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Update ISA-TAB configuration files and fix export
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The ISA-TAB configuration files were updated to the latest version and the export
format was also fixed. #175
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@timeu
timeu committed Sep 4, 2016
1 parent 513442a commit 506d722
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Showing 5 changed files with 631 additions and 559 deletions.
38 changes: 37 additions & 1 deletion genophenbrowser-server/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
<supercsv.version>2.2.1</supercsv.version>
<apache.commons.math>3.4</apache.commons.math>
<apache.commons.exec>1.3</apache.commons.exec>
<isatab.version>1.7.8-SPECIAL</isatab.version>
<isatab.version>1.7.9-SPECIAL</isatab.version>
</properties>


Expand Down Expand Up @@ -463,6 +463,42 @@
<groupId>com.explodingpixels</groupId>
<artifactId>scroller</artifactId>
</exclusion>
<exclusion>
<groupId>net.java.dev.fuse</groupId>
<artifactId>fuse-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-rt</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-tools</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.felix</groupId>
<artifactId>org.apache.felix.framework</artifactId>
</exclusion>
<exclusion>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
</exclusion>
<exclusion>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</exclusion>
<exclusion>
<groupId>javax.jws</groupId>
<artifactId>jsr181-api</artifactId>
</exclusion>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.jersey.contribs</groupId>
<artifactId>jersey-multipart</artifactId>
</exclusion>
<!--
<exclusion>
<groupId>uk.ac.ebi</groupId>
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90 changes: 43 additions & 47 deletions ...rver/src/main/java/com/gmi/nordborglab/browser/server/data/isatab/IsaTabExporterImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
import org.isatools.isacreator.ontologymanager.BioPortal4Client;
import org.isatools.isacreator.ontologymanager.OntologyManager;
import org.isatools.isacreator.ontologymanager.OntologySourceRefObject;
import org.isatools.isacreator.ontologymanager.common.OntologyTerm;
import org.isatools.isacreator.ontologymanager.utils.OntologyUtils;
import org.isatools.isacreator.settings.ISAcreatorProperties;
import org.isatools.isacreator.spreadsheet.model.ReferenceData;
Expand Down Expand Up @@ -99,42 +100,30 @@ public class IsaTabExporterImpl implements IsaTabExporter {
static final String INVESTIGATION_FILE = "i_investigation.txt";
static final String STUDY_FILE = "s_study.txt";
static final String ASSAY_FILE = "a_assay.txt";
static final String TRAIT_DEF_FILE = "t_trait_def.txt";
static final String TRAIT_DEF_FILE = "tdf.txt";
static final String DERVIVED_DATA_FILE = "d_derived_data.txt";
static URL CONFIG_DIRECTORY;
static final Pattern derivedTraitPattern = Pattern.compile("Trait Value\\[(.*)\\]");

final static String[] STUDY_HEADER = new String[]{"Source Name", "Characteristics[Organism]", "Term Source REF", "Term Accession Number", "Characteristics[Infra-specific name]", "Term Source REF", "Term Accession Number", "Characteristics[Organism part]", "Term Source REF", "Term Accession Number", "Protocol REF", "Sample Name"};
final static String[] ASSAY_HEADER = new String[]{"Sample Name", "Protocol REF", "Assay Name", "Comment[Trait Definition File]", "Raw Data File", "Protocol REF", "Normalization Name", "Data Transformation Name", "Derived Data File"};
final static String[] TRAIT_DEF_HEADER = new String[]{"Measurement Type", "Term Source REF", "Term Accession Number", "Technology Type", "Term Source REF", "Term Accession Number", "Unit Name", "Term Source REF", "Term Accession Number"};
private static ImmutableSet<OntologySourceRefObject> ontologySources = null;
//private static final OntologySourceRefObject traitOntologySource = new OntologySourceRefObject("TO","http://www.ontobee.org/browser/index.php?o=TO","","Gramene trait ontology");
//private static final OntologySourceRefObject accOntologySource = new OntologySourceRefObject("ARA","http://www.ontobee.org/browser/index.php?o=TO","","Taxonomy trait ontology");
private static final OntologySourceRefObject obiOntologySource = new OntologySourceRefObject("OBI", "http://data.bioontology.org/ontologies/OBI", "", "Ontology for Biomedical Investigations\n");
private static final OntologySourceRefObject taxOntologySource = new OntologySourceRefObject("NCBITAXON", "http://data.bioontology.org/ontologies/NCBITAXON", "", "National Center for Biotechnology Information (NCBI) Organismal Classification");
final static String[] STUDY_HEADER = new String[]{"Source Name", "Characteristics[Organism]", "Characteristics[Infraspecific name]", "Characteristics[Seed origin]", "Characteristics[Study start]", "Characteristics[Study duration]", "Characteristics[Growth facility]", "Characteristics[Geographic location]", "Sample Name"};
final static String[] ASSAY_HEADER = new String[]{"Sample Name", "Characteristics[Organism Part]", "Assay Name", "Raw Data File", "Protocol REF", "Parameter Value[Trait Definition File]", "Derived Data File"};
final static String[] TRAIT_DEF_HEADER = new String[]{"Variable ID", "Trait", "Term Source REF", "Term Accession Number", "Method", "Term Source REF", "Term Accession Number", "Scale", "Term Source REF", "Term Accession Number"};
private static final OntologySourceRefObject accOntologySource = new OntologySourceRefObject("ARA", "http://gwas.gmi.oeaw.ac.at/#/taxonomy/1/passports?alleleAssayId=0", "", "Catalogue of Arabidopsis accessions");


public IsaTabExporterImpl() {
CONFIG_DIRECTORY = getClass().getResource("/ISA_TAB/");
try {
ConfigurationManager.loadConfigurations(CONFIG_DIRECTORY.getPath());
if (ontologySources == null) {
ontologySources = ImmutableSet.<OntologySourceRefObject>builder()
.add(obiOntologySource)
// .add(traitOntologySource)
// .add(accOntologySource)
.add(taxOntologySource)
.build();
}

final BioPortal4Client client = new BioPortal4Client();
Collection<Ontology> ontologies = client.getAllOntologies();
List<OntologySourceRefObject> list = new ArrayList();
list.add(accOntologySource);
for (Ontology ontology : ontologies) {
list.add(OntologyUtils.convertOntologyToOntologySourceReferenceObject(ontology));
}
ISAcreatorProperties.setProperty(ISAcreatorProperties.ONTOLOGY_TERM_URI, "true");
ISAcreatorProperties.setProperty(ISAcreatorProperties.ONTOLOGY_TERM_URI, "false");
OntologyManager.setOntologySources(ImmutableSet.copyOf(list));
//OntologyManager.getOntologySelectionHistory().put("OBI",OntologyManager.getOntologyTerm("OBI"));

} catch (Exception e) {
e.printStackTrace();
Expand All @@ -155,7 +144,7 @@ public String save(Experiment experiment, boolean isZip) throws IOException {
fileOutput.saveISAFiles(false, investigation);
List<TraitUom> traitUoms = Lists.newArrayList(aclManager.filterByAcl(traitUomRepository.findByExperimentId(experiment.getId())));
List<String[]> traitDefinitions = createTraitDefinitions(traitUoms);
List<String[]> dervivedValues = createDervivedValues(experiment, traitUoms);
List<String[]> dervivedValues = createDerivedValues(experiment, traitUoms);
saveCsvToFile(baseDirectory + File.separator + TRAIT_DEF_FILE, traitDefinitions);
saveCsvToFile(baseDirectory + File.separator + DERVIVED_DATA_FILE, dervivedValues);
if (isZip) {
Expand Down Expand Up @@ -201,7 +190,7 @@ private String zip(String baseDirectory, Experiment experiment) {
private void saveCsvToFile(String filename, List<String[]> rows) throws IOException {
try (
FileWriter fout = new FileWriter(filename);
ICsvListWriter listWriter = new CsvListWriter(fout, CsvPreference.STANDARD_PREFERENCE)
ICsvListWriter listWriter = new CsvListWriter(fout, CsvPreference.TAB_PREFERENCE)
) {
// write the header
listWriter.writeHeader(rows.get(0));
Expand Down Expand Up @@ -460,22 +449,30 @@ private Study createStudy(Experiment experiment) {
final Study study = new Study(experiment.getId().toString(), experiment.getName(), "", "", "", "");
study.setSampleFileName(STUDY_FILE);
study.setStudyDesigns(Lists.newArrayList(new StudyDesign(experiment.getDesign())));
final Assay studySample = new Assay(ASSAY_FILE,
final Assay studySample = new Assay(STUDY_FILE,
ConfigurationManager.selectTROForUserSelection(MappingObject.STUDY_SAMPLE));
String[] header = studySample.getTableReferenceObject().getHeaders().toArray(new String[]{"Source Name", "Characteristics[Organism]", "Term Source REF", "Term Accession Number", "Characteristics[Infra-specific name]", "Term Source REF", "Term Accession Number", "Characteristics[Organism part]", "Term Source REF", "Term Accession Number", "Protocol REF", "Sample Name"});
//String[] header = studySample.getTableReferenceObject().getHeaders().toArray(STUDY_HEADER);
for (ObsUnit obsUnit : experiment.getObsUnits()) {
Passport passport = obsUnit.getStock().getPassport();
String taxonomy = passport.getTaxonomy().getGenus() + " " + passport.getTaxonomy().getSpecies();
// FIXME required to add passport id because otherwise OntologyManager outputs the wrong id
String accename = passport.getAccename() + "_" + passport.getId();
// TODO don't harcode it
OntologyManager.addToOntologyTerms(taxonomy, new OntologyTerm(taxonomy, "3702", "http://purl.obolibrary.org/obo/NCBITaxon_3702", OntologyManager.getOntologySourceReferenceObjectByAbbreviation("NCBITaxon")));
OntologyManager.addToOntologyTerms(accename, new OntologyTerm(accename, passport.getId().toString(), String.format("https://gwas.gmi.oeaw.ac.at/#/passport/%s/overview", passport.getId()), OntologyManager.getOntologySourceReferenceObjectByAbbreviation("ARA")));
studySample.getTableReferenceObject()
.addRowData(
STUDY_HEADER,
new String[]{"source" + obsUnit.getId(),
//passport.getTaxonomy().getGenus() + " " + passport.getTaxonomy().getSpecies(),
"4932",
"NCBITAXON",
"http://purl.obolibrary.org/obo/NCBITaxon_3702",
passport.getId().toString(),
"ARA", passport.getId().toString(), // change to div_passport_acc
"", "", "", "", "sample" + obsUnit.getId()
new String[]{
"source" + obsUnit.getId(),
taxonomy,
accename,
"",
"",
"",
"",
"",
"sample" + obsUnit.getId()
}
);
}
Expand All @@ -493,20 +490,17 @@ private List<Assay> createAssays(Experiment experiment) {
final Vector<String> assayHeaderVector = assay
.getTableReferenceObject().getHeaders();

final String[] assayHeaderArray = assayHeaderVector
.toArray(ASSAY_HEADER);
/*final String[] assayHeaderArray = assayHeaderVector
.toArray(ASSAY_HEADER);*/
for (ObsUnit obsUnit : experiment.getObsUnits()) {
Passport passport = obsUnit.getStock().getPassport();
assay.getTableReferenceObject().addRowData(
ASSAY_HEADER,
new String[]{"sample" + obsUnit.getId(),
"",
"phenotyping" + obsUnit.getId(),
TRAIT_DEF_FILE,
"",
"",
"",
"assay" + obsUnit.getId(),
"",
"Data transformation",
TRAIT_DEF_FILE,
DERVIVED_DATA_FILE}
);
}
Expand All @@ -519,32 +513,34 @@ private List<String[]> createTraitDefinitions(List<TraitUom> traitUoms) {
for (TraitUom traitUom : traitUoms) {
String[] row = new String[TRAIT_DEF_HEADER.length];
row[0] = traitUom.getLocalTraitName();
row[1] = row[0];
if (traitUom.getToAccession() != null && !traitUom.getToAccession().isEmpty()) {
row[1] = "TO";
row[2] = traitUom.getToAccession();
row[2] = "TO";
row[3] = traitUom.getToAccession();
}
row[3] = traitUom.getTraitProtocol();
row[4] = traitUom.getTraitProtocol();
if (traitUom.getUnitOfMeasure() != null) {
row[6] = traitUom.getUnitOfMeasure().getUnitType();
row[5] = traitUom.getUnitOfMeasure().getUnitType();
//TODO retrieve Unit of measure
}
traitDefinitions.add(row);
}
return traitDefinitions;
}

private List<String[]> createDervivedValues(Experiment experiment, List<TraitUom> traitUoms) {
private List<String[]> createDerivedValues(Experiment experiment, List<TraitUom> traitUoms) {
Map<TraitUom, Long> statisticMap = getStatisticTypeFromTrait(traitUoms);
List<String[]> dervivedValues = Lists.newArrayList();
String[] header = new String[traitUoms.size() + 1];
header[0] = "Assay Name";
for (int i = 1; i <= traitUoms.size(); i++) {
header[i] = String.format("Trait Value[%s]", traitUoms.get((i - 1)).getLocalTraitName());
header[i] = String.format("%s", traitUoms.get((i - 1)).getLocalTraitName());
}
dervivedValues.add(header);
for (ObsUnit obsUnit : experiment.getObsUnits()) {
Passport passport = obsUnit.getStock().getPassport();
String[] row = new String[header.length];
row[0] = "phenotyping" + obsUnit.getId().toString();
row[0] = "assay" + obsUnit.getId().toString();
for (int i = 1; i < header.length; i++) {
TraitUom traitUom = traitUoms.get(i - 1);
row[i] = getTraitValue(obsUnit.getTraits(), traitUom.getId(), statisticMap.get(traitUom));
Expand Down
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