diff --git a/CHANGELOG b/CHANGELOG
index af4ff48bca5d91abcc556a3791c83031cf93620c..d1c2ef7c9e211bf29e25e3806bd7fc429d408167 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,211 +1,218 @@
-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
+
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
index e6d3655a19c8da6a8ed2a98aebaed3c3cef0e9b9..ee307c12d466ca203e66d33bf4bd1ffce016a4e2 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
@@ -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);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
index 3c8b521e144a99725ba4a3d7910c72872828b5dc..a694153509919fc90df21c47f164e66b84715a75 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
@@ -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();
+ throw e;
+ }
+ }
@Test
public void testGetNameWhenProblemWithDb() throws Exception {
@@ -137,128 +137,129 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
}
}
- @Test
- public void testGetNameForInvalidTax() throws Exception {
- try {
- String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "-a-"));
- assertNull(name);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNameForInvalidInputData() throws Exception {
- try {
- String name = taxonomyBackend.getNameForTaxonomy(null);
- assertNull(name);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByName2() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("homo sapiens");
- assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByName3() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("bla bla kiwi");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByMusMusculusName() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("Mus musculus");
- assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByMouseName() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("Mouse");
- assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- String result = taxonomyBackend.refreshCacheQuery(TaxonomyBackend.TAXONOMY_CACHE_PREFIX + "homo sapiens");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery2() throws Exception {
- try {
- String result = taxonomyBackend.refreshCacheQuery(TaxonomyBackend.TAXONOMY_NAME_CACHE_PREFIX + TaxonomyBackend.HUMAN_TAXONOMY.getResource());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery3() throws Exception {
- try {
- String result = taxonomyBackend.refreshCacheQuery("http://google.pl/");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- taxonomyBackend.refreshCacheQuery("unk_query");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- taxonomyBackend.refreshCacheQuery(new Object());
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testGetNameForInvalidTax() throws Exception {
+ try {
+ String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "-a-"));
+ assertNull(name);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetNameForInvalidInputData() throws Exception {
+ try {
+ String name = taxonomyBackend.getNameForTaxonomy(null);
+ assertNull(name);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByName2() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("homo sapiens");
+ assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByName3() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("bla bla kiwi");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByMusMusculusName() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("Mus musculus");
+ assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByMouseName() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("Mouse");
+ assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ String result = taxonomyBackend.refreshCacheQuery(TaxonomyBackend.TAXONOMY_CACHE_PREFIX + "homo sapiens");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery2() throws Exception {
+ try {
+ String result = taxonomyBackend
+ .refreshCacheQuery(TaxonomyBackend.TAXONOMY_NAME_CACHE_PREFIX + TaxonomyBackend.HUMAN_TAXONOMY.getResource());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery3() throws Exception {
+ try {
+ String result = taxonomyBackend.refreshCacheQuery("http://google.pl/");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ taxonomyBackend.refreshCacheQuery("unk_query");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ taxonomyBackend.refreshCacheQuery(new Object());
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
@Test
public void testRefreshCacheQueryNotAvailable() throws Exception {
@@ -278,15 +279,15 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
}
}
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, taxonomyBackend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, taxonomyBackend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
@Test
public void testSimulateDownStatus() throws Exception {
diff --git a/checkstyle.xml b/checkstyle.xml
index cf13403c2f932c8bf48a761e81ef0b95ba94ae76..b4ae1463262e7beed047c9c943c4a4abc7d7b2f1 100644
--- a/checkstyle.xml
+++ b/checkstyle.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE module PUBLIC "-//Puppy Crawl//DTD Check Configuration 1.3//EN" "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
-<!--
- This configuration file was written by the eclipse-cs plugin configuration editor
+<!--
+ This configuration file was written by the eclipse-cs plugin configuration editor
-->
-<!--
- Checkstyle-Configuration: MapViewer checkstyle
- Description: none
+<!--
+ Checkstyle-Configuration: MapViewer checkstyle
+ Description: none
-->
<module name="Checker">
<property name="severity" value="warning"/>
diff --git a/converter-CellDesigner/.settings/org.eclipse.wst.common.component b/converter-CellDesigner/.settings/org.eclipse.wst.common.component
index 21d6d142e0167ea7171a1ec7140e8ab92072fcde..547a0c08e066ce2bbb19695db30871b995ff9509 100644
--- a/converter-CellDesigner/.settings/org.eclipse.wst.common.component
+++ b/converter-CellDesigner/.settings/org.eclipse.wst.common.component
@@ -1,6 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
- <wb-module deploy-name="MapViewer-converter-CellDesigner">
- <wb-resource deploy-path="/" source-path="/src/main/java"/>
- <wb-resource deploy-path="/" source-path="/src/main/resources"/>
- </wb-module>
-</project-modules>
+<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
+ <wb-module deploy-name="MapViewer-converter-CellDesigner">
+ <wb-resource deploy-path="/" source-path="/src/main/java"/>
+ </wb-module>
+</project-modules>
diff --git a/converter-graphics/.settings/org.eclipse.wst.common.component b/converter-graphics/.settings/org.eclipse.wst.common.component
index 26ce8011de8cd0cfe1fc284ae00b6fd6876cde02..2faa3f2b4556a750b4d43d4248dd12fe2fcfb759 100644
--- a/converter-graphics/.settings/org.eclipse.wst.common.component
+++ b/converter-graphics/.settings/org.eclipse.wst.common.component
@@ -1,6 +1,5 @@
-<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
- <wb-module deploy-name="MapViewer-converter-graphics">
- <wb-resource deploy-path="/" source-path="/src/main/java"/>
- <wb-resource deploy-path="/" source-path="/src/main/resources"/>
- </wb-module>
-</project-modules>
+<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
+ <wb-module deploy-name="MapViewer-converter-graphics">
+ <wb-resource deploy-path="/" source-path="/src/main/java"/>
+ </wb-module>
+</project-modules>
diff --git a/debian/create-debian-pkg.sh b/debian/create-debian-pkg.sh
index 1a6936e6fc9fa7c2cd17bd88b313eb2a8acc7a19..654df170b9de5f453019e137908583eb9650cc6b 100755
--- a/debian/create-debian-pkg.sh
+++ b/debian/create-debian-pkg.sh
@@ -9,6 +9,8 @@ versionCompLt() {
[ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
}
+# file with bash code generating DB schema diffs for different versions
+dbschemadiff=management_scripts/db_schema_and_diff.sh
#Where source file of the debian package should be placed
SRC_DIR=debian/src
@@ -54,22 +56,9 @@ cp debian/scripts/common.sh $SRC_DIR/
#copy changelog file
cp CHANGELOG $ROOT_DIR/debian/template/changelog
-#this variable will contain all available versions of the package
-versions=();
-
-#this is current (latest) version of the package
-current_version=-1;
-
-#find all available versions
-
-for version in `ls $DB_SCHEMA_DIR | sort -V`;
-do
- if [ -d "$DB_SCHEMA_DIR/$version" ]
- then
- versions+=($version);
- current_version=$version;
- fi
-done
+# set $versions and $current_version; generate upgrade scripts in SRC_DIR
+DBSCRIPT_DEST_DIR=$SRC_DIR
+source $dbschemadiff
echo "Current version: " $current_version
@@ -81,47 +70,6 @@ then
exit 1;
fi
-#--------------------------------------
-# GENERATE DB schemas and diff files
-#--------------------------------------
-
-#last version (used for generating db diff files)
-last_version=-1;
-for version_A in ${versions[*]}
-do
- #main update file (used to create this version - it's a diff
- #between base.sql and current version)
- update_file=$SRC_DIR/db_0_to_$current_version".sql";
-
- #now iterate through all versions
- for file in `ls $DB_SCHEMA_DIR/$version_A | sort -V`;
- do
- if [ -f "$DB_SCHEMA_DIR/$version_A/$file" ]
- then
- #add differemce tp current db schema diff
- printf "\n\n-- UPDATE $version_A/$file\n\n" >>$update_file;
- cat $DB_SCHEMA_DIR/$version_A/$file >> $update_file;
-
- #and now iterate again through all versions to add diffs
- #between previous versions and current one
- for version_B in ${versions[*]}
- do
- #update from version_B should contain all db changes that appeard
- #after #version_B (so version_A must be later)
- if versionCompLt $version_B $version_A
- then
- upd_file=$SRC_DIR/db_"$version_B"_to_$current_version".sql";
- printf "\n\n-- UPDATE $version_A/$file\n\n" >>$upd_file;
- cat $DB_SCHEMA_DIR/$version_A/$file >> $upd_file;
-
- fi
- done
- fi
- done
-
- last_version=$version_A
-done
-
#------------------------------------------
# Now we have all db schema diff files. Let's start preparing
# debian package
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index b533358e8ae4ea67767851406e6567696d52e951..97e626f51715551c80431c453095d07363e8a540 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1178,7 +1178,7 @@ ServerConnector.getReactions = function (params) {
var filterParams = {
id: params.ids,
columns: params.columns,
- participantId: params.participantId
+ participantId: params.participantId,
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index 2746a2973a215bca9d456dae973d620111695edd..c5c7167867ed2a964ecb728470c5536619155de5 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -638,8 +638,9 @@ AbstractCustomMap.prototype._showSelectedLayout = function (layoutId, index, len
return Promise.each(layoutReactions, function (layoutReaction) {
if (layoutReaction.getModelId() === self.getId()) {
return self.getModel().getReactionById(layoutReaction.getId()).then(function (reactionData) {
+ var surface;
var element = new IdentifiedElement(reactionData);
- var surface = new ReactionSurface({
+ return ReactionSurface.create({
layoutReaction: layoutReaction,
reaction: reactionData,
map: self,
@@ -649,10 +650,11 @@ AbstractCustomMap.prototype._showSelectedLayout = function (layoutId, index, len
return self.getTopMap().callListeners("onBioEntityClick", element);
}],
customized: (length === 1)
+ }).then(function(result){
+ surface = result;
+ self.selectedLayoutOverlays[layoutId].push(surface);
+ surface.show();
});
-
- self.selectedLayoutOverlays[layoutId].push(surface);
- surface.show();
});
}
});
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 6a5f9e5d47e7e78847d06badd4899f3a55596478..b884e97df68cb43985ae0aded88aae7a19b347d9 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -1303,7 +1303,7 @@ CustomMap.prototype.createSurfaceForDbOverlay = function (element, dbOverlay) {
});
} else if (element.getType() === "REACTION") {
return map.getModel().getReactionById(element.getId()).then(function (reactionData) {
- var result = new ReactionSurface({
+ return ReactionSurface.create({
reaction: reactionData,
map: map,
customized: true,
@@ -1313,10 +1313,12 @@ CustomMap.prototype.createSurfaceForDbOverlay = function (element, dbOverlay) {
}, function () {
return self.callListeners("onBioEntityClick", element);
}]
+ }).then(function(surface){
+ result = surface;
+ result.show();
+ dbOverlay.mapOverlays[element.getType()][element.getId()] = result;
+ return result;
});
- result.show();
- dbOverlay.mapOverlays[element.getType()][element.getId()] = result;
- return result;
});
} else if (element.getType() === "POINT") {
throw new Error("Not implemented");
diff --git a/frontend-js/src/main/js/map/surface/ReactionSurface.js b/frontend-js/src/main/js/map/surface/ReactionSurface.js
index de28af972e8ff53628b7301cfbb98c14cf903edc..c858a0a739bd15023e8875f5aa059d96fb185d05 100644
--- a/frontend-js/src/main/js/map/surface/ReactionSurface.js
+++ b/frontend-js/src/main/js/map/surface/ReactionSurface.js
@@ -11,7 +11,7 @@ var IdentifiedElement = require('../data/IdentifiedElement');
/**
* Class representing overlay of the reaction on the map relevant for a specific
* layout.
- *
+ *
* @param layoutReaction
* {@link LayoutReaction} for which overlay is created
* @param reactionData
@@ -39,7 +39,6 @@ function ReactionSurface(params) {
if (overlayData.width) {
this.width = overlayData.width;
}
- color = functions.overlayToColor(overlayData);
}
if (color === undefined) {
color = "#0000FF";
@@ -58,11 +57,11 @@ ReactionSurface.prototype.constructor = ReactionSurface;
/**
* Returns {@link google.maps.Bounds bounds} of all google maps elements
* included in the object.
- *
+ *
* @returns {@link google.maps.Bounds bounds} of all google maps elements
* included in the object
*/
-ReactionSurface.prototype.getBounds = function() {
+ReactionSurface.prototype.getBounds = function () {
var bounds = new google.maps.LatLngBounds();
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
@@ -74,23 +73,23 @@ ReactionSurface.prototype.getBounds = function() {
return bounds;
};
-ReactionSurface.prototype.setCustomized = function(customized) {
+ReactionSurface.prototype.setCustomized = function (customized) {
this.customized = customized;
};
/**
* Sets color to be used by the reaction overlay visualization when visualized
* in customized mode.
- *
+ *
* @param color
* new color value
*/
-ReactionSurface.prototype.setColor = function(color) {
+ReactionSurface.prototype.setColor = function (color) {
this._color = color;
var gmapObjects = this.getGoogleMapObjects();
for (var i = 0; i < gmapObjects.length; i++) {
gmapObjects[i].setOptions({
- strokeColor : color,
+ strokeColor: color,
});
}
this.customized = true;
@@ -99,11 +98,11 @@ ReactionSurface.prototype.setColor = function(color) {
/**
* Sets width of line to be used by the reaction overlay visualization when
* visualized in customized mode.
- *
+ *
* @param width
* new width value
*/
-ReactionSurface.prototype.setWidth = function(width) {
+ReactionSurface.prototype.setWidth = function (width) {
if (width !== undefined || width !== null) {
this.width = width;
} else {
@@ -114,19 +113,19 @@ ReactionSurface.prototype.setWidth = function(width) {
/**
* Returns color that should be used when visualized in customized mode.
- *
+ *
* @returns color that should be used when visualized in customized mode.
*/
-ReactionSurface.prototype.getColor = function() {
+ReactionSurface.prototype.getColor = function () {
return this._color;
};
/**
* Returns width that should be used when visualized in customized mode.
- *
+ *
* @returns width that should be used when visualized in customized mode.
*/
-ReactionSurface.prototype.getWidth = function() {
+ReactionSurface.prototype.getWidth = function () {
return this.width;
};
@@ -138,7 +137,7 @@ ReactionSurface.prototype.getWidth = function() {
* of reaction should turn to some default mode where we know that reaction is
* highlighted, but we have no more information. In this way user will know that
* he should investigate the reaction manually.
- *
+ *
* @param startX
* see {AliasSurface} class for details, in this implementation the
* only important information is that when there are more than one
@@ -150,7 +149,7 @@ ReactionSurface.prototype.getWidth = function() {
* layout visualized at least one of the two parameters (startX,endX)
* will differ from {0.0, 1.0} values
*/
-ReactionSurface.prototype.setBoundsForAlias = function(startX, endX) {
+ReactionSurface.prototype.setBoundsForAlias = function (startX, endX) {
if (this.isCustomized() && (startX > 0 || endX < 1)) {
this.changedToDefault();
} else if (!this.isCustomized() && (startX <= 0 && endX >= 1)) {
@@ -162,11 +161,11 @@ ReactionSurface.prototype.setBoundsForAlias = function(startX, endX) {
* Changes visualization of the ReactionSurface to default mode where we mark
* reaction as highlighted, but we skip customized reaction layout data.
*/
-ReactionSurface.prototype.changedToDefault = function() {
+ReactionSurface.prototype.changedToDefault = function () {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
this.getGoogleMapObjects()[i].setOptions({
- strokeColor : "#0000FF",
- strokeWeight : 5,
+ strokeColor: "#0000FF",
+ strokeWeight: 5,
});
}
this.customized = false;
@@ -179,8 +178,8 @@ ReactionSurface.prototype.changedToDefault = function() {
ReactionSurface.prototype.changedToCustomized = function() {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
this.getGoogleMapObjects()[i].setOptions({
- strokeColor : this.getColor(),
- strokeWeight : this.getWidth(),
+ strokeColor: this.getColor(),
+ strokeWeight: this.getWidth(),
});
}
this.customized = true;
@@ -188,7 +187,7 @@ ReactionSurface.prototype.changedToCustomized = function() {
/**
* Creates {google.maps.Polyline} from input data.
- *
+ *
* @param line
* raw data about line taken from server
* @param color
@@ -199,41 +198,41 @@ ReactionSurface.prototype.changedToCustomized = function() {
* {google.maps.Map} where line should be visualized
* @returns {google.maps.Polyline} from input data
*/
-ReactionSurface.createLine = function(line, color, width, map) {
+ReactionSurface.createLine = function (line, color, width, map) {
var pointA = new google.maps.Point(line.start.x, line.start.y);
var pointB = new google.maps.Point(line.end.x, line.end.y);
var latLngA = map.fromPointToLatLng(pointA);
var latLngB = map.fromPointToLatLng(pointB);
- var path = [ latLngA, latLngB ];
+ var path = [latLngA, latLngB];
var googleLine = new google.maps.Polyline({
- strokeColor : color,
- strokeOpacity : 1.0,
- strokeWeight : width,
- path : path,
- map : map.map
+ strokeColor: color,
+ strokeOpacity: 1.0,
+ strokeWeight: width,
+ path: path,
+ map: map.map
});
return googleLine;
};
/**
* Returns {@link Reaction} data for this marker.
- *
+ *
* @returns {@link Reaction} data for this marker
*/
-ReactionSurface.prototype.getReactionData = function() {
+ReactionSurface.prototype.getReactionData = function () {
return this.reactionData;
};
-ReactionSurface.prototype.getId = function() {
+ReactionSurface.prototype.getId = function () {
return this._id;
};
-ReactionSurface.prototype.setId = function(id) {
+ReactionSurface.prototype.setId = function (id) {
this._id = id;
};
-ReactionSurface.prototype.setReactionData = function(value) {
+ReactionSurface.prototype.setReactionData = function (value) {
if (value === undefined || value === null) {
throw new Error("Reaction must be defined");
}
@@ -241,11 +240,11 @@ ReactionSurface.prototype.setReactionData = function(value) {
this.setId(value.getId());
};
-ReactionSurface.prototype.isCustomized = function() {
+ReactionSurface.prototype.isCustomized = function () {
return this.customized;
};
-ReactionSurface.prototype.init = function() {
+ReactionSurface.prototype.init = function () {
var i;
var line;
var googleLine;
@@ -269,4 +268,24 @@ ReactionSurface.prototype.init = function() {
}
};
+ReactionSurface.create = function (params) {
+ var overlayData = params.layoutReaction;
+
+ var promise = Promise.resolve(params.color);
+ if (overlayData !== undefined && overlayData !== null) {
+ if (overlayData.width) {
+ this.width = overlayData.width;
+ }
+ promise = functions.overlayToColor(overlayData);
+ }
+ return promise.then(function (color) {
+ logger.debug(color);
+ if (color === undefined) {
+ color = "#0000FF";
+ }
+ params.color = color;
+ return new ReactionSurface(params);
+ });
+};
+
module.exports = ReactionSurface;
diff --git a/frontend-js/src/test/js/map/data/MapModel-test.js b/frontend-js/src/test/js/map/data/MapModel-test.js
index 267e598a481881805dfd6bb0ae5f51010faa8658..46f6ae592091ffdb458c9267aaa878ccdaecac21 100644
--- a/frontend-js/src/test/js/map/data/MapModel-test.js
+++ b/frontend-js/src/test/js/map/data/MapModel-test.js
@@ -1,6 +1,6 @@
"use strict";
-require("../../mocha-config.js");
+require("../../mocha-config");
var IdentifiedElement = require('../../../../main/js/map/data/IdentifiedElement');
var LayoutData = require('../../../../main/js/map/data/LayoutData');
diff --git a/frontend-js/src/test/js/map/surface/ReactionSurface-test.js b/frontend-js/src/test/js/map/surface/ReactionSurface-test.js
index 724cf409071a95550ce673f5177953ec043e2b78..c2e3290e116151eca5a8039557f3a8f1ef916ea1 100644
--- a/frontend-js/src/test/js/map/surface/ReactionSurface-test.js
+++ b/frontend-js/src/test/js/map/surface/ReactionSurface-test.js
@@ -1,22 +1,21 @@
"use strict";
+require("../../mocha-config");
var ReactionSurface = require('../../../../main/js/map/surface/ReactionSurface');
var assert = require('assert');
var logger = require('../../logger');
-describe('ReactionSurface', function() {
- it("Constructor", function() {
+describe('ReactionSurface', function () {
+ it("Constructor", function () {
var map = helper.createAbstractCustomMap();
var reaction = helper.createReaction(map);
- var layoutReaction = helper.createLayoutReaction(reaction);
var reactionOverlay = new ReactionSurface({
- overlayData : layoutReaction,
- reaction : reaction,
- map : map,
- customized : false
+ reaction: reaction,
+ map: map,
+ customized: false
});
assert.ok(reactionOverlay.getGoogleMapObjects().length > 0);
@@ -26,19 +25,41 @@ describe('ReactionSurface', function() {
assert.ok(reactionOverlay.getReactionData());
assert.ok(reactionOverlay.getCustomMap());
assert.ok(reactionOverlay.getId());
+ assert.ok(typeof reactionOverlay.getColor() === "string");
+ });
+ it("create", function () {
+ var map = helper.createAbstractCustomMap();
+ var reaction = helper.createReaction(map);
+ var layoutReaction = helper.createLayoutReaction(reaction);
+ return ReactionSurface.create({
+ layoutReaction: layoutReaction,
+ reaction: reaction,
+ map: map,
+ customized: false
+ }).then(function(reactionOverlay){
+
+ assert.ok(reactionOverlay.getGoogleMapObjects().length > 0);
+ assert.ok(reactionOverlay.getColor());
+ assert.ok(reactionOverlay.getWidth());
+ assert.ok(reactionOverlay.getBounds());
+ assert.ok(reactionOverlay.getReactionData());
+ assert.ok(reactionOverlay.getCustomMap());
+ assert.ok(reactionOverlay.getId());
+ assert.ok(typeof reactionOverlay.getColor() === "string");
+ });
});
- it("show", function() {
+ it("show", function () {
var map = helper.createCustomMap();
var reaction = helper.createReaction(map);
var layoutReaction = helper.createLayoutReaction(reaction);
var reactionOverlay = new ReactionSurface({
- overlayData : layoutReaction,
- reaction : reaction,
- map : map,
- customized : false
+ overlayData: layoutReaction,
+ reaction: reaction,
+ map: map,
+ customized: false
});
reactionOverlay.hide();
@@ -61,10 +82,10 @@ describe('ReactionSurface', function() {
var layoutReaction = helper.createLayoutReaction(reaction);
var reactionOverlay = new ReactionSurface({
- overlayData : layoutReaction,
- reaction : reaction,
- map : map,
- customized : false
+ overlayData: layoutReaction,
+ reaction: reaction,
+ map: map,
+ customized: false
});
reactionOverlay.changedToCustomized();
@@ -76,13 +97,13 @@ describe('ReactionSurface', function() {
var map = helper.createAbstractCustomMap();
var line = ReactionSurface.createLine({
- start : {
- x : 0,
- y : 10
+ start: {
+ x: 0,
+ y: 10
},
- end : {
- x : 100,
- y : 100
+ end: {
+ x: 100,
+ y: 100
},
}, "#000000", 3, map);
diff --git a/management_scripts/db_schema_and_diff.sh b/management_scripts/db_schema_and_diff.sh
new file mode 100644
index 0000000000000000000000000000000000000000..c6c0783e00fec80662cdb30d86aec5ed637e53a2
--- /dev/null
+++ b/management_scripts/db_schema_and_diff.sh
@@ -0,0 +1,77 @@
+# shell snippet which extracts all available MINERVA versions from
+# subdirectories available in DB_SCHEMA_DIR (typically
+# `persist/src/db`) and generates database upgrade scripts (diff
+# files)
+
+# Precondition: the following variables have to be correctly initialised
+# * DB_SCHEMA_DIR set to the directory containing database initialisation and upgrade sql commands
+# * DBSCRIPT_DEST_DIR set to the directory that will be populated with database upgrade scripts
+
+# Postcondition:
+# * versions is set to the available MINERVA versions (bash array)
+# * current_version is set to the latest available version
+# * DBSCRIPT_DEST_DIR contains script to initialise the database from any version to the current version
+
+
+#this variable will contain all available versions of the package
+versions=();
+
+#this is current (latest) version of the package
+current_version=-1;
+
+#find all available versions
+
+for version in `ls "$DB_SCHEMA_DIR" | sort -V`;
+do
+ if [ -d "$DB_SCHEMA_DIR/$version" ]
+ then
+ versions+=($version);
+ current_version=$version;
+ fi
+done
+
+#--------------------------------------
+# GENERATE DB schemas and diff files
+#--------------------------------------
+
+versionCompLte() {
+ [ "$1" = "`echo -e "$1\n$2" | sort -V | head -n1`" ]
+}
+
+
+versionCompLt() {
+ [ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
+}
+
+#last version (used for generating db diff files)
+for version_A in ${versions[*]}
+do
+ #main update file (used to create this version - it's a diff
+ #between base.sql and current version)
+ update_file="$DBSCRIPT_DEST_DIR/db_0_to_${current_version}.sql";
+
+ #now iterate through all versions
+ for file in `ls "$DB_SCHEMA_DIR/$version_A" | sort -V`;
+ do
+ if [ -f "$DB_SCHEMA_DIR/$version_A/$file" ]
+ then
+ #add difference to current db schema diff
+ printf "\n\n-- UPDATE $version_A/$file\n\n" >> "$update_file";
+ cat "$DB_SCHEMA_DIR/$version_A/$file" >> "$update_file";
+
+ #and now iterate again through all versions to add diffs
+ #between previous versions and current one
+ for version_B in ${versions[*]}
+ do
+ #update from version_B should contain all db changes that appeared
+ #after #version_B (so version_A must be later)
+ if versionCompLt $version_B $version_A
+ then
+ upd_file="$DBSCRIPT_DEST_DIR/db_${version_B}_to_${current_version}.sql";
+ printf "\n\n-- UPDATE $version_A/$file\n\n" >> "$upd_file";
+ cat "$DB_SCHEMA_DIR/$version_A/$file" >> "$upd_file";
+ fi
+ done
+ fi
+ done
+done
diff --git a/persist/src/db/11.0.4/fix_db_20171109.sql b/persist/src/db/11.0.4/fix_db_20171109.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/11.0.4/fix_db_20171109.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
diff --git a/rpm/INSTALL.rst b/rpm/INSTALL.rst
new file mode 100644
index 0000000000000000000000000000000000000000..11116e05510ccd5a849e643b27b14355ff8d7acf
--- /dev/null
+++ b/rpm/INSTALL.rst
@@ -0,0 +1,120 @@
+MINERVA installation instructions using RPM Package Manager
+===========================================================
+
+These instructions guide you through the installation process of
+`MINERVA <https://git-r3lab.uni.lu/piotr.gawron/minerva>`_ on Red Hat
+Enterprise Linux 7 or CentOS 7. The server will also host the database
+required for the functioning of MINERVA.
+
+.. note::
+
+ Content visualization of MINERVA platform is supported by Google
+ Maps API. Users of MINERVA platform are obliged to comply with the
+ `Google Maps/Google Earth APIs Terms of Service
+ <https://www.google.com/intl/en-US_US/help/terms_maps.html>`_.
+
+
+Overview
+--------
+
+The main steps are
+
+* Install `PostgreSQL <https://www.postgresql.org/>`_ and set up a
+ database.
+* Install and configure `Apache Tomcat <https://tomcat.apache.org/>`_.
+* Install the MINERVA RPM.
+
+
+PostgreSQL
+----------
+
+Install PostgreSQL and initialise it with
+
+.. code:: shell
+
+ yum install -y postgresql-server
+ postgresql-setup initdb
+
+Ensure that the database authentication on IPv4 on ``localhost`` is
+done with md5-based passwords by adding the following line to
+``/var/lib/pgsql/data/pg_hba.conf``
+
+.. code::
+
+ host all all 127.0.0.1/32 md5
+
+
+Enable and start postgresql
+
+.. code:: shell
+
+ systemctl enable postgresql
+ systemctl start postgresql
+
+Create the MINERVA database user and the database
+
+.. code:: shell
+
+ su - postgres -c "createuser -d -r -s map_viewer"
+ su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql"
+ su - postgres -c "createdb -O map_viewer map_viewer"
+
+.. warning::
+
+ Currently the password for the database user ``map_viewer`` is
+ hardcoded, therefore make sure the database cannot be accessed
+ from distrusted hosts.
+
+
+Apache Tomcat
+-------------
+
+Install and enable (don't start yet) Apache Tomcat with
+
+.. code:: shell
+
+ yum install -y tomcat
+ systemctl enable tomcat
+
+In ``/etc/sysconfig/tomcat``, adjust the memory settings, e.g.
+
+.. code::
+
+ JAVA_OPTS="-Xms2048M -Xmx4096M"
+
+Make sure to open the port (by default port 8080) to allow incoming
+connections, e.g. using ``firewalld`` this can be accomplished with
+
+.. code:: shell
+
+ firewall-cmd --permanent --zone=public --add-port=8080/tcp
+
+.. warning::
+
+ Currently the administrator password of MINERVA is hardcoded,
+ therefore make sure the MINERVA cannot be accessed from distrusted
+ hosts until the password was changed.
+
+MINERVA
+-------
+
+Install MINERVA using ``yum``
+
+.. code:: shell
+
+ yum install -y minerva-X.Y.Z-1.el7.centos.noarch.rpm
+
+and start tomcat
+
+.. code:: shell
+
+ systemctl start tomcat
+
+Now point your browser to the newly installed service, e.g. on a local
+network this could be `<http://192.168.0.42:8080/minerva/>`_.
+
+.. warning::
+
+ This way of installing MINERVA does **not** ensure that security
+ updates are installed with ``yum update``, therefore you have to
+ establish a process to install such updates manually.
diff --git a/rpm/buildrpm.sh b/rpm/buildrpm.sh
new file mode 100755
index 0000000000000000000000000000000000000000..eb3166272ad7a7d7dab709facd55f6340cfe7f32
--- /dev/null
+++ b/rpm/buildrpm.sh
@@ -0,0 +1,60 @@
+#!/bin/bash
+
+set -e
+
+MINERVA_SRC_DIR="$(dirname "$(dirname "$0")")"
+
+# where generated files will be written
+RPMBUILD_TEMP="${RPMBUILD_TEMP:-$MINERVA_SRC_DIR/rpm/rpmbuildtemp}"
+
+if [[ "$RPMBUILD_TEMP" =~ ' ' ]]; then
+ echo "RPMBUILD_TEMP contains whitespace: '$RPMBUILD_TEMP'"
+ echo "This is not allowed. Please provide a different directory to create the RPM with"
+ echo " RPMBUILD_TEMP=/path/without/whitespace/ \"$0\""
+ exit 1
+fi
+
+# current date (for automatic changelog)
+CURDATE=$(date +"%a %b %d %Y")
+
+# file that should be deployed on tomcat
+TOMCAT_FILE="$MINERVA_SRC_DIR/web/target/web-1.0.war"
+
+# file with bash code generating DB schema diffs for different versions
+dbschemadiff="$MINERVA_SRC_DIR/management_scripts/db_schema_and_diff.sh"
+
+# directory with database schema
+DB_SCHEMA_DIR="$MINERVA_SRC_DIR/persist/src/db"
+
+# destination directory for database upgrade scripts
+DBSCRIPT_DEST_DIR="$RPMBUILD_TEMP/BUILD/sql"
+
+# clean build directories
+rm -rf "$RPMBUILD_TEMP"
+
+# create directory
+mkdir -p "$RPMBUILD_TEMP/"{BUILD,SPECS}
+
+# copy war file and other files
+cp "$TOMCAT_FILE" "$RPMBUILD_TEMP/BUILD/minerva.war"
+cp "$MINERVA_SRC_DIR/README.md" "$MINERVA_SRC_DIR/CHANGELOG" "$MINERVA_SRC_DIR/rpm/INSTALL.rst" "$MINERVA_SRC_DIR/rpm/logrotate_minerva" "$RPMBUILD_TEMP/BUILD"
+
+mkdir -p "$DBSCRIPT_DEST_DIR"
+# copy base sql schema
+cp "$DB_SCHEMA_DIR/base.sql" "$DBSCRIPT_DEST_DIR/db_0.sql"
+
+# set $versions and $current_version; generate upgrade scripts in DBSCRIPT_DEST_DIR
+source "$dbschemadiff"
+
+# create RPM spec file
+cp "$MINERVA_SRC_DIR/rpm/minerva.spec.in" "$RPMBUILD_TEMP/SPECS/minerva.spec"
+sed -i "s/__CURRENT_VERSION__/$current_version/g" "$RPMBUILD_TEMP/SPECS/minerva.spec"
+sed -i "s/__DATE__/$CURDATE/g" "$RPMBUILD_TEMP/SPECS/minerva.spec"
+
+# build RPM
+RPMBUILD_TEMP_ABS="$(readlink -f "$RPMBUILD_TEMP")"
+echo "****** Building miverva $current_version RPM in $RPMBUILD_TEMP_ABS ****** "
+set -x
+rpmbuild -bb --define "_topdir $RPMBUILD_TEMP_ABS" "$RPMBUILD_TEMP_ABS/SPECS/minerva.spec"
+set +x
+echo "****** Finished building RPM ****** "
diff --git a/rpm/logrotate_minerva b/rpm/logrotate_minerva
new file mode 100644
index 0000000000000000000000000000000000000000..001adf1a0734bbf445836bf465621a49565c98c2
--- /dev/null
+++ b/rpm/logrotate_minerva
@@ -0,0 +1,10 @@
+/var/log/tomcat/minerva.txt {
+ copytruncate
+ size 32k
+ weekly
+ dateext
+ rotate 52
+ compress
+ missingok
+ create 0640 tomcat tomcat
+}
diff --git a/rpm/minerva.spec.in b/rpm/minerva.spec.in
new file mode 100644
index 0000000000000000000000000000000000000000..2edcdf292154137850bb234c22e28361f72d51ac
--- /dev/null
+++ b/rpm/minerva.spec.in
@@ -0,0 +1,95 @@
+Name: minerva
+Version: __CURRENT_VERSION__
+Release: 1%{?dist}
+Summary: Platform for visualization and curation of molecular interaction networks
+
+License: AGPLv3
+URL: http://r3lab.uni.lu/web/minerva-website/
+Source0: https://git-r3lab.uni.lu/piotr.gawron/minerva/repository/archive.tar.gz?ref=v%{version}
+
+Requires: tomcat, postgresql
+BuildArch: noarch
+
+%description
+Web application for visualization, exploration and management of
+molecular networks encoded in SBGN-compliant format. The resource is
+used and managed via a webbrowser.
+
+%pre -p /bin/bash
+# check that postgres is started and tomcat is stopped, otherwise abort installation/upgrade
+if ! $(systemctl -q is-active postgresql); then
+ echo "postgresql not running, aborting installation/upgrade of minerva" >&2
+ exit -1
+fi
+if $(systemctl -q is-active tomcat); then
+ echo "tomcat is running, aborting installation/upgrade of minerva" >&2
+ exit -1
+fi
+# make sure the user `map_viewer` has the required permissions
+attributes_map_viewer=$(su - postgres -c "psql -F $'\t' --no-align -t -c '\du map_viewer'" | cut -f 2)
+if ! [[ $attributes_map_viewer == *"Superuser"* ]] || ! [[ $attributes_map_viewer == *"Create role"* ]] || ! [[ $attributes_map_viewer == *"Create DB"* ]]; then
+ echo "Postgres user map_viewer does not exist or does not have the required attributes." >&2
+ echo "Make sure to create map_viewer with the permission 'Superuser, Create role, Create DB'." >&2
+ echo "Attributes are: '$attributes_map_viewer'" >&2
+ echo "Aborting installation/upgrade of minerva." >&2
+ exit -1
+fi
+# make sure the database map_viewer exists
+if ! su - postgres -c "psql --dbname map_viewer -q -c '\q'" 2> /dev/null; then
+ echo "Database map_viewer does not exist, aborting installation/upgrade of minerva." >&2
+ exit -1
+fi
+
+%preun -p /bin/bash
+# save version information of the old package to make sure we run the correct DB-update script after installation
+if [ $1 == 1 ]; then
+ mkdir -p %{_sharedstatedir}/rpm-state/%{name}
+ echo -n %{version} > %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION
+fi
+
+%posttrans -p /bin/bash
+LOGFILE=%{_localstatedir}/log/minerva-install.log
+if [ -e %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION ]; then
+ OLD_VERSION=$(cat %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION)
+ echo $(date) "Upgrading minerva from $OLD_VERSION to %{version}" >> $LOGFILE
+ if [ ! -e %{_datadir}/%{name}/schema/db_${OLD_VERSION}_to_%{version}.sql ]; then
+ echo "ERROR: missing DB-update script %{_datadir}/%{name}/schema/db_${OLD_VERSION}_to_%{version}.sql" >&2
+ exit -1
+ fi
+ su - postgres -c "psql map_viewer -f %{_datadir}/%{name}/schema/db_${OLD_VERSION}_to_%{version}.sql" >> $LOGFILE 2>&1
+ rm -f %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION
+ rmdir %{_sharedstatedir}/rpm-state/%{name}
+else
+ echo $(date) "Installing minerva %{version}" >> $LOGFILE
+ if [ $(su - postgres -c "psql --dbname map_viewer -F $'\t' --no-align -t -c '\dt'" | wc -l) -gt 51 ]; then
+ echo "The database map_viewer is not empty, aborting initialisation of database." >&2
+ echo "The database map_viewer is not empty, aborting initialisation of database." >> $LOGFILE
+ exit -1
+ fi
+ # install base version of the framework
+ su - postgres -c "psql map_viewer -f %{_datadir}/%{name}/schema/db_0.sql" >> $LOGFILE 2>&1
+ # install patch to current version
+ su - postgres -c "psql map_viewer -f %{_datadir}/%{name}/schema/db_0_to_%{version}.sql" >> $LOGFILE 2>&1
+fi
+
+%install
+rm -rf %{buildroot}
+mkdir -p %{buildroot}/%{_datadir}/%{name}/schema
+install -m 0644 sql/*.sql %{buildroot}/%{_datadir}/%{name}/schema
+install -m 0644 %{name}.war %{buildroot}/%{_datadir}/%{name}/%{name}.war
+mkdir -p %{buildroot}/%{_sysconfdir}/logrotate.d
+install -m 0644 logrotate_minerva %{buildroot}/%{_sysconfdir}/logrotate.d/minerva
+mkdir -p %{buildroot}/%{_sharedstatedir}/tomcat/webapps
+ln -s %{_datadir}/%{name}/%{name}.war %{buildroot}/%{_sharedstatedir}/tomcat/webapps/
+
+%files
+%defattr(-,root,root,-)
+%doc README.md CHANGELOG INSTALL.rst
+%{_datadir}/%{name}/%{name}.war
+%{_datadir}/%{name}/schema/*
+%config(noreplace) %{_sysconfdir}/logrotate.d/minerva
+%attr(-,tomcat,tomcat) %{_sharedstatedir}/tomcat/webapps/%{name}.war
+
+%changelog
+* __DATE__ - %{version}-%{release}
+- Automatically packaged