Commit 7e33272e authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch 'devel_11.1.x'

parents dbe7164f ef9d76d7
Pipeline #2576 passed with stage
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minerva (11.0.3) stable; urgency=medium
* Bug fix: removing empty project removed images from all projects
* Bug fix: clicking on map when left panel was hidden threw error
* Bug fix: links to invalid annotations were opening invalid web page
* Bug fix: service resolving miriam resources doesn't worki over http
anymore
* Bug fux: chebi annotator doesn't work over http anymore
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Oct 2017 13:50:00 +0200
minerva (11.0.2) stable; urgency=medium
* Bug fix: login issues when default page is in secure area
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 25 Sep 2017 12:00:00 +0200
minerva (11.0.1) stable; urgency=medium
* Bug fix: logout caused issues with session data
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
by the userlogin
* 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)
* Selecting an element on the map shows info about it in the bottom left
corner (when Search tab is not open)
* Upload of data overlays allows to upload just names of the proteins
(or other elements), it can be done via file or just by typing in the
proper text box
* Layout changes: the main one is that there are only 3 tab panels
(search, overlay, info), so it should be easier to navigate
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
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
* Overlay presents description field if possible
-- Piotr Gawron <piotr.gawron@uni.lu> Sat, 04 Mar 2017 12:00:00 +0200
minerva (10.0.4) stable; urgency=medium
* Bug fix: overlays colors are centered in white (not black)
* Bug fix: export to CellDesigner fixed
* Bug fix: DrugBank connector updated due to change in DrugBank website
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Dec 2016 17:01:16 +0200
minerva (10.0.3) stable; urgency=medium
* Bug fix: login cannot contain whitespace
* Bug fix: search for multiple drugs will not return more drugs than
queried for
* Bug fix: drug list for some proteins (like RHOA) hung webpage
* Bug fix: comments on submaps issue
* Bug fix: link to submap from comment panel
* Overlay coloring can be defined in Configuration
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 15 Dec 2016 15:01:16 +0200
minerva (10.0.2) stable; urgency=medium
* Bug fix: markers for mirna targets visibility
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Sep 2016 10:01:16 +0200
minerva (10.0.1) stable; urgency=medium
* Bug fix: export to image
* Bug fix: trigger reaction and physical stimulation reactions are no
longer allowed (CellDesigner data model issue)
* Bug fix: clicking on reactions in submaps
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 21 Sep 2016 13:01:16 +0200
minerva (10) stable; urgency=medium
* Project info tab available for users
* Management of overlays in admin panel
* Bug fix: Visualization of text mining
* Bug fix: Exception when accessing non-existing project
* Bug fix: Zooming issue when searching for results on submaps
* Bug fix: Out of memory when caching a lot of data
* Bug fix: Corrupted drug names
* Bug fix: Unexpected errors when uploading layouts
* Bug fix: Coordinates in url
* Bug fix: Hiding left panel
* Bug fix: CellDesigner font size is processed properly
* Bug fix: Search by reaction id is not case sensitive
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Aug 2016 13:01:16 +0200
minerva (9) stable; urgency=medium
* Fix on install script of version 8 that crashed some new installations
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 29 Jun 2016 09:58:34 +0200
minerva (8) stable; urgency=medium
* Micro RNA interface
* Toxic chemicals interdace
* Data sets (layouts) visualized dynamically in the browser
* Reverse query for drugs, chemicals, micro RNAs interfaces
* Small bug fixes
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Apr 2016 13:03:55 +0200
minerva (7) stable; urgency=low
* Uploaded datasets are available for download
* Entrez annotator
* Ensembl annotator
* Valid/required annotations and used annotations saved in user profile
* Export to pdf/png/jpg/svg
* New web interface
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 3 Dec 2015 22:00:00 +0200
minerva (6) stable; urgency=low
* Searching by annotations
* Errors from parsing data forwarded to client
* Notification email system added
* Warnings are downloadable
* Complex map (composed from many small maps)
* Visualization of Recon specific annotations
* Versioning system
* Galaxy connector
* Miriam types report
* Advanced annotation options
* 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: 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
* Bug fix: Recon annotations of reactions
* Bug fix: Login problem when browsing not default map
* Bug fix: Multimers are available for every element
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 21 Jul 2015 22:00:00 +0200
minerva (5) stable; urgency=low
* Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
* Popup window in admin panel that list warnings
* Information about build
* Parsing and annotation warnings for models in admin panel
* Custom reaction visualization in upload overlay
* Bug fix: Problem with touch interface on Windows 8.1
* Bug fix: Google Maps API problem with floating bubbles
* Bug fix: Error handling in admin panel
* Bug fix: Reaction color in CellDesigner file
* Bug fix: Reaction line width
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Dec 2014 22:00:00 +0200
minerva (4) stable; urgency=low
* Export of the part of the map into CellDesigner file
* Logo files managable 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: 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
* Bug fix: Export problem
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 11 Sep 2014 22:00:00 +0200
minerva (3) stable; urgency=low
* Drug targeting interface
* Export to CellDesigner
* Status page of all dependent services
* Configuration page
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 5 Jun 2014 22:00:00 +0200
minerva (2) stable; urgency=low
* Upload of the CellDesigner map
* Bug fix: Problem with touch interface after update of browsers engine
* Bug fix: Problem in Safari when searching for elements
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 2 Apr 2014 22:00:00 +0200
minerva (1) stable; urgency=low
* Initial release
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Dec 2013 22:00:00 +0200
minerva (11.0.4) stable; urgency=medium
* Bug fix: fix on connection to taxonomy database
* Bug fix: color coding for reactions (wrong color was chosen)
* Bug fix: overlays with many reactions did not work properly
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 09 Nov 2017 14:50:00 +0200
minerva (11.0.3) stable; urgency=medium
* Bug fix: removing empty project removed images from all projects
* Bug fix: clicking on map when left panel was hidden threw error
* 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
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Oct 2017 13:50:00 +0200
minerva (11.0.2) stable; urgency=medium
* Bug fix: login issues when default page is in secure area
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 25 Sep 2017 12:00:00 +0200
minerva (11.0.1) stable; urgency=medium
* Bug fix: logout caused issues with session data
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
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: mesh connector
* Rest API (documentation can be found here:
https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
* Selecting an element on the map shows info about it in the bottom left
corner (when Search tab is not open)
* Upload of data overlays allows to upload just names of the proteins
(or other elements), it can be done via file or just by typing in the
proper text box
* Layout changes: the main one is that there are only 3 tab panels
(search, overlay, info), so it should be easier to navigate
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 28 Aug 2017 12:00:00 +0200
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
* Overlay presents description field if possible
-- Piotr Gawron <piotr.gawron@uni.lu> Sat, 04 Mar 2017 12:00:00 +0200
minerva (10.0.4) stable; urgency=medium
* Bug fix: overlays colors are centered in white (not black)
* Bug fix: export to CellDesigner fixed
* Bug fix: DrugBank connector updated due to change in DrugBank website
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Dec 2016 17:01:16 +0200
minerva (10.0.3) stable; urgency=medium
* Bug fix: login cannot contain whitespace
* Bug fix: search for multiple drugs will not return more drugs than
queried for
* Bug fix: drug list for some proteins (like RHOA) hung webpage
* Bug fix: comments on submaps issue
* Bug fix: link to submap from comment panel
* Overlay coloring can be defined in Configuration
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 15 Dec 2016 15:01:16 +0200
minerva (10.0.2) stable; urgency=medium
* Bug fix: markers for mirna targets visibility
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 29 Sep 2016 10:01:16 +0200
minerva (10.0.1) stable; urgency=medium
* Bug fix: export to image
* Bug fix: trigger reaction and physical stimulation reactions are no
longer allowed (CellDesigner data model issue)
* Bug fix: clicking on reactions in submaps
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 21 Sep 2016 13:01:16 +0200
minerva (10) stable; urgency=medium
* Project info tab available for users
* Management of overlays in admin panel
* Bug fix: Visualization of text mining
* Bug fix: Exception when accessing non-existing project
* Bug fix: Zooming issue when searching for results on submaps
* Bug fix: Out of memory when caching a lot of data
* Bug fix: Corrupted drug names
* Bug fix: Unexpected errors when uploading layouts
* Bug fix: Coordinates in url
* Bug fix: Hiding left panel
* Bug fix: CellDesigner font size is processed properly
* Bug fix: Search by reaction id is not case sensitive
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Aug 2016 13:01:16 +0200
minerva (9) stable; urgency=medium
* Fix on install script of version 8 that crashed some new installations
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 29 Jun 2016 09:58:34 +0200
minerva (8) stable; urgency=medium
* Micro RNA interface
* Toxic chemicals interface
* Data sets (layouts) visualized dynamically in the browser
* Reverse query for drugs, chemicals, micro RNAs interfaces
* Small bug fixes
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 14 Apr 2016 13:03:55 +0200
minerva (7) stable; urgency=low
* Uploaded datasets are available for download
* Entrez annotator
* Ensembl annotator
* Valid/required annotations and used annotations saved in user profile
* Export to pdf/png/jpg/svg
* New web interface
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 3 Dec 2015 22:00:00 +0200
minerva (6) stable; urgency=low
* Searching by annotations
* Errors from parsing data forwarded to client
* Notification email system added
* Warnings are downloadable
* Complex map (composed from many small maps)
* Visualization of Recon specific annotations
* Versioning system
* Galaxy connector
* Miriam types report
* Advanced annotation options
* 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: 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
* Bug fix: Recon annotations of reactions
* Bug fix: Login problem when browsing not default map
* Bug fix: Multimers are available for every element
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 21 Jul 2015 22:00:00 +0200
minerva (5) stable; urgency=low
* Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
* Popup window in admin panel that list warnings
* Information about build
* Parsing and annotation warnings for models in admin panel
* Custom reaction visualization in upload overlay
* Bug fix: Problem with touch interface on Windows 8.1
* Bug fix: Google Maps API problem with floating bubbles
* Bug fix: Error handling in admin panel
* Bug fix: Reaction color in CellDesigner file
* Bug fix: Reaction line width
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Dec 2014 22:00:00 +0200
minerva (4) stable; urgency=low
* Export of the part of the map into CellDesigner file
* Logo files managable 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: 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
* Bug fix: Export problem
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 11 Sep 2014 22:00:00 +0200
minerva (3) stable; urgency=low
* Drug targeting interface
* Export to CellDesigner
* Status page of all dependent services
* Configuration page
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 5 Jun 2014 22:00:00 +0200
minerva (2) stable; urgency=low
* Upload of the CellDesigner map
* Bug fix: Problem with touch interface after update of browsers engine
* Bug fix: Problem in Safari when searching for elements
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 2 Apr 2014 22:00:00 +0200
minerva (1) stable; urgency=low
* Initial release
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Dec 2013 22:00:00 +0200
......@@ -180,9 +180,8 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
try {
String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + miriamData.getResource();
logger.debug(url);
String page = getWebPageContent(url);
Pattern idPattern = Pattern.compile("<h2>([A-Za-z0-9\\ \\.]+)</h2>");
Pattern idPattern = Pattern.compile("<title>Taxonomy browser \\(([A-Za-z0-9\\ \\.]+)\\)</title>");
Matcher matcher = idPattern.matcher(page);
if (!matcher.find()) {
logger.warn("Unknown organism: " + miriamData);
......
......@@ -27,96 +27,96 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
public class TaxonomyBackendTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(TaxonomyBackendTest.class);
@Autowired
TaxonomyBackend taxonomyBackend;
GeneralCacheInterface cache;
@Before
public void setUp() throws Exception {
cache = taxonomyBackend.getCache();
// exclude first cached value
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
}
@After
public void tearDown() throws Exception {
taxonomyBackend.setCache(cache);
}
@Test
public void testByName() throws Exception {
try {
MiriamData md = taxonomyBackend.getByName("Human");
assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByComplexName() throws Exception {
try {
assertNotNull(taxonomyBackend.getByName("Aplysia californica (Sea Hare)"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByCommonName() throws Exception {
try {
assertNotNull(taxonomyBackend.getByName("Rat"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByEmptyName() throws Exception {
try {
assertNull(taxonomyBackend.getByName(null));
assertNull(taxonomyBackend.getByName(""));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByAbreviationName() throws Exception {
try {
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("C. elegans"));
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("D. sechellia"));
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("P. pacificus"));
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("T. castaneum"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetName() throws Exception {
try {
String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
assertTrue(name.contains("Homo sapiens"));
assertNotNull(taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9605")));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
Logger logger = Logger.getLogger(TaxonomyBackendTest.class);
@Autowired
TaxonomyBackend taxonomyBackend;
GeneralCacheInterface cache;
@Before
public void setUp() throws Exception {
cache = taxonomyBackend.getCache();
// exclude two first cached values
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 2));
}
@After
public void tearDown() throws Exception {
taxonomyBackend.setCache(cache);
}
@Test
public void testByName() throws Exception {
try {
MiriamData md = taxonomyBackend.getByName("Human");
assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByComplexName() throws Exception {
try {
assertNotNull(taxonomyBackend.getByName("Aplysia californica (Sea Hare)"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByCommonName() throws Exception {
try {
assertNotNull(taxonomyBackend.getByName("Rat"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByEmptyName() throws Exception {
try {
assertNull(taxonomyBackend.getByName(null));
assertNull(taxonomyBackend.getByName(""));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testByAbreviationName() throws Exception {
try {
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("C. elegans"));
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("D. sechellia"));
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("P. pacificus"));
taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
assertNotNull(taxonomyBackend.getByName("T. castaneum"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetName() throws Exception {
try {
String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
assertTrue(name.contains("Homo sapiens"));
assertNotNull(taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9605")));
} catch (Exception e) {
e.printStackTrace();