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Commit 518c3ef7 authored by Piotr Gawron's avatar Piotr Gawron
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Merge remote-tracking branch 'origin/master' into 1016-refactor-test-framework

parents 51adac30 94a0142c
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.gitlab-ci.yml
View file @ 518c3ef7
......@@ -34,6 +34,8 @@ test:frontend:
- postgres:9.6
stage: test
coverage: '/(\d+.\d+) \% covered/'
before_script:
- mvn dependency:purge-local-repository -DmanualInclude="lcsb.mapviewer"
.jdk_11_template: &jdk_11_definition
image: maven:3.6.0-jdk-11
......@@ -41,6 +43,8 @@ test:frontend:
- postgres:9.6
stage: test
coverage: '/(\d+.\d+) \% covered/'
before_script:
- mvn dependency:purge-local-repository -DmanualInclude="lcsb.mapviewer"
.hsql_template: &hsql_definition
image: maven:3.6.0-jdk-11
......
CHANGELOG
View file @ 518c3ef7
minerva (16.0.0~alpha.0) stable; urgency=medium
* Bug fix: md5 hash function of plugin was not computed properly
minerva (15.0.0~beta.2) stable; urgency=medium
* Bug fix: newt use incorrect attributes when exporting render information
that could not be parsed by minevra (#1127)
* Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
* Bug fix: upload logs for SBGN parser were not translated properly to new
structured log form
* Bug fix: antisenseRNA shape is infered from SBGN when antisenseRNA 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
same were not handled properly (#1131)
* Bug fix: exporting map to CellDesigner from GPML file created not-editable
compartments (#1146)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 27 Feb 2020 14:00:00 +0200
minerva (15.0.0~beta.1) stable; urgency=medium
* Bug fix: conflict on libraries caused some features to stop working in
production (like parsing text notes of species, regresion in
15.0.0~alpha.1, #1139)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 26 Feb 2020 13:00:00 +0200
minerva (15.0.0~beta.0) stable; urgency=medium
* Feature removal: old connection to CTD is removed and replaced with
minerva (15.1.0) unstable; urgency=medium
* Small improvement: annotations are exported in SBGN extension that can be
opened by newt (#1296)
* Small improvement: plugin API allows to add/remove data overlays (#1153)
* Small improvement: logged user can change password (#1119)
* Small improvement: possibility to reset password added (#275)
* Small improvement: import SBML uses render:fill color for compartment
(#1254)
* Small improvement: in SBML render stroke color for glyphs is used for
defining font color
* Small improvement: when SBML with layout contains different glyph text and
species name those two values are assigned to name and full name (#1275)
* Small improvement: process rectangle can be specified in SBML with reaction
bounding box (#1292)
* Small improvement: API allows to remove plugin data entry (#1298)
* Small improvement: transport/translation/transcription reactions are
exported to SBGN PD (#1302)
* Small improvement: Unknown Transition Reaction is exported to GPML as
CONVERSION (#1300)
* Small improvement: when uploading complex map with images warnings are
raised if images are not referenced in coords.txt file (#1308)
* Small improvement: hitting enter after filling credentials automatically
tries to log in (#1312)
* Small improvement: rest API provides information about element glyph and z
index
* Small improvement: pathways with glyphs and z index below 0 are not
clickable (#1314)
* Bug fix: export to image from selected polygon contained all elements
inside rectangle bounded by the polygon coordinates (#1096)
* Bug fix: continuous refreshing list of project when uploading/removing
project did not allow to change other project details (#996)
* Bug fix: when multi extension did not contain species type list import of
SBML crashed
* Bug fix: when content of element popover is too wide the scrollbar is
visible (#1269)
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 18 Jun 2020 16:00:00 +0200
minerva (15.0.2) stable; urgency=medium
* Bug fix: annotations using identifiers.org urls sometimes required http and
sometimes required https url (#1297)
* Bug fix: map notes were not exported to GPML
* Bug fix: reaction notes were not imported from GPML
* Bug fix: export of notes could create invalid GPML file (#1299)
* Bug fix: there was an issue with exporting color and line type of reaction
additional reactant/product (#1303)
* Bug fix: coordinates of children in compact complexes in CellDesigner were
wrong (#1304)
* Bug fix: user data overlays were not removed when user was deleted (#1301)
* Bug fix: kinetic parameters exported to SBML created invalid SBML file
(#1305)
* Bug fix: text area were not converted to GPML using conversion API (#1306)
* Bug fix: name provided by user in comment dialog was not visible in admin
panel (#1245)
* Bug fix: bqmodel:isInstanceOf and bqmodel:hasInstance relation types were
not handled properly (#1281)
* Bug fix: "bqmodel:isInstanceOf", "bqmodel:hasInstance",
"bqbiol:hasProperty", "bqbiol:isPropertyOf" and "bqbiol:hasTaxon" relation
types are not supported by CellDedigner 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)
* Bug fix: complex/compartment with empty name was incorrectly exported to
CellDesigner (#1310)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 1 Jul 2020 16:00:00 +0200
minerva (15.0.1) stable; urgency=medium
* Bug fix: when there was problem with DAPI minerva threw unexpected error
(#1316)
* Bug fix: DAPI connection must go over HTTPS (#1316)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 26 Jun 2020 11:00:00 +0200
minerva (15.0.0) stable; urgency=medium
* Backward incompatible: old connection to CTD is removed and replaced with
new Data-API interface that closely check license compliance
* Feature removal: some custom fields (like transparency zoom level) are not
exported to CellDesigner file (#1071)
* Backward incompatible: old connection to DrugBank is removed and replaced
with new Data-API interface that closely check license compliance
* Backward incompatible: some custom fields (like transparency zoom level)
are not exported to CellDesigner file (#1071)
* Backward incompatible: truncation/association/dissociation points are
represented as a dot in all new images/uploaded maps (#1265)
* Backward incompatible: and/split points are represented as a dot in all new
images/uploaded maps (#1253)
* Backward incompatible: reaction will be on top of elements in maps uploaded
from formats that does not contain z-index (#1251)
* Backward incompatible: when uploading complex map with submap there is no
possibility to change submap name (#947)
* Improvement: logs provided for validation data model are structured (#325)
* Improvement: import/export of GPML implemented
* Improvement: API allows to merge files (#1208)
* Improvement: export to SBGN/SBML/GPML format provides popup with list of
warnings occurred in the translation process (#713)
* Improvement: support for rendering colors in SBGNML added (#1009)
* Small improvement: compartments in not layouted SBML file are more
scattered (#326)
* Small improvement: when downloading a map results in too big file (>1MB)
the content is compressed and returned as a zip file (#348)
* Small improvement: confirmation dialog when removing "general view"
overlays contain proper warning (#809)
* Small improvement: CellDesigner text area object can have "BorderColor"
property defined (#806)
* Small improvement: list of submaps is sorted alphabetically (#962)
* Small improvement: notification about new releases of minerva added in
admin panel (#961)
* Small improvement: font awesome upgraded to 5.1 (new icon styles)
* Small improvement: header contains login/logout button and access admin
panel button (#982)
* Small improvement: autocomplete for chemical searches is enabled (#841)
* Small improvement: "bqbiol:occursIn" and "bqmodel:isDerivedFrom" and
handled in annotations (#1190),
* Small improvement: 3DMET, Evidence Code Ontology, Kegg Glycan, LipidBank,
Chemical Component Dictionary annotations are supported (#1190)
* Small improvement: SWISS-model annotations are supported (#1249),
* Small Improvement: SBO annotation support added (#1194)
* Small improvement: support for annotations added: ChemIDplus, EcoGene,
FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein,
PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
* Small Improvement: additional annotation uri qualifiers added: hasProperty,
isPropertyOf (#1193)
* Small improvement: small css improvement in info tab (#1104)
* Small improvement: import/export to SBML of unit of information obtained
from SBGN source is supported (#1088)
* Small improvement: rounded rectangle is used to visualize Simple chemicals
in SBGN-like view according to the newest SBGN specification (#1094)
* Small improvement: after removing project is confirmed the system enforce
waiting until remove status is confirmed (#1106)
* Bug fix: import from SBGN assigned invalid name to species that didn't have
label defined (#1093)
* Bug fix: drawing protein in SBGN-like style didn't handle properly
dimension of the species for multimers bigger than 2 (#1091)
* Bug fix: drawing of structural state in SBGN-like style uses
RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095)
* Bug fix: export to GPML provided invalid font size and pathviosio could not
open it (#1108)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 28 Jan 2020 13:00:00 +0200
minerva (15.0.0~alpha.2) stable; urgency=medium
* Feature removal: old connection to DrugBank is removed and replaced with
new Data-API interface that closely check license compliance
* Small improvement: when typing drug, list of autocomplete drugs should be
available limited to the drugs targetting something on the map (#641)
available limited to the drugs that target something on the map (#641)
* Small improvement: data not compliant with database constraints (for
instance too long species identifiers) will be automatically adjust instead
of crashing project upload (#1041)
* Small improvement: reaction lines in SBML files without layout are set
outside of the species (not in the center, #1023)
* Bug fix: import from CellDesigner rounded alias dimension to integer
* Bug fix: old project with structural state couldn't be removed (regression
15.0.0~alpha.1, #1021)
* Bug fix: processing sbgn file with render information was breaking sometimes
(regression 15.0.0~alpha.1, #1020)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 22 Jan 2020 13:00:00 +0200
minerva (15.0.0~alpha.1) stable; urgency=medium
* Feature removal: when uploading complex map with submap there is no
possibility to change submap name (#947)
* Improvement: support for rendering colors in SBGNML added (#1009)
* Small improvement: sort order of tables in admin panel is preserved among
sessions (#836)
* Small improvement: simple molecules in sbgn compliant view are drawn as
* 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
......@@ -86,15 +154,52 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
about the plugins (name, version)
* Small improvement: there is possibility to define default plugins loaded
with every opening of a map (#967)
* Small improvement: support for annotations added: ChemIDplus, EcoGene,
FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein,
PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
* Bug fix: pathways are visualized in image converter (#1266)
* Bug fix: conversion of file containing BOM did not work (#1264)
* Bug fix: proper color is parsed from CellDesigner species marked as 'brief'
* Bug fix: upload of SBGN files didn't process unicode characters properly
when server was running with encoding different than UTF-8 (#1142)
* Bug fix: kinetic equation in reaction that referenced complex (instead of
target species) crashed CellDesigner upload (#1212)
* Bug fix: kinetic equation in SBML that used speciesReference id crashed
upload (#1190)
* Bug fix: layout reaction with duplicated reaction element crashed SBML
upload (#1190)
* Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228)
* Bug fix: Select annotation dialog width is at least 840px (#1210)
* Bug fix: modifiers joined by operator were exported to SBML without line
corresponding to the operator (#1199)
* Bug fix: first state variable that does not match modification residue is
translated to structural state when importing from SBGNML (#1088)
* Bug fix: exported SBML was not compliant with the standard when element
name was empty (#1147)
* Bug fix: invalid data overlays in uploaded zip file created "valid" project
that could not be opened (#1086)
* Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157)
* Bug fix: notes from SBML are parsed with all html tags (#1196)
* Bug fix: converter API append conversion warnings to generated output notes
* 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
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
same were not handled properly (#1131)
* Bug fix: more than one authors in CellDesigner file were not parsed
properly (#1156)
* Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
* Bug fix: import from SBGN assigned invalid name to species that didn't have
label defined (#1093)
* Bug fix: drawing protein in SBGN-like style didn't handle properly
dimension of the species for multimers bigger than 2 (#1091)
* Bug fix: drawing of structural state in SBGN-like style uses
RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095)
* Bug fix: import from CellDesigner rounded alias dimension to integer
* Bug fix: compartments limited by corner (left-top corner compartment, etc)
are parsed properly from CellDesigner files
* Bug fix: structural states of proteins are imported properly from SBGNML PD
(#995)
* Bug fix: clear button icon, refresh comments button and show overview
button icons were missing (regression 15.0.0~alpha.0)
* Bug fix: export to CellDesigner names with new line is properly handled
(#930)
* Bug fix: layout of the exported reactome pathways is fixed when reactome
......@@ -103,36 +208,61 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
visualized with proper line type across all included modifiers (#957)
* Bug fix: dimension of the modifications is the same as in minerva when
exporting to SBGNML-PD (#554)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 15 Nov 2019 9:00:00 +0200
minerva (15.0.0~alpha.0) stable; urgency=medium
* Improvement: logs provided for validation data model are structurized (#325)
* Improvement: import/export of GPML implemented
* Small improvement: compartments in not layouted SBML file are more
scattered (#326)
* Small improvement: when downloading a map results in too big file (>1MB)
the content is compressed and returned as a zip file (#348)
* Small improvement: confirmation dialog when removing "general view"
overlays contain proper warning (#809)
* Small improvement: CellDesigner text area object can have "BorderColor"
property defined (#806)
* Small improvement: list of submaps is sorted alphabetically (#962)
* Small improvement: notification about new releases of minerva added in
admin panel (#961)
* Small improvement: font awesome upgraded to 5.1 (new icon styles)
* Small improvement: header contains login/logout button and access admin
panel button (#982)
* Bug fix: position of structural state is preserved on upload CellDesigner
file (#671)
* Bug fix: problematic notes doesn't crash CellDesigner upload (#968)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 4 Nov 2019 11:00:00 +0200
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Jun 2020 11:00:00 +0200
minerva (14.0.13) stable; urgency=medium
* Bug fix: chrome modified default css and service looked ugly in chrome
(#1260)
* Bug fix: uploaded HGNC identifiers that looks like "HGNC:HGNC:1234" are
changed to "HGNC:1234" (#1252)
* Bug fix: creating comment with too long name/email resulted in Internal
Server Error - now the proper error message is returned (#1245)
* Bug fix: user cannot put too long name in a comment dialog (#1245)
* Bug fix: when url contained invalid submap id unhandled error was raised
(#1243)
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 3 Jun 2020 17:00:00 +0200
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
CellDesigner (#1227)
* Bug fix: doi annotation was inproperly 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
(#1211)
-- 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
(#1198)
* Bug fix: export to CellDesigner deal with CellDesigner issue that does not
allow compartment species alias to be shorter than 2 characters (#1204)
* Bug fix: kinetic parameters with INFINITY values could not be uploaded to
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
missing (#1201)
* Bug fix: refreshing minerva page with more than one plugin opened might
led to an error due to race condition (#1197)
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 31 Mar 2020 09:00:00 +0200
minerva (14.0.10) stable; urgency=medium
* Bug fix: reaction without ports in SBGN crashed upload (#1065)
* Bug fix: annotations using newer identifiers.org uri schema were truncated
by one character (#1191)
* Bug fix: long annotation string broke listing of annotations (#1155)
-- Piotr Gawron <piotr.gawron@uni.lu> Tue, 27 Feb 2020 10:00:00 +0200
-- 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
......
CellDesigner-plugin/build.xml
View file @ 518c3ef7
......@@ -2,34 +2,18 @@
<project name="CellDesigner plugin" default="main" basedir=".">
<property environment="env"/>
<property name="build.dir" value="target" />
<property name="mvn.home" value="${env.M2_HOME}" />
<property name="celldesigner.home" value="C:/Program Files (x86)/CellDesigner4.4/" />
<property name="celldesigner.deploy.dir" value="${celldesigner.home}/plugin/" />
<property name="plugin.name" value="mv_plugin" />
<property name="jar.file" value="CellDesigner-plugin-1.0-jar-with-dependencies.jar" />
<target name="maven-build">
<exec executable="${mvn.home}/bin/mvn.bat" >
<exec executable="mvn" >
<arg line="clean" />
</exec>
<exec executable="${mvn.home}/bin/mvn.bat" >
<exec executable="mvn" >
<arg line="-Dmaven.test.skip=true install" />
</exec>
</target>
<target name="jar-exists">
<available file="${celldesigner.home}/plugin/${plugin.name}.jar" property="jar.exists"/>
</target>
<target name="remove-jar" depends="jar-exists" if="jar.exists">
<delete file="${celldesigner.home}/plugin/${plugin.name}.jar" />
</target>
<target name="deploy" depends="remove-jar">
<copy file="${build.dir}/${jar.file}" todir="${celldesigner.deploy.dir}" />
<move file="${celldesigner.deploy.dir}/${jar.file}" tofile="${celldesigner.deploy.dir}/${plugin.name}.jar"/>
</target>
<target name="main" depends="maven-build, deploy"/>
<target name="main" depends="maven-build"/>
</project>
\ No newline at end of file
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
View file @ 518c3ef7
......@@ -99,7 +99,7 @@ public class InfoPlugin extends CellDesignerPlugin {
for (int i = 0; i < Math.min(aliasList.size(), MAX_VISIBLE_ELEMENTS); i++) {
PluginSpeciesAlias alias = (PluginSpeciesAlias) aliasList.get(i);
v.add(alias);
newId += alias.getSpecies().getName();
newId += alias.getAliasID();
}
// if the cache is exactly the same as in the previous run then
// don't update infoframe
......
README.md
View file @ 518c3ef7
......@@ -10,7 +10,7 @@ Documentation for minerva can be found here: https://minerva.pages.uni.lu/doc/
After cloning repo you need to install following tools:
* postgresql (>=9.1)
* tomcat (tested on tomcat7, tomcat8)
* tomcat (tested on tomcat8, tomcat9)
* Java8 - works on OpenJDK 8, Oracle Java 8, OpenJDK 11
* maven
* ant
......
annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
View file @ 518c3ef7
......@@ -143,7 +143,13 @@ public class WebPageDownloader {
Future<String> future = executor.submit(new Task());
try {
String result = future.get(HTTP_CONNECTION_TIMEOUT_SEC, TimeUnit.SECONDS);
int timeout = HTTP_CONNECTION_TIMEOUT_SEC;
// dapi is slow for now
if (accessUrl.indexOf("dapi.lcsb.uni.lu") >= 0) {
timeout *= 10;
}
String result = future.get(timeout, TimeUnit.SECONDS);
executor.shutdownNow();
return result;
} catch (Exception e) {
......
annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
View file @ 518c3ef7
......@@ -98,8 +98,6 @@ public class XmlSerializer<T> {
}
try {
return (T) jaxbUnmarshaller.unmarshal(node);
} catch (JAXBException e) {
throw new SerializationException(e);
} catch (Exception e) { // the library can throw NPE sometimes...
logger.error(e, e);
return null;
......
annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
View file @ 518c3ef7
......@@ -29,7 +29,7 @@ public class Drug implements Serializable, TargettingStructure {
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(Drug.class);
private static Logger logger = LogManager.getLogger();
/**
* Source of the data.
......@@ -47,7 +47,7 @@ public class Drug implements Serializable, TargettingStructure {
private String description;
/**
* Status of blood brain barries for the drug.
* Status of blood brain barriers for the drug.
*/
private String bloodBrainBarrier = "N/A";
......
annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
View file @ 518c3ef7
......@@ -12,6 +12,7 @@ import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.*;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.*;
/**
......@@ -36,6 +37,8 @@ public final class MiriamConnector extends CachableInterface implements IExterna
* Default class logger.
*/
private Logger logger = LogManager.getLogger(MiriamConnector.class);
XmlAnnotationParser xap = new XmlAnnotationParser();
/**
* Default class constructor. Prevent initialization.
......@@ -90,13 +93,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
} else if (miriamData.getDataType().getUris().size() == 0) {
throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
}
String id;
if (miriamData.getDataType().getNamespace().isEmpty()) {
id = miriamData.getResource();
} else {
id = miriamData.getDataType().getNamespace() + ":" + miriamData.getResource();
}
String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
String result = getCacheValue(query);
if (result != null) {
......@@ -106,7 +102,8 @@ public final class MiriamConnector extends CachableInterface implements IExterna
return result;
}
try {
result = getRedirectURL("https://identifiers.org/" + id);
String identifiersOrgUrl = xap.getIdentifiersOrgUrl(miriamData);
result = getRedirectURL(identifiersOrgUrl);
if (result != null) {
setCacheValue(query, result);
......@@ -123,7 +120,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
}
private String getRedirectURL(String address) throws IOException {
URL url = new URL(address);
URL url = new URL(address.replaceAll("\n", ""));
HttpURLConnection con = (HttpURLConnection) url.openConnection();
con.setInstanceFollowRedirects(false);
con.setRequestProperty("User-Agent", "minerva-framework");
......
annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
View file @ 518c3ef7
......@@ -43,7 +43,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* Version of the remote API that is supported by this connecting class.
*/
static final String SUPPORTED_VERSION = "6.2";
static final String SUPPORTED_VERSION = "6.3";
static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
/**
* Length of {@link #PUBMED_PREFIX} string.
......
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
View file @ 518c3ef7
......@@ -36,7 +36,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
/**
* Version of the rest API that is supported by this annotator.
*/
static final String SUPPORTED_VERSION = "11.2";
static final String SUPPORTED_VERSION = "12.0";
/**
* Url address of ensembl restful service.
......
annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/ChemicalParser.java
View file @ 518c3ef7
......@@ -152,7 +152,8 @@ public class ChemicalParser {
if (target.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
targets.add(target);
} else {
throw new InvalidArgumentException("Only those identifiers are accepted: " + MiriamType.HGNC_SYMBOL);
throw new InvalidArgumentException(
"Only those identifiers are accepted: " + MiriamType.HGNC_SYMBOL + ". Found: " + target);
}
return targets;
}
......@@ -196,7 +197,7 @@ public class ChemicalParser {
if (disease == null) {
throw new InvalidArgumentException("disease cannot be null");
}
if (!dapiConnector.isValidConnection()) {
return null;
}
......@@ -230,7 +231,8 @@ public class ChemicalParser {
private List<Chemical> fetchChemicals(ListChemicalEntityDto list, MiriamData disease) throws DapiConnectionException {
List<Chemical> result = new ArrayList<>();
for (ChemicalEntityDto entity : list.getContent()) {
Chemical chemical = getByIdentifier(MiriamType.getMiriamDataFromPrefixIdentifier(entity.getSourceIdentifier()), disease);
Chemical chemical = getByIdentifier(MiriamType.getMiriamDataFromPrefixIdentifier(entity.getSourceIdentifier()),
disease);
if (chemical == null) {
logger.warn("Invalid chemical identifier: " + entity.getSourceIdentifier());
} else {
......@@ -252,8 +254,8 @@ public class ChemicalParser {
Chemical chemical = chemicalEntityDtoConverter.dtoToChemical(result);
Set<Target> targetsToRemove = new HashSet<>();
for (Target t:chemical.getTargets()) {
if (disease!=null && !Objects.equals(t.getAssociatedDisease(), disease)) {
for (Target t : chemical.getTargets()) {
if (disease != null && !Objects.equals(t.getAssociatedDisease(), disease)) {
targetsToRemove.add(t);
}
}
......
annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/DapiConnectorImpl.java
View file @ 518c3ef7
......@@ -26,7 +26,7 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
private static Logger logger = LogManager.getLogger();
private static final String DAPI_DOMAIN = "dapi.lcsb.uni.lu";
private static final String DAPI_BASE_URL = "http://" + DAPI_DOMAIN + "/api/";
private static final String DAPI_BASE_URL = "https://" + DAPI_DOMAIN + "/api/";
private ConfigurationDao configurationDao;