resizeable
+reupload
+revalidated
+reverseReaction
+RFAM
+RGD
+RHOA
+RK
+RNAi
+RNAs
+RoundedRectangle
+SABIO
+Saccharomyces
+SBGN
+SBGNML
+SBML
+SBO
+ScerTF
+Schizosaccharomyces
+SCOP
+scrollbar
+scrollbars
+SearchListener
+selectable
+SemanticZoomLevelTransparency
+ShapeType
+SIDER
+SitEx
+smegmatis
+SMTP
+SNOMED
+SNP
+sortable
+SoyBase
+specific
+speciesReference
+SSL
+STAP
+subfolders
+submap
+submaps
+submodel
+submodels
+substanceUnits
+SubstrateDB
+SubtiList
+SubtiWiki
+superfamily
+SUPFAM
+svg
+SwissLipids
+symlink
+Tair
+TAIR
+TarBase
+targetting
+Taxnomy
+Tetrahymena
+TFDB
+TIGRFAMS
+timeouted
+TOPDB
+TopFind
+ToS
+ToxoDB
+TransparencyZoomLevelVisibility
+TreeBASE
+TreeFam
+TrichDB
+TriTrypDB
+TTD
+txt
+UBERON
+uBio
+ubuntu
+uid
+un
+unhandled
+unicode
+UNII
+Unimod
+UniParc
+UniPathway
+UniProt
+UniSTS
+uri
+url
+urlencoded
+urls
+USPTO
+UTF
+VariO
+Vbase
+VBRC
+Vetinary
+VFDB
+viewBox
+ViralZone
+VIRsiRNA
+vmh
+webpage
+whitespace
+WikiGenes
+Worfdb
+WormBase
+Wormpep
+www
+Xenbase
+xml
+xsd
+xss
+YDPM
+YeTFasCo
+YRC
+ZFIN
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9cc9e8425e1690a6ca7b625230ebcc513ce1a7f6..6ca6e7bc57c5c3571dac89b5fdca46a56340029e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -589,3 +589,8 @@ test_postgres_14_compatibility:
<<: *test_database_definition
services:
- postgres:14
+
+changelog_spelling:
+ stage: test
+ script:
+ - sh test_spelling.sh
diff --git a/CHANGELOG b/CHANGELOG
index 099c8dae1c784f6b8f21953a5b8ed47f88e19e74..d41d21eea55be638142d83da216ec5be6d3734f1 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -56,7 +56,7 @@ 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
@@ -65,7 +65,7 @@ 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)
@@ -84,7 +84,7 @@ 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
@@ -270,7 +270,7 @@ 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)
@@ -420,8 +420,8 @@ 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
@@ -451,7 +451,7 @@ 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)
@@ -464,7 +464,7 @@ 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
@@ -509,14 +509,14 @@ 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)
@@ -588,15 +588,15 @@ 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)
@@ -627,11 +627,11 @@ 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)
@@ -710,7 +710,7 @@ 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)
@@ -747,7 +747,7 @@ 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
@@ -796,9 +796,9 @@ 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
@@ -807,7 +807,7 @@ 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)
@@ -815,7 +815,7 @@ 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)
@@ -831,7 +831,7 @@ 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)
@@ -862,7 +862,7 @@ 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
@@ -896,13 +896,13 @@ 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)
@@ -911,7 +911,7 @@ 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)
@@ -921,7 +921,7 @@ 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
@@ -936,7 +936,7 @@ 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)
@@ -948,7 +948,7 @@ 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)
@@ -984,7 +984,7 @@ 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
@@ -1048,7 +1048,7 @@ 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
@@ -1122,7 +1122,7 @@ 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
@@ -1163,7 +1163,7 @@ 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)
@@ -1172,7 +1172,7 @@ 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)
@@ -1187,19 +1187,19 @@ 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)
@@ -1223,8 +1223,8 @@ 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)
@@ -1276,7 +1276,7 @@ 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)
@@ -1347,7 +1347,7 @@ 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)
@@ -1433,7 +1433,7 @@ 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
@@ -1465,8 +1465,8 @@ 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
@@ -1500,7 +1500,7 @@ 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
@@ -1512,7 +1512,7 @@ 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
@@ -1525,7 +1525,7 @@ 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
@@ -1594,7 +1594,7 @@ 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
@@ -1615,7 +1615,7 @@ 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
@@ -1631,7 +1631,7 @@ 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
@@ -1711,17 +1711,17 @@ 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
@@ -1740,7 +1740,7 @@ 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
@@ -1758,7 +1758,7 @@ 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)
@@ -1776,7 +1776,7 @@ 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
@@ -1804,7 +1804,7 @@ 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
@@ -1873,15 +1873,15 @@ 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
@@ -1909,12 +1909,12 @@ 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/test_spelling.sh b/test_spelling.sh
new file mode 100644
index 0000000000000000000000000000000000000000..f837444d6efe4df08b101c8c238adf84711d46fb
--- /dev/null
+++ b/test_spelling.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+lines=`cat CHANGELOG | aspell --lang=en --encoding=utf-8 --add-extra-dicts=./.aspell.en.pws list|wc -l`
+if [ $lines -ne 0 ]
+then
+ echo "Unknown words:"
+ echo
+ cat CHANGELOG | aspell --lang=en --encoding=utf-8 --add-extra-dicts=./.aspell.en.pws list
+ exit 1
+fi
+
diff --git a/web/pom.xml b/web/pom.xml
index e27cbc3630e83d35a148baf6b7879bd9934a63d5..b74fc20700f665af7ec539da14ee039964e61725 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -1,6 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
@@ -71,14 +69,14 @@
</dependency>
<dependency>
- <groupId>javax.el</groupId>
- <artifactId>javax.el-api</artifactId>
- <version>${el.version}</version>
+ <groupId>javax.el</groupId>
+ <artifactId>javax.el-api</artifactId>
+ <version>${el.version}</version>
</dependency>
<dependency>
- <groupId>org.glassfish.web</groupId>
- <artifactId>javax.el</artifactId>
- <version>${el.version}</version>
+ <groupId>org.glassfish.web</groupId>
+ <artifactId>javax.el</artifactId>
+ <version>${el.version}</version>
</dependency>
<dependency>
@@ -374,8 +372,8 @@
<directory>${project.basedir}/../</directory>
<targetPath>.</targetPath>
<includes>
- <include>CHANGELOG</include>
- </includes>
+ <include>CHANGELOG</include>
+ </includes>
</resource>
</webResources>
<archive>
@@ -442,6 +440,29 @@
</configuration>
</plugin>
+
+ <plugin>
+ <groupId>org.jboss.maven.plugins</groupId>
+ <artifactId>maven-spellChecker-plugin</artifactId>
+ <version>1.2-SNAPSHOT</version>
+ <executions>
+ <execution>
+ <id>spellChecker:check</id>
+ <phase>package</phase>
+ <goals>
+ <goal>check</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <outputDir>${project.build.directory}/log</outputDir>
+ <reportFileName>log.txt</reportFileName>
+ <dirForScan>${project.basedir}</dirForScan>
+ <includes>
+ <include>CHANGELOG</include>
+ </includes>
+ </configuration>
+ </plugin>
</plugins>
</build>