From 4a084ab5f114649f165b3793a76204743b2b046b Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Thu, 6 Feb 2014 17:12:06 +0000 Subject: [PATCH 01/16] Updates to 1.7.6. Fixed small issues in ontology browsing code that were observed when upgrading the configurator. --- pom.xml | 2 +- .../WSOntologyTreeCreator.java | 35 ++++++------------- .../BioPortalSearchResultHandler.java | 1 + .../io/ProgrammaticISATabCreationTest.java | 3 +- 4 files changed, 13 insertions(+), 28 deletions(-) diff --git a/pom.xml b/pom.xml index f6ea2f59..fdc6a9d6 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.isatools ISAcreator bundle - 1.7.5 + 1.7.6 ISAcreator http://www.isa-tools.org diff --git a/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java b/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java index 32b6ffa9..cf6c16ce 100644 --- a/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java +++ b/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java @@ -74,7 +74,7 @@ public class WSOntologyTreeCreator implements OntologyTreeCreator, TreeSelection private Map ontologies; private Container browser; - private static OntologyService bioportalClient; + private static BioPortal4Client bioportalClient; private JTree tree; @@ -116,16 +116,14 @@ private void initiateOntologyVisualization() { RecommendedOntology recommendedOntology = ontologies.get(ontology); System.out.println("initialising ontology visualisation for " + recommendedOntology.getOntology().getOntologyDisplayLabel()); - System.out.println("Ontology version is: " + recommendedOntology.getOntology().getOntologyVersion()); + System.out.println("Ontology ID: " + recommendedOntology.getOntology().getOntologyID()); + System.out.println("Ontology Abbreviation: " + recommendedOntology.getOntology().getOntologyAbbreviation()); // if ontology has no branch specified, query the whole ontology. Map rootTerms; String nodeLabel = recommendedOntology.getOntology().getOntologyDisplayLabel(); - OntologyService service = getCorrectOntologyService(recommendedOntology.getOntology()); - - if (recommendedOntology.getBranchToSearchUnder() != null) { nodeLabel += " under " + recommendedOntology.getBranchToSearchUnder().getBranchName(); @@ -138,12 +136,10 @@ private void initiateOntologyVisualization() { System.out.println("Going to search for " + branchIdentifier + " in " + recommendedOntology.getOntology().getOntologyDisplayLabel()); - rootTerms = service.getTermChildren(branchIdentifier, getCorrectQueryString(service, recommendedOntology.getOntology())); + rootTerms = bioportalClient.getTermChildren(branchIdentifier, recommendedOntology.getOntology().getOntologyAbbreviation()); } else { - rootTerms = service.getOntologyRoots( - getCorrectQueryString(service, recommendedOntology.getOntology())); - + rootTerms = bioportalClient.getOntologyRoots(recommendedOntology.getOntology().getOntologyAbbreviation()); } DefaultMutableTreeNode ontologyNode = new DefaultMutableTreeNode(nodeLabel); @@ -177,14 +173,6 @@ private void initiateOntologyVisualization() { } } - private OntologyService getCorrectOntologyService(Ontology ontology) { - return bioportalClient; - } - - private String getCorrectQueryString(OntologyService service, Ontology ontology) { - return ontology.getOntologyVersion(); - } - public void updateTree() { DefaultMutableTreeNode root = (DefaultMutableTreeNode) treeModel.getRoot(); TreePath path = new TreePath(root.getPath()); @@ -204,9 +192,8 @@ private void preloadNextOntologyLevel(String termAccession, DefaultMutableTreeNo Ontology ontology = extractOntologyFromNode(parentTerm); - OntologyService service = getCorrectOntologyService(ontology); - Map termChildren = service.getTermChildren(termAccession, getCorrectQueryString(service, ontology)); + Map termChildren = bioportalClient.getTermChildren(termAccession, ontology.getOntologyAbbreviation()); // add the level of non visible nodes for (String accession : termChildren.keySet()) { @@ -277,9 +264,8 @@ public void expandTreeToReachTerm(OntologyTerm term) { Ontology ontology = new Ontology("", term.getOntologyVersionId(), term.getOntologySourceInformation().getSourceName(), term.getOntologySourceInformation().getSourceDescription()); - OntologyService service = getCorrectOntologyService(ontology); - Map nodeParentsFromRoot = service.getAllTermParents(term.getOntologyTermAccession(), term.getOntologySourceInformation().getSourceVersion()); + Map nodeParentsFromRoot = bioportalClient.getAllTermParents(term.getOntologyTermAccession(), term.getOntologySourceInformation().getSourceVersion()); TreePath lastPath = null; for (OntologyTerm node : nodeParentsFromRoot.values()) { @@ -327,16 +313,15 @@ public void valueChanged(TreeSelectionEvent treeSelectionEvent) { // load children only for leaf nodes and those that have not been marked as processed if (node.isLeaf() && node.getAllowsChildren()) { - OntologyService service = getCorrectOntologyService(ontologyTerm.getOntology()); // load children. if no children, set allowsChildren to false - Map termChildren = service.getTermChildren(ontologyTerm.getBranch().getBranchIdentifier(), - getCorrectQueryString(service, ontologyTerm.getOntology())); + Map termChildren = bioportalClient.getTermChildren(ontologyTerm.getBranch().getBranchIdentifier(), + ontologyTerm.getOntology().getOntologyAbbreviation()); if (termChildren.size() > 0) { node.setAllowsChildren(true); } } - // olsDialog.loadMetaData(nodeInfo.getTermId(), OLSDialog.OLS_DIALOG_BROWSE_ONTOLOGY); + } else { rootNode.removeAllChildren(); treeModel.reload(); diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java index 55c63dd4..da8ae576 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java @@ -295,6 +295,7 @@ public Map getOntologyRoots(String ontologyAbbreviation) { Map roots = new HashMap(); String queryContents = generalQueryEndpoint(BioPortal4Client.REST_URL + "ontologies/" + ontologyAbbreviation + "/classes/roots?apikey=" + API_KEY); + System.out.println(BioPortal4Client.REST_URL + "ontologies/" + ontologyAbbreviation + "/classes/roots?apikey=" + API_KEY); StringReader reader = new StringReader(queryContents); JsonReader rdr = Json.createReader(reader); JsonArray rootArray = rdr.readArray(); diff --git a/src/test/java/org/isatools/isacreator/io/ProgrammaticISATabCreationTest.java b/src/test/java/org/isatools/isacreator/io/ProgrammaticISATabCreationTest.java index a53289d2..d8eaf38b 100644 --- a/src/test/java/org/isatools/isacreator/io/ProgrammaticISATabCreationTest.java +++ b/src/test/java/org/isatools/isacreator/io/ProgrammaticISATabCreationTest.java @@ -37,8 +37,7 @@ public void createISATabProgrammatically() { } } - ISAcreator isAcreator = new ISAcreator(Mode.NORMAL_MODE, null, baseDir + ISAcreator.CONFIG_DIR); - + ConfigurationManager.loadConfigurations(baseDir + "/Configurations/isaconfig-default_v2014-01-16/"); Investigation investigation = new Investigation("gis-investigation", "GIS investigation test"); investigation.addContact(new InvestigationContact("maguire", "eamonn", "J", "eamonnmag@gmail.com", "", "", "", "Oxford University", "")); From dd704a21ffeb816ab7f562259089ab673a055724 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Wed, 12 Feb 2014 10:07:20 +0000 Subject: [PATCH 02/16] Automatically generates an ID for the investigation if not present. --- .../isacreator/gui/io/importisa/ISAtabFilesImporterFromGUI.java | 2 -- src/main/java/org/isatools/isacreator/model/Investigation.java | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/gui/io/importisa/ISAtabFilesImporterFromGUI.java b/src/main/java/org/isatools/isacreator/gui/io/importisa/ISAtabFilesImporterFromGUI.java index f012f329..84f3f841 100644 --- a/src/main/java/org/isatools/isacreator/gui/io/importisa/ISAtabFilesImporterFromGUI.java +++ b/src/main/java/org/isatools/isacreator/gui/io/importisa/ISAtabFilesImporterFromGUI.java @@ -57,7 +57,6 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi public class ISAtabFilesImporterFromGUI extends ISAtabImporter { private DataEntryEnvironment dataEntryEnvironment; - private ISAcreator isacreator; /** * ImportISAFiles provides a facility for you to import ISATAB files @@ -66,7 +65,6 @@ public class ISAtabFilesImporterFromGUI extends ISAtabImporter { * @param isacreator - a reference to the Main entry point of the Application */ public ISAtabFilesImporterFromGUI(ISAcreator isacreator){ - this.isacreator = isacreator; this.dataEntryEnvironment = new DataEntryEnvironment(); isacreator.setCurDataEntryPanel(dataEntryEnvironment); } diff --git a/src/main/java/org/isatools/isacreator/model/Investigation.java b/src/main/java/org/isatools/isacreator/model/Investigation.java index 1b1e923b..524e6421 100755 --- a/src/main/java/org/isatools/isacreator/model/Investigation.java +++ b/src/main/java/org/isatools/isacreator/model/Investigation.java @@ -103,7 +103,7 @@ public Investigation(String investigationId, String investigationTitle, String i String submissionDate, String publicReleaseDate) { super(); - setInvestigationId(investigationId); + setInvestigationId(investigationId.equals("") ? String.valueOf(System.currentTimeMillis()) : investigationId); setInvestigationTitle(investigationTitle.equals("") ? "Investigation" : investigationTitle); setInvestigationDescription(investigationDescription); setSubmissionDate(submissionDate); From 4970a2e688d870791537180cf9b69acd423be498 Mon Sep 17 00:00:00 2001 From: Alejandra Gonzalez-Beltran Date: Wed, 12 Feb 2014 10:28:48 +0000 Subject: [PATCH 03/16] Setting default investigation id when importing --- .../io/importisa/StructureToInvestigationMapper.java | 4 ++++ .../org/isatools/isacreator/model/Investigation.java | 10 +++++++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/isatools/isacreator/io/importisa/StructureToInvestigationMapper.java b/src/main/java/org/isatools/isacreator/io/importisa/StructureToInvestigationMapper.java index cceb119c..1bfb2082 100644 --- a/src/main/java/org/isatools/isacreator/io/importisa/StructureToInvestigationMapper.java +++ b/src/main/java/org/isatools/isacreator/io/importisa/StructureToInvestigationMapper.java @@ -39,6 +39,7 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi import org.apache.commons.collections15.OrderedMap; import org.apache.commons.collections15.map.ListOrderedMap; +import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; import org.isatools.errorreporter.model.ErrorLevel; import org.isatools.errorreporter.model.ErrorMessage; @@ -162,6 +163,9 @@ private Pair, Investigation> processInvestigationSection(OrderedMap< Map record = getRecord(investigationSection, 0); investigation.addToFields(record); + if (StringUtils.trimToNull(investigation.getInvestigationId()) == null) { + investigation.setDefaultInvestigationId(); + } Map> ontologyFields = IOUtils.getOntologyTerms(sectionFields); diff --git a/src/main/java/org/isatools/isacreator/model/Investigation.java b/src/main/java/org/isatools/isacreator/model/Investigation.java index 524e6421..acac826a 100755 --- a/src/main/java/org/isatools/isacreator/model/Investigation.java +++ b/src/main/java/org/isatools/isacreator/model/Investigation.java @@ -103,7 +103,11 @@ public Investigation(String investigationId, String investigationTitle, String i String submissionDate, String publicReleaseDate) { super(); - setInvestigationId(investigationId.equals("") ? String.valueOf(System.currentTimeMillis()) : investigationId); + + if (investigationId.equals("")) + setDefaultInvestigationId(); + else + setInvestigationId(investigationId); setInvestigationTitle(investigationTitle.equals("") ? "Investigation" : investigationTitle); setInvestigationDescription(investigationDescription); setSubmissionDate(submissionDate); @@ -120,6 +124,10 @@ private void initialise() { publications = new ArrayList(); } + public void setDefaultInvestigationId(){ + setInvestigationId( String.valueOf(System.currentTimeMillis()) ); + } + @Override public void setReferenceObjectForSection() { setReferenceObject(ApplicationManager.getInvestigationDataEntryReferenceObject()); From d4a430fdce7a97281bb1707e77af6dcaad17c1ac Mon Sep 17 00:00:00 2001 From: Alejandra Gonzalez-Beltran Date: Sun, 16 Feb 2014 02:46:16 +0000 Subject: [PATCH 04/16] Fixed bug introduced in previous commit --- .../spreadsheet/model/TableReferenceObject.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/spreadsheet/model/TableReferenceObject.java b/src/main/java/org/isatools/isacreator/spreadsheet/model/TableReferenceObject.java index 5489ee6c..e8fc40c0 100644 --- a/src/main/java/org/isatools/isacreator/spreadsheet/model/TableReferenceObject.java +++ b/src/main/java/org/isatools/isacreator/spreadsheet/model/TableReferenceObject.java @@ -340,10 +340,12 @@ public void addRowData(String[] headers, String[] rowData) { rowDataModified.set(prevValLoc, s + ":" + prevVal); } } else if (headers[i].toLowerCase().trim().contains("term accession number")) { - //if (!s.equals("")) { + if (!s.equals("")) { + //if the value of 'term accession number' column is not empty, deal with the column String prevVal = rowDataModified.get(prevValLoc); - if (prevVal.contains(":")) { + //if prevVal correspond to an ontology term, it will have the short from : + if (prevVal.contains(":")){ String[] parts = prevVal.split(":"); if (parts.length > 1) { @@ -368,7 +370,7 @@ public void addRowData(String[] headers, String[] rowData) { } } - //} + } } else { rowDataModified.add(s); prevValLoc = rowDataModified.size() - 1; From fde50f59afaf9692cca60447ce25e150a65d0b0c Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Mon, 10 Mar 2014 14:17:06 +0000 Subject: [PATCH 05/16] Updating the annotator given the changes to the bioportal api. Removing deprecated classes. --- .../ontologymanager/BioPortalClient.java | 546 ------------------ .../io/AcceptedOntologiesLoader.java | 1 - .../BioPortalAnnotatorResultHandler.java | 28 +- .../utils/OntologyTermHarvestingPool.java | 8 +- .../BioPortalAnnotatorResultHandler.java | 124 ---- .../BioPortalClassBeanResultHandler.java | 232 -------- .../BioPortalOntologyListResultHandler.java | 202 ------- .../BioPortalSearchBeanResultHandler.java | 134 ----- .../ontologymanager/common/OntologyTerm.java | 2 +- .../ontologymanager/BioPortalClient4Test.java | 8 +- .../ontologymanager/BioPortalClientTest.java | 255 -------- 11 files changed, 22 insertions(+), 1518 deletions(-) delete mode 100644 src/main/java/org/isatools/isacreator/ontologymanager/BioPortalClient.java delete mode 100644 src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalAnnotatorResultHandler.java delete mode 100644 src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalClassBeanResultHandler.java delete mode 100644 src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalOntologyListResultHandler.java delete mode 100644 src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalSearchBeanResultHandler.java delete mode 100644 src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClientTest.java diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/BioPortalClient.java b/src/main/java/org/isatools/isacreator/ontologymanager/BioPortalClient.java deleted file mode 100644 index a64a2bbf..00000000 --- a/src/main/java/org/isatools/isacreator/ontologymanager/BioPortalClient.java +++ /dev/null @@ -1,546 +0,0 @@ -/** - ISAcreator is a component of the ISA software suite (http://www.isa-tools.org) - - License: - ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL) - - EXHIBIT A. CPAL version 1.0 - The contents of this file are subject to the CPAL version 1.0 (the License); - you may not use this file except in compliance with the License. You may obtain a - copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html. - The License is based on the Mozilla Public License version 1.1 but Sections - 14 and 15 have been added to cover use of software over a computer network and - provide for limited attribution for the Original Developer. In addition, Exhibit - A has been modified to be consistent with Exhibit B. - - Software distributed under the License is distributed on an AS IS basis, - WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for - the specific language governing rights and limitations under the License. - - The Original Code is ISAcreator. - The Original Developer is the Initial Developer. The Initial Developer of the - Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com; - Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com; - http://www.isa-tools.org). All portions of the code written by the ISA Team are - Copyright (c) 2007-2011 ISA Team. All Rights Reserved. - - EXHIBIT B. Attribution Information - Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team - Attribution Phrase: Developed by the ISA Team - Attribution URL: http://www.isa-tools.org - Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png - Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL. - - Sponsors: - The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone). - */ -package org.isatools.isacreator.ontologymanager; - -import org.apache.commons.collections15.map.ListOrderedMap; -import org.apache.log4j.Logger; -import org.isatools.isacreator.configuration.Ontology; -import org.isatools.isacreator.configuration.RecommendedOntology; -import org.isatools.isacreator.ontologymanager.bioportal.utils.BioPortalXMLModifier; -import org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers.BioPortalClassBeanResultHandler; -import org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers.BioPortalOntologyListResultHandler; -import org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers.BioPortalSearchBeanResultHandler; -import org.isatools.isacreator.ontologymanager.common.OntologyTerm; -import uk.ac.ebi.utils.io.DownloadUtils; - -import java.io.File; -import java.util.*; - - -public class BioPortalClient implements OntologyService { - - private static final Logger log = Logger.getLogger(BioPortalClient.class); - - public static final int PARENTS = 0; - - public static final int CHILDREN = 1; - - public static final String REST_URL = "http://rest.bioontology.org/bioportal/"; - public static final String API_KEY = "apikey=fd88ee35-6995-475d-b15a-85f1b9dd7a42"; - - public static final String OWL_EXT = ".owl"; - - private Set noChildren; - - private static List ontologies; - - // - private static Map ontologyNames = new HashMap(); - private static Map ontologyVersions = new HashMap(); - private static Map ontologyFiles = new HashMap(); - - - private Map searchResults; - private Map> cachedNodeChildrenQueries; - - public static final String DIRECT_ONTOLOGY_URL = "http://bioportal.bioontology.org/ontologies/"; - - /** - * Constructor - */ - public BioPortalClient() { - searchResults = new HashMap(); - cachedNodeChildrenQueries = new HashMap>(); - noChildren = new HashSet(); - } - - - public List getAllOntologies() { - - if (ontologies == null || ontologies.size() == 0) { - - String searchString = REST_URL + "ontologies/?" + API_KEY; - - log.info("Getting all ontologies: query string is " + searchString); - - DownloadUtils.downloadFile(searchString, DownloadUtils.DOWNLOAD_FILE_LOC + "ontologies" + DownloadUtils.XML_EXT); - - BioPortalOntologyListResultHandler parser = new BioPortalOntologyListResultHandler(); - - ontologies = parser.parseFile(DownloadUtils.DOWNLOAD_FILE_LOC + "ontologies" + DownloadUtils.XML_EXT); - - if (ontologies != null) { - for (Ontology ontology : ontologies) { - ontologyNames.put(ontology.getOntologyAbbreviation(), ontology.getOntologyDisplayLabel()); - ontologyVersions.put(ontology.getOntologyAbbreviation(), ontology.getOntologyVersion()); - ontologyFiles.put(ontology.getOntologyAbbreviation(), ontology.getOntologyID()); - } - } - } - - return ontologies; - } - - public Ontology getOntologyById(String ontologyId) { - if (!ontologyId.isEmpty()) { - - String searchString = REST_URL + "virtual/ontology/" + ontologyId + "/?" + API_KEY; - - log.info("Getting ontology by id : query string is " + searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + "ontology" + ontologyId + DownloadUtils.XML_EXT; - - DownloadUtils.downloadFile(searchString, downloadLocation); - - BioPortalOntologyListResultHandler parser = new BioPortalOntologyListResultHandler(); - - List ontologies = parser.parseFile(downloadLocation); - - if (ontologies != null && !ontologies.isEmpty()) { - return ontologies.get(0); - } - } - - return null; - } - - public String getLatestOntologyVersion(String ontologyId) { - - Ontology o = getOntologyById(ontologyId); - - if (o == null) { - return null; - } else { - return o.getOntologyVersion(); - } - } - - public Map getOntologyNames() { - if (ontologyNames.size() == 0) { - getAllOntologies(); - } - return ontologyNames; - } - - public OntologyTerm getTerm(String termId, String ontology) { - return null; - } - - public Map> exactSearch(String term, String ontology) { - return null; - } - - public String getOntologySourceFile(String sourceName) { - if (ontologyFiles.size() == 0) { - getAllOntologies(); - } - return "http://bioportal.bioontology.org/ontologies/"+ontologyFiles.get(sourceName); - } - - public String getOntologyDescription(String sourceName) { - if (ontologyFiles.size() == 0) { - getAllOntologies(); - } - return ontologyNames.get(sourceName); - } - - public String getOntologyVersion(String sourceName) { - if (ontologyFiles.size() == 0) { - getAllOntologies(); - } - return ontologyVersions.get(sourceName); - } - - public Map getOntologyVersions() { - if (ontologyVersions.size() == 0) { - getAllOntologies(); - } - - return ontologyVersions; - } - - public Map getTermMetadata(String termAccession, String ontology) { - - OntologyTerm ontologyResult = getTermInformation(termAccession, ontology); - Map result = new ListOrderedMap(); - result.put("accession", termAccession); - result.putAll(ontologyResult.getComments()); - return result; - } - - public OntologyTerm getTermInformation(String termAccession, String ontologyVersion) { - OntologyTerm bpo; - if (searchResults.containsKey(ontologyVersion + "-" + termAccession)) { - bpo = searchResults.get(ontologyVersion + "-" + termAccession); - if (bpo != null) { - if (bpo.getOntologyTermURI() == null || - bpo.getOntologyTermURI().trim().equals("")) { - bpo = performMetadataQuery(termAccession, ontologyVersion); - - searchResults.put(ontologyVersion + "-" + termAccession, bpo); - } else { - return bpo; - } - } - } else { - bpo = performMetadataQuery(termAccession, ontologyVersion); - searchResults.put(ontologyVersion + "-" + termAccession, - bpo); - } - return bpo; - } - - private OntologyTerm performMetadataQuery(String termAccession, String ontology) { - String searchString = REST_URL + "concepts/" + ontology + "/" + termAccession + "/?" + API_KEY; - - System.out.println(searchString); - - log.info("Getting term information for " + termAccession + " -> " + searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontology + "-" + termAccession + DownloadUtils.XML_EXT; - - DownloadUtils.downloadFile(searchString, downloadLocation); - - File fileWithNameSpace = BioPortalXMLModifier.addNameSpaceToFile(new File(downloadLocation), "http://bioontology.org/bioportal/classBeanSchema#", ""); - - if (fileWithNameSpace != null) { - - BioPortalClassBeanResultHandler handler = new BioPortalClassBeanResultHandler(); - - return handler.parseMetadataFile(fileWithNameSpace.getAbsolutePath()); - } else { - return null; - } - } - - - public Map> getTermsByPartialNameFromSource(String term, List recommendedOntologies) { - - term = correctTermForHTTPTransport(term); - - // need to accommodate more complicated search strings in the case where the recommended source contains the branch - // to search under as well! - Map> result = new HashMap>(); - - // need to do a loop over all branches and do a single query on those recommended ontologies only defined - // by the source, not the branch. - for (RecommendedOntology ro : recommendedOntologies) { - - if (ro.getOntology() != null) { - - StringBuilder searchString = new StringBuilder(); - - searchString.append(REST_URL); - - searchString.append("search/").append(term).append("/?ontologyids=").append(ro.getOntology().getOntologyID()); - - - if (ro.getBranchToSearchUnder() != null && !ro.getBranchToSearchUnder().getBranchIdentifier().equals("")) { - String branch = ro.getBranchToSearchUnder().getBranchIdentifier(); - searchString.append("&subtreerootconceptid=").append(branch); - } - - searchString.append("&").append(API_KEY); - - System.out.println("sending query: " + searchString); - - Map> searchResult = downloadAndProcessBranch(term, searchString.toString()); - - if (searchResult != null) { - result.putAll(searchResult); - } - } - } - return result; - } - - - private Map> downloadAndProcessBranch(String term, String searchString) { - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + term + DownloadUtils.XML_EXT; - DownloadUtils.downloadFile(searchString, downloadLocation); - - BioPortalSearchBeanResultHandler handler = new BioPortalSearchBeanResultHandler(); - - File fileWithNameSpace = BioPortalXMLModifier.addNameSpaceToFile(new File(downloadLocation), "http://bioontology.org/bioportal/resultBeanSchema#", ""); - - if (fileWithNameSpace != null) { - return handler.getSearchResults(fileWithNameSpace.getAbsolutePath()); - } - - return new HashMap>(); - - } - - public Map> getTermsByPartialNameFromSource(String term, String source, boolean reverseOrder) { - - System.out.println("Searching for source: " + source); - - term = correctTermForHTTPTransport(term); - - String searchString = REST_URL + "search/" + term + - (((source == null) || source.trim().equalsIgnoreCase("") - || source.trim().equalsIgnoreCase("all")) - ? "?" : "/?ontologyids=" +source + "&") + API_KEY; - - log.info("search string " + searchString); - System.out.println("search string " + searchString); - - Map> searchResult = downloadAndProcessBranch(term, searchString); - - log.info("found " + (searchResult == null ? "0" : searchResult.size()) + " ontology terms"); - - return searchResult == null ? new HashMap>() : searchResult; - } - - /** - * Finds the root in an ontology - * - * @param ontology - ontology to search in as its version ID e.g. 39002 for BRO - * @return Map representing ontology term accession to term label mappings. - */ - public Map getOntologyRoots(String ontology) { - - if (!cachedNodeChildrenQueries.containsKey(ontology)) { - - String searchString = REST_URL + "concepts/" + ontology + "/root/?" + API_KEY; - - - System.out.println("Search string is: " + searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontology + "-roots" + DownloadUtils.XML_EXT; - - DownloadUtils.downloadFile(searchString, downloadLocation); - - File fileWithNameSpace = BioPortalXMLModifier.addNameSpaceToFile(new File(downloadLocation), "http://bioontology.org/bioportal/classBeanSchema#", ""); - - BioPortalClassBeanResultHandler handler = new BioPortalClassBeanResultHandler(); - - if (fileWithNameSpace == null) { - return new HashMap(); - } - - Map result = handler.parseRootConceptFile(fileWithNameSpace.getAbsolutePath(), noChildren); - - if (result != null) { - searchResults.putAll(result); - cachedNodeChildrenQueries.put(ontology, result); - } - - return result; - } else { - System.out.println("using cached version for display."); - return cachedNodeChildrenQueries.get(ontology); - } - } - - public Map getTermParent(String termAccession, String ontology) { - return getTermChildOrParent(termAccession, ontology, PARENTS); - } - - - /** - * Return the children of a term with gathering extra metadata information about the term. - * This makes creating tree views quicker, although it's primarily for BioPortal WS queries since - * it requires an extra query per child term to resolve the PURLs etc. - * - * @param termAccession - term to search under - * @param ontology - ontology term is located in - * @return Map with mappings from term accession to the term label - */ - public Map getTermChildren(String termAccession, String ontology) { - return getTermChildOrParent(termAccession, ontology, CHILDREN); - } - - /** - * Gets the children or parents of a term - * - * @param termAccession - accession of term e.g. snap:Continuant - * @param ontology - ontology version id e.g. 40832 for OBI - * @param type - @see PARENTS, CHILDREN - what type of search to make - * @return Map> from Ontology Source object -> List of found terms - */ - public Map getTermChildOrParent(String termAccession, String ontology, int type) { - - if (!noChildren.contains(termAccession)) { - if (!cachedNodeChildrenQueries.containsKey(ontology + "-" + termAccession)) { - - String searchString = REST_URL + "concepts/" + ((type == PARENTS) ? "parents/" : "") + "" + ontology + "?conceptid=" + termAccession + "&" + API_KEY; - - System.out.println("Searching for : " + searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontology + "-" + termAccession + DownloadUtils.XML_EXT; - - DownloadUtils.downloadFile(searchString, downloadLocation); - - BioPortalClassBeanResultHandler handler = new BioPortalClassBeanResultHandler(); - - File fileWithNameSpace = BioPortalXMLModifier.addNameSpaceToFile(new File(downloadLocation), - "http://bioontology.org/bioportal/classBeanSchema#", ""); - - if (fileWithNameSpace != null) { - - Map result = handler.parseRootConceptFile(fileWithNameSpace.getAbsolutePath(), noChildren); - - if (result != null) { - searchResults.putAll(result); - cachedNodeChildrenQueries.put(ontology + "-" + termAccession, result); - } - - return result; - } else { - return new HashMap(); - } - } else { - return cachedNodeChildrenQueries.get(ontology + "-" + termAccession); - } - } else { - return new HashMap(); - } - - } - - /** - * Method will search the Ontology space to determine the parents of a given term. This can then be used in searches to make - * location of a term within an Ontology much quicker. - * - * @param termAccession - the accession of the term being searched on e.g. ENVO:00003073 - * @param ontology - version access for the ontology you wish to query e.g. 40832 for OBI - * @return Map representing the parents of the Term - */ - public Map getAllTermParents(String termAccession, String ontology) { - String searchString = REST_URL + "path/" + ontology + "/?source=" + termAccession + "&target=root&" + API_KEY; - - System.out.println("Searching for parent terms: " + searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontology + "-all-parents-" + termAccession + DownloadUtils.XML_EXT; - - DownloadUtils.downloadFile(searchString, downloadLocation); - - File fileWithNameSpace = BioPortalXMLModifier.addNameSpaceToFile(new File(downloadLocation), "http://bioontology.org/bioportal/classBeanSchema#", ""); - - BioPortalClassBeanResultHandler handler = new BioPortalClassBeanResultHandler(); - - return handler.parseOntologyParentPathFile(fileWithNameSpace.getAbsolutePath()); - } - - - public void downloadOntology(String ontologyVersion){ - String searchString = REST_URL + "ontologies/download/"+ ontologyVersion + "?" + API_KEY; - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontologyVersion + OWL_EXT; - - log.info("Downloading ontology whose version is "+ontologyVersion+ " at location "+ downloadLocation); - - DownloadUtils.downloadFile(searchString, downloadLocation); - } - - public void downloadLatestVersionOntology(String ontologyVirtualID){ - String searchString = REST_URL + "virtual/download/" + ontologyVirtualID + "?" + API_KEY; - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontologyVirtualID + OWL_EXT; - - log.info("Downloading latest ontology version for virtual identifier "+ontologyVirtualID+ " at location "+ downloadLocation); - - DownloadUtils.downloadFile(searchString, downloadLocation); - } - - /** - * Retrieves a list with the namespace prefixes - * - * @param ontologyVersion - * @return - */ - public List getOntologyNamespacePrefixes(String ontologyVersion){ - - String searchString = REST_URL + "ontologies/namespaces/" + ontologyVersion + "?" + API_KEY; - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontologyVersion + "--namespaces" + DownloadUtils.XML_EXT; - - System.out.println("Getting namespaces for ontology whose version is "+ontologyVersion+ " at location "+ downloadLocation); - - DownloadUtils.downloadFile(searchString, downloadLocation); - - return null; - } - - public void getRDFTerm(String ontologyVersion, String termAccession){ - //examples: - //http://rest.bioontology.org/bioportal/rdf/47799/?conceptid=NEMO_1398000&apikey=YourAPIKey - //http://rest.bioontology.org/bioportal/rdf/47893/?conceptid=obo:OBI_0000634&apikey=fd88ee35-6995-475d-b15a-85f1b9dd7a42 - - String searchString = REST_URL + "rdf/" + ontologyVersion + "/?conceptid=" + termAccession + "&" + API_KEY; - - log.debug("searchString="+searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontologyVersion + "--" + termAccession + DownloadUtils.XML_EXT; - - log.debug("downloadLocation="+downloadLocation); - - log.info("Getting RDF information for term "+ termAccession + " in the ontology whose version is "+ontologyVersion+ " at location "+ downloadLocation); - - DownloadUtils.downloadFile(searchString, downloadLocation); - } - - public String getTermIRI(String ontologyVersion, String termAccession){ - //http://rest.bioontology.org/bioportal/concepts/47893?conceptid=obo:OBI_0000634&apikey=fd88ee35-6995-475d-b15a-85f1b9dd7a42 - String searchString = REST_URL + "concepts/" + ontologyVersion + "?conceptid=" + termAccession + "&" + API_KEY; - - log.debug("searchString="+searchString); - - String downloadLocation = DownloadUtils.DOWNLOAD_FILE_LOC + ontologyVersion + "-" + correctTermForHTTPTransport(termAccession) + DownloadUtils.XML_EXT; - - DownloadUtils.downloadFile(searchString, downloadLocation); - - log.debug("downloadLocation="+downloadLocation); - - BioPortalClassBeanResultHandler handler = new BioPortalClassBeanResultHandler(); - - File fileWithNameSpace = BioPortalXMLModifier.addNameSpaceToFile(new File(downloadLocation), - "http://bioontology.org/bioportal/classBeanSchema#", ""); - - return handler.getTermURL(fileWithNameSpace.getAbsolutePath()); - } - - private String correctTermForHTTPTransport(String term) { - return term.replaceAll("[\\s]+", "%20"); - } - - public String getOntologyURL() { - return DIRECT_ONTOLOGY_URL; - } - -} diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/io/AcceptedOntologiesLoader.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/io/AcceptedOntologiesLoader.java index 5401c774..8ef78f3e 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/io/AcceptedOntologiesLoader.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/io/AcceptedOntologiesLoader.java @@ -2,7 +2,6 @@ import org.isatools.isacreator.configuration.Ontology; import org.isatools.isacreator.ontologymanager.BioPortal4Client; -import org.isatools.isacreator.ontologymanager.BioPortalClient; import org.w3c.dom.Attr; import org.w3c.dom.Document; import org.w3c.dom.Element; diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java index a8adb5d9..1f301f06 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java @@ -1,5 +1,7 @@ package org.isatools.isacreator.ontologymanager.bioportal.jsonresulthandlers; +import org.isatools.isacreator.ontologymanager.OntologyManager; +import org.isatools.isacreator.ontologymanager.OntologySourceRefObject; import org.isatools.isacreator.ontologymanager.bioportal.io.AcceptedOntologies; import org.isatools.isacreator.ontologymanager.bioportal.model.AnnotatorResult; import org.isatools.isacreator.ontologymanager.common.OntologyTerm; @@ -31,6 +33,7 @@ public Map> getSearchResults(String queryCo StringReader reader = new StringReader(queryContents); + System.out.println(queryContents); JsonReader rdr = Json.createReader(reader); JsonArray obj = rdr.readArray(); @@ -41,7 +44,7 @@ public Map> getSearchResults(String queryCo if (annotatorResult != null) { - String originalTerm = originalText.substring(annotatorResult.getStartIndex()-1, annotatorResult.getEndIndex()); + String originalTerm = originalText.substring(annotatorResult.getStartIndex() - 1, annotatorResult.getEndIndex()); if (originalTerms.contains(originalTerm)) { if (!result.containsKey(originalTerm)) { @@ -61,27 +64,24 @@ public Map> getSearchResults(String queryCo } private AnnotatorResult extractAnnotatorResult(JsonObject resultItem) { - JsonObject annotatedClass = resultItem.getJsonObject("annotatedClass"); JsonObject links = annotatedClass.getJsonObject("links"); String ontologyId = links.getJsonString("ontology").toString(); - OntologyTerm ontologyTerm = searchHandler.getTermMetadata(annotatedClass.getString("@id"), ontologyId); - - if (ontologyTerm != null) { + OntologySourceRefObject sourceRefObject = OntologyManager.getOntologySourceReferenceObjectByAbbreviation(ontologyId); + OntologyTerm ontologyTerm = new OntologyTerm(annotatedClass.getString("prefLabel"), annotatedClass.getString("@id"), annotatedClass.getString("@id"), sourceRefObject); - JsonNumber from = null, to = null; + JsonNumber from = null, to = null; - for (JsonObject annotation : resultItem.getJsonArray("annotations").getValuesAs(JsonObject.class)) { - from = annotation.getJsonNumber("from"); - to = annotation.getJsonNumber("to"); - } + for (JsonObject annotation : resultItem.getJsonArray("annotations").getValuesAs(JsonObject.class)) { + from = annotation.getJsonNumber("from"); + to = annotation.getJsonNumber("to"); + } - if (from != null && to != null) { - return new AnnotatorResult(ontologyTerm, AcceptedOntologies.getAcceptedOntologies().get(ontologyId), 1, - from.intValue(), to.intValue()); - } + if (from != null && to != null) { + return new AnnotatorResult(ontologyTerm, AcceptedOntologies.getAcceptedOntologies().get(ontologyId), 1, + from.intValue(), to.intValue()); } return null; diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/utils/OntologyTermHarvestingPool.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/utils/OntologyTermHarvestingPool.java index f726809c..5730d1fd 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/utils/OntologyTermHarvestingPool.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/utils/OntologyTermHarvestingPool.java @@ -38,7 +38,7 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi package org.isatools.isacreator.ontologymanager.bioportal.utils; -import org.isatools.isacreator.ontologymanager.BioPortalClient; +import org.isatools.isacreator.ontologymanager.BioPortal4Client; import org.isatools.isacreator.ontologymanager.common.OntologyTerm; import java.util.Map; @@ -53,14 +53,14 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi */ public class OntologyTermHarvestingPool implements Runnable { - private BioPortalClient client; + private BioPortal4Client client; private String ontology; private Map toProcess; private ExecutorService threadPool; private Thread executor; - public OntologyTermHarvestingPool(BioPortalClient client) { + public OntologyTermHarvestingPool(BioPortal4Client client) { this.client = client; threadPool = Executors.newFixedThreadPool(3); } @@ -87,7 +87,7 @@ class OntologyHandler implements Runnable { } public void run() { - OntologyTerm term = client.getTermInformation(termAccession, ontology); + OntologyTerm term = client.getTerm(termAccession, ontology); addToResults(termAccession, term); } } diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalAnnotatorResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalAnnotatorResultHandler.java deleted file mode 100644 index 8493f66b..00000000 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalAnnotatorResultHandler.java +++ /dev/null @@ -1,124 +0,0 @@ -package org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers; - -import bioontology.bioportal.annotator.schema.AnnotationBeanDocument; -import bioontology.bioportal.annotator.schema.ConceptDocument; -import bioontology.bioportal.annotator.schema.OntologyUsedBeanDocument; -import bioontology.bioportal.annotator.schema.SuccessDocument; -import org.isatools.isacreator.configuration.Ontology; -import org.isatools.isacreator.ontologymanager.bioportal.io.AcceptedOntologies; -import org.isatools.isacreator.ontologymanager.bioportal.model.AnnotatorResult; -import org.isatools.isacreator.ontologymanager.common.OntologyTerm; - -import java.io.File; -import java.util.HashMap; -import java.util.Map; -import java.util.Set; - -public class BioPortalAnnotatorResultHandler { - - public SuccessDocument getDocument(String fileLocation) { - SuccessDocument resultDocument = null; - try { - resultDocument = SuccessDocument.Factory.parse(new File(fileLocation)); - } catch (org.apache.xmlbeans.XmlException e) { - System.err.println("XML Exception encountered"); - } catch (java.io.IOException e) { - System.err.println("IO Exception: " + e.getMessage()); - } - - return resultDocument; - } - - public Map> getSearchResults(String fileLocation, Set originalTerms) { - SuccessDocument resultDocument = getDocument(fileLocation); - - Map ontologies = getOntologyInformation(resultDocument); - - // map from search term to a map of full id to the ontology term. - Map> result = new HashMap>(); - // for each token, we wan to find the matches and add them to the list - - String originalTextToAnnotate = extractOriginalSearchText(resultDocument); - - if (resultDocument != null) { - if (resultDocument.getSuccess().getData().getAnnotatorResultBean().getAnnotations() != null) { - AnnotationBeanDocument.AnnotationBean[] searchResults = resultDocument.getSuccess().getData().getAnnotatorResultBean().getAnnotations() - .getAnnotationBeanArray(); - - for (AnnotationBeanDocument.AnnotationBean annotationBean : searchResults) { - - AnnotatorResult annotatorResult = extractAnnotatorResult(annotationBean, ontologies); - - if (annotatorResult != null) { - - String originalTerm = originalTextToAnnotate.substring(annotatorResult.getStartIndex() - 1, annotatorResult.getEndIndex()); - - if (originalTerms.contains(originalTerm)) { - - if (!result.containsKey(originalTerm)) { - result.put(originalTerm, new HashMap()); - } - - String ontologyId = annotatorResult.getOntologySource().getOntologyID(); - - if (!result.get(originalTerm).containsKey(ontologyId)) { - result.get(originalTerm).put(ontologyId, annotatorResult); - } - } - } - } - } - } - - return result; - } - - private String extractOriginalSearchText(SuccessDocument resultDocument) { - if (resultDocument.getSuccess() == null) { - return ""; - } - return resultDocument.getSuccess().getData().getAnnotatorResultBean().getParameters().getTextToAnnotate(); - } - - private AnnotatorResult extractAnnotatorResult(AnnotationBeanDocument.AnnotationBean annotation, Map ontologies) { - ConceptDocument.Concept concept = annotation.getConcept(); - - if (ontologies.containsKey(concept.getLocalOntologyId().toString())) { - OntologyTerm ontologyTerm = new OntologyTerm(concept.getPreferredName(),concept.getLocalConceptId(), concept.getFullId(), null); - - Ontology ontologySource = ontologies.get(concept.getLocalOntologyId().toString()); - - return new AnnotatorResult(ontologyTerm, ontologySource, new Integer(annotation.getScore().toString()), - new Integer(annotation.getContext().getFrom().toString()), new Integer(annotation.getContext().getTo().toString())); - } - - return null; - } - - private Map getOntologyInformation(SuccessDocument document) { - Map ontologies = new HashMap(); - - if (document != null) { - for (OntologyUsedBeanDocument.OntologyUsedBean ontology : document.getSuccess().getData().getAnnotatorResultBean().getOntologies().getOntologyUsedBeanArray()) { - Ontology newOntology = new Ontology(); - newOntology.setOntologyDisplayLabel(ontology.getName()); - newOntology.setOntologyID(ontology.getVirtualOntologyId().toString()); - newOntology.setOntologyVersion(ontology.getLocalOntologyId().toString()); - - - for (Ontology accceptedOntology : AcceptedOntologies.values()) { - if (accceptedOntology.toString().equals(newOntology.getOntologyID())) { - newOntology.setOntologyAbbreviation(accceptedOntology.getOntologyAbbreviation()); - ontologies.put(ontology.getLocalOntologyId().toString(), newOntology); - break; - } - } - - } - } - - return ontologies; - } - - -} diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalClassBeanResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalClassBeanResultHandler.java deleted file mode 100644 index a3662032..00000000 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalClassBeanResultHandler.java +++ /dev/null @@ -1,232 +0,0 @@ -/** - ISAcreator is a component of the ISA software suite (http://www.isa-tools.org) - - License: - ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL) - - EXHIBIT A. CPAL version 1.0 - The contents of this file are subject to the CPAL version 1.0 (the License); - you may not use this file except in compliance with the License. You may obtain a - copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html. - The License is based on the Mozilla Public License version 1.1 but Sections - 14 and 15 have been added to cover use of software over a computer network and - provide for limited attribution for the Original Developer. In addition, Exhibit - A has been modified to be consistent with Exhibit B. - - Software distributed under the License is distributed on an AS IS basis, - WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for - the specific language governing rights and limitations under the License. - - The Original Code is ISAcreator. - The Original Developer is the Initial Developer. The Initial Developer of the - Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com; - Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com; - http://www.isa-tools.org). All portions of the code written by the ISA Team are - Copyright (c) 2007-2011 ISA Team. All Rights Reserved. - - EXHIBIT B. Attribution Information - Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team - Attribution Phrase: Developed by the ISA Team - Attribution URL: http://www.isa-tools.org - Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png - Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL. - - Sponsors: - The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone). - */ - - -package org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers; - -import bioontology.bioportal.classBean.schema.*; -import org.apache.commons.collections15.map.ListOrderedMap; -import org.isatools.isacreator.ontologymanager.common.OntologyTerm; - -import java.io.File; -import java.util.HashMap; -import java.util.Map; -import java.util.Set; - -public class BioPortalClassBeanResultHandler { - - - public SuccessDocument getDocument(String fileLocation) { - SuccessDocument resultDocument = null; - try { - resultDocument = bioontology.bioportal.classBean.schema.SuccessDocument.Factory.parse(new File(fileLocation)); - } catch (org.apache.xmlbeans.XmlException e) { - System.err.println("XML Exception encountered "+ e.getMessage()); - e.printStackTrace(); - } catch (java.io.IOException e) { - System.err.println("IO Exception: " + e.getMessage()); - } - - return resultDocument; - } - - - public String getTermURL(String fileLocation){ - SuccessDocument resultDocument = getDocument(fileLocation); - return resultDocument.getSuccess().getData().getClassBean().getFullIdArray(0); - } - - public OntologyTerm parseMetadataFile(String fileLocation) { - SuccessDocument resultDocument = getDocument(fileLocation); - ClassBeanDocument.ClassBean classBean = resultDocument.getSuccess().getData().getClassBean(); - - OntologyTerm ontology = createOntologyFromClassBean(classBean); - - for (RelationsDocument.Relations relation : classBean.getRelationsArray()) { - for (EntryDocument.Entry entry : relation.getEntryArray()) { - if (entry.getStringArray().length > 0) { - String entryType = entry.getStringArray(0); - if (entry.getListArray().length > 0) { - for (ListDocument.List listItem : entry.getListArray()) { - for (String item : listItem.getStringArray()) { - ontology.addToComments(entryType, item); - } - } - } - } - } - } - - if (classBean.getDefinitionsArray() != null) { - for (DefinitionsDocument.Definitions definition : classBean.getDefinitionsArray()) { - for (String definitionString : definition.getStringArray()) { - ontology.addToComments("definition", definitionString); - } - - } - } - - return ontology; - } - - public Map parseRootConceptFile(String fileLocation, Set termHasNoChildren) { - SuccessDocument resultDocument = getDocument(fileLocation); - - Map result = new HashMap(); - - if (resultDocument == null) { - return result; - } - - ClassBeanDocument.ClassBean upperLevelClass = resultDocument.getSuccess().getData().getClassBean(); - - for (RelationsDocument.Relations relation : upperLevelClass.getRelationsArray()) { - for (EntryDocument.Entry entry : relation.getEntryArray()) { - if (entry.getStringArray().length > 0) { - String entryType = entry.getStringArray(0); - - if (entryType.equalsIgnoreCase("subclass")) { - if (entry.getListArray().length > 0) { - for (ListDocument.List listItem : entry.getListArray()) { - - for (ClassBeanDocument.ClassBean classBeanItem : listItem.getClassBeanArray()) { - - OntologyTerm ontology = createOntologyFromClassBean(classBeanItem); - - result.put(classBeanItem.getIdArray(0), ontology); - for (RelationsDocument.Relations classBeanRelation : classBeanItem.getRelationsArray()) { - for (EntryDocument.Entry relationEntry : classBeanRelation.getEntryArray()) { - if (relationEntry.getStringArray(0).equals("ChildCount")) { - - - // if there are no children, add the term accession to quicken up later queries - if (relationEntry.getInt().intValue() == 0) { - termHasNoChildren.add(ontology.getOntologyTermAccession()); - break; - } - - - } - } - } - } - } - } - } - } - } - } - - return result; - } - - public Map parseOntologyParentPathFile(String fileLocation) { - SuccessDocument resultDocument = getDocument(fileLocation); - - Map result = new ListOrderedMap(); - - if (resultDocument == null) { - return result; - } - - ClassBeanDocument.ClassBean upperLevelClass = resultDocument.getSuccess().getData().getClassBean(); - - result = getOntologyTermParents(result, upperLevelClass); - - return result; - } - - private Map getOntologyTermParents(Map terms, ClassBeanDocument.ClassBean upperLevelClass) { - for (RelationsDocument.Relations relation : upperLevelClass.getRelationsArray()) { - for (EntryDocument.Entry entry : relation.getEntryArray()) { - if (entry.getStringArray().length > 0) { - String entryType = entry.getStringArray(0); - if (entryType.equalsIgnoreCase("subclass")) { - OntologyTerm ontology = createOntologyFromClassBean(upperLevelClass); - - if (!ontology.getOntologyTermName().equals(OntologyTerm.THING)) { - terms.put(ontology.getOntologyTermAccession(), ontology); - } - - if (entry.getListArray().length > 0) { - ListDocument.List[] items = entry.getListArray(); - - for (ListDocument.List listItem : items) { - for (ClassBeanDocument.ClassBean bean : listItem.getClassBeanArray()) { - terms.putAll(getOntologyTermParents(terms, bean)); - } - } - } - } - } - } - } - - return terms; - } - - - public OntologyTerm createOntologyFromClassBean(ClassBeanDocument.ClassBean classToConvert) { - - String termName = null; - String termAccession = null; - String purl = null; - OntologyTerm ontologyTerm = null; - - - if (classToConvert.getIdArray().length > 0) { - termAccession = classToConvert.getIdArray(0); - } - if (classToConvert.getLabelArray().length > 0) { - termName = classToConvert.getLabelArray(0); - } - if (classToConvert.getFullIdArray().length > 0) { - purl = classToConvert.getFullIdArray(0); - } - ontologyTerm = new OntologyTerm(termName, termAccession, purl, null); - - return ontologyTerm; - } - - private boolean proceedWithProcessing(SuccessDocument successDoc) { - return successDoc != null && - successDoc.getSuccess() != null && - successDoc.getSuccess().getData() != null; - - } - -} diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalOntologyListResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalOntologyListResultHandler.java deleted file mode 100644 index 38003085..00000000 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalOntologyListResultHandler.java +++ /dev/null @@ -1,202 +0,0 @@ -/** - ISAcreator is a component of the ISA software suite (http://www.isa-tools.org) - - License: - ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL) - - EXHIBIT A. CPAL version 1.0 - ÒThe contents of this file are subject to the CPAL version 1.0 (the ÒLicenseÓ); - you may not use this file except in compliance with the License. You may obtain a - copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html. - The License is based on the Mozilla Public License version 1.1 but Sections - 14 and 15 have been added to cover use of software over a computer network and - provide for limited attribution for the Original Developer. In addition, Exhibit - A has been modified to be consistent with Exhibit B. - - Software distributed under the License is distributed on an ÒAS ISÓ basis, - WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for - the specific language governing rights and limitations under the License. - - The Original Code is ISAcreator. - The Original Developer is the Initial Developer. The Initial Developer of the - Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com; - Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com; - http://www.isa-tools.org). All portions of the code written by the ISA Team are - Copyright (c) 2007-2011 ISA Team. All Rights Reserved. - - EXHIBIT B. Attribution Information - Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team - Attribution Phrase: Developed by the ISA Team - Attribution URL: http://www.isa-tools.org - Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png - Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL. - - Sponsors: - The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone). - */ - -package org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers; - -import org.apache.log4j.Logger; -import org.isatools.isacreator.configuration.Ontology; -import org.isatools.isacreator.configuration.OntologyFormats; -import org.xml.sax.Attributes; -import org.xml.sax.SAXException; -import org.xml.sax.helpers.DefaultHandler; - -import javax.xml.parsers.ParserConfigurationException; -import javax.xml.parsers.SAXParser; -import javax.xml.parsers.SAXParserFactory; -import java.io.IOException; -import java.util.ArrayList; -import java.util.List; - -/** - * @author eamonnmaguire - * @date Jul 17, 2009 - */ - - -public class BioPortalOntologyListResultHandler extends DefaultHandler { - private static final Logger log = Logger.getLogger(BioPortalOntologyListResultHandler.class.getName()); - // maps an ontology with it's name to a Search result object - - private Ontology currentOntologyEntry; - private List result; - - private static final int READING_ONTOLOGY = 1; - private static final int READING_ONT_ID = 2; - private static final int READING_ONT_LABEL = 3; - private static final int READING_ONT_ABBREVIATION = 4; - private static final int READING_ONT_VERSION = 5; - private static final int READING_IS_FOUNDRY = 6; - private static final int READING_FORMAT = 7; - private static final int READING_CONTACT = 8; - private static final int READING_CONTACT_EMAIL = 9; - private static final int READING_URL = 10; - private static final int READING_IS_VIEW = 11; - - private static final int IGNORE_READ = -1; - - private int currentReadStatus = -1; - - - /** - * Parse the config.xml file - * - * @param fileLoc - location of file to be parsed! - */ - public List parseFile(String fileLoc) { - result = new ArrayList(); - SAXParserFactory spf = SAXParserFactory.newInstance(); - - try { - SAXParser sp = spf.newSAXParser(); - sp.parse(fileLoc, this); - return result; - } catch (SAXException se) { - log.error("SAX Exception Caught: \n Details are: \n" + - se.getMessage()); - } catch (ParserConfigurationException pce) { - log.error( - "Parser Configuration Exception Caught: \n Details are: \n" + - pce.getMessage()); - } catch (IOException ioe) { - log.error("File not found: \n Details are: \n" + - ioe.getMessage()); - } - - return null; - } - - /** - * Process start element to determine if information about tables or mappings is being read in. - * - * @param namespaceURI * - * @param localName * - * @param qName - qualifier name for XML tag. - * @param atts - Attributes of element. - */ - public void startElement(String namespaceURI, String localName, - String qName, Attributes atts) { - if (qName.equalsIgnoreCase("ontologyBean")) { - currentReadStatus = READING_ONTOLOGY; - currentOntologyEntry = new Ontology(); - } else if (qName.equalsIgnoreCase("ontologyId")) { - currentReadStatus = READING_ONT_ID; - } else if (qName.equalsIgnoreCase("displayLabel")) { - currentReadStatus = READING_ONT_LABEL; - } else if (qName.equalsIgnoreCase("abbreviation")) { - currentReadStatus = READING_ONT_ABBREVIATION; - } else if (qName.equalsIgnoreCase("id")) { - currentReadStatus = READING_ONT_VERSION; - } else if (qName.equalsIgnoreCase("isFoundry")) { - currentReadStatus = READING_IS_FOUNDRY; - } else if (qName.equalsIgnoreCase("format")) { - currentReadStatus = READING_FORMAT; - } else if (qName.equalsIgnoreCase("homepage")) { - currentReadStatus = READING_URL; - } else if (qName.equalsIgnoreCase("contactName")) { - currentReadStatus = READING_CONTACT; - } else if (qName.equalsIgnoreCase("contactEmail")) { - currentReadStatus = READING_CONTACT_EMAIL; - } else if (qName.equalsIgnoreCase("isView")) { - currentReadStatus = READING_IS_VIEW; - } - } - - @Override - public void endElement(String namespaceURI, String localName, - String qName) throws SAXException { - if (qName.equalsIgnoreCase("ontologyBean")) { - - if (!currentOntologyEntry.getOntologyAbbreviation().contains("test") && - !currentOntologyEntry.getOntologyDisplayLabel().contains("test")) - result.add(currentOntologyEntry); - currentReadStatus = IGNORE_READ; - } - } - - public void characters(char[] ch, int start, int length) { - String data = new String(ch, start, length).trim(); - if (!data.equals("")) { - if (currentReadStatus == READING_ONT_ID) { - currentOntologyEntry.setOntologyID(data); - } else if (currentReadStatus == READING_ONT_LABEL) { - currentOntologyEntry.setOntologyDisplayLabel(data); - } else if (currentReadStatus == READING_ONT_ABBREVIATION) { - currentOntologyEntry.setOntologyAbbreviation(data); - } else if (currentReadStatus == READING_ONT_VERSION) { - currentOntologyEntry.setOntologyVersion(data); - } else if (currentReadStatus == READING_IS_FOUNDRY) { - boolean isFoundry = data.trim().equals("1"); - currentOntologyEntry.setFoundry(isFoundry); - } else if (currentReadStatus == READING_FORMAT) { - String trimmedSource = data.contains("-") ? data.substring(0, data.indexOf("-")).trim().toUpperCase() : data.trim().toUpperCase(); - if (isFormatSupported(trimmedSource)) { - currentOntologyEntry.setFormat(OntologyFormats.valueOf(trimmedSource)); - } - } else if (currentReadStatus == READING_CONTACT) { - currentOntologyEntry.setContactName(data); - } else if (currentReadStatus == READING_CONTACT_EMAIL) { - currentOntologyEntry.setContactEmail(data); - } else if (currentReadStatus == READING_URL) { - currentOntologyEntry.setHomePage(data); - } else if (currentReadStatus == READING_IS_VIEW) { - boolean isView = Boolean.valueOf(data); - currentOntologyEntry.setIsView(isView); - } - currentReadStatus = IGNORE_READ; - } - } - - private boolean isFormatSupported(String format) { - for (OntologyFormats of : OntologyFormats.values()) { - if (of.getFormat().equalsIgnoreCase(format)) { - return true; - } - } - return false; - } - -} diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalSearchBeanResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalSearchBeanResultHandler.java deleted file mode 100644 index f145ec88..00000000 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/xmlresulthandlers/BioPortalSearchBeanResultHandler.java +++ /dev/null @@ -1,134 +0,0 @@ -/** - ISAcreator is a component of the ISA software suite (http://www.isa-tools.org) - - License: - ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL) - - EXHIBIT A. CPAL version 1.0 - The contents of this file are subject to the CPAL version 1.0 (the License); - you may not use this file except in compliance with the License. You may obtain a - copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html. - The License is based on the Mozilla Public License version 1.1 but Sections - 14 and 15 have been added to cover use of software over a computer network and - provide for limited attribution for the Original Developer. In addition, Exhibit - A has been modified to be consistent with Exhibit B. - - Software distributed under the License is distributed on an AS IS basis, - WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for - the specific language governing rights and limitations under the License. - - The Original Code is ISAcreator. - The Original Developer is the Initial Developer. The Initial Developer of the - Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com; - Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com; - http://www.isa-tools.org). All portions of the code written by the ISA Team are - Copyright (c) 2007-2011 ISA Team. All Rights Reserved. - - EXHIBIT B. Attribution Information - Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team - Attribution Phrase: Developed by the ISA Team - Attribution URL: http://www.isa-tools.org - Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png - Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL. - - Sponsors: - The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone). - */ - - -package org.isatools.isacreator.ontologymanager.bioportal.xmlresulthandlers; - -import bioontology.bioportal.searchBean.schema.SearchBeanDocument; -import bioontology.bioportal.searchBean.schema.SearchResultListDocument; -import bioontology.bioportal.searchBean.schema.SuccessDocument; -import org.isatools.isacreator.ontologymanager.BioPortalClient; -import org.isatools.isacreator.ontologymanager.OntologyManager; -import org.isatools.isacreator.ontologymanager.OntologySourceRefObject; -import org.isatools.isacreator.ontologymanager.bioportal.io.AcceptedOntologies; -import org.isatools.isacreator.ontologymanager.common.OntologyTerm; -import org.isatools.isacreator.ontologymanager.bioportal.model.BioPortalSearchResult; - -import java.io.File; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * BioPortalSearchBeanHandler - * - * @author eamonnmaguire - * @date Feb 25, 2010 - */ - - -public class BioPortalSearchBeanResultHandler { - - public SuccessDocument getDocument(String fileLocation) { - SuccessDocument resultDocument = null; - try { - resultDocument = SuccessDocument.Factory.parse(new File(fileLocation)); - } catch (org.apache.xmlbeans.XmlException e) { - System.err.println("XML Exception encountered"); - e.printStackTrace(); - } catch (java.io.IOException e) { - System.err.println("IO Exception: " + e.getMessage()); - } - - return resultDocument; - } - - public Map> getSearchResults(String fileLocation) { - SuccessDocument resultDocument = getDocument(fileLocation); - - BioPortalSearchResult result = new BioPortalSearchResult(); - - if (resultDocument != null) { - if (resultDocument.getSuccess().getData().getPage() != null) { - SearchResultListDocument.SearchResultList[] searchResults = resultDocument.getSuccess().getData().getPage() - .getContents().getSearchResultListArray(); - - for (SearchResultListDocument.SearchResultList searchResult : searchResults) { - for (SearchBeanDocument.SearchBean searchBean : searchResult.getSearchBeanArray()) { - OntologyTerm ontologyTerm = createBioPortalOntologyFromSearchResult(searchBean); - OntologySourceRefObject sourceRefObject = createOntologySourceReferenceFromSearchResult(searchBean); - - if (ontologyTerm != null) { - ontologyTerm.setOntologySourceInformation(sourceRefObject); - result.addToResult(sourceRefObject, ontologyTerm); - } - } - } - } - } - - return result.getResult() == null ? new HashMap>() : result.getResult(); - } - - private OntologyTerm createBioPortalOntologyFromSearchResult(SearchBeanDocument.SearchBean searchResult) { - OntologyTerm ontologyTerm = null; - if (AcceptedOntologies.getOntologyAbbreviationFromId(searchResult.getOntologyId()) != null) { - - ontologyTerm = new OntologyTerm(searchResult.getPreferredName(),searchResult.getConceptIdShort(), searchResult.getConceptId(), null); - ontologyTerm.addToComments("Service Provider", OntologyManager.BIO_PORTAL); - return ontologyTerm; - - } - return null; - } - - private OntologySourceRefObject createOntologySourceReferenceFromSearchResult(SearchBeanDocument.SearchBean searchResult) { - OntologySourceRefObject refObject = new OntologySourceRefObject(); - - if (AcceptedOntologies.getAcceptedOntologies().get(searchResult.getPreferredName()) != null) { - refObject.setSourceName(AcceptedOntologies.getOntologyAbbreviationFromId(searchResult.getOntologyId())); - refObject.setSourceDescription(searchResult.getOntologyDisplayLabel()); - refObject.setSourceVersion(searchResult.getOntologyVersionId()); - refObject.setSourceFile(BioPortalClient.DIRECT_ONTOLOGY_URL + searchResult.getOntologyVersionId()); - - return refObject; - } - - return null; - } - -} diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/common/OntologyTerm.java b/src/main/java/org/isatools/isacreator/ontologymanager/common/OntologyTerm.java index 1c1a12cc..9cc520a0 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/common/OntologyTerm.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/common/OntologyTerm.java @@ -124,7 +124,7 @@ public String getOntologyTermName() { public String getOntologyTermURI() { if (ontologyTermIRI==null){ - String iri = OntologyTermUtils.getURI(this); + String iri = ""; //System.out.println("term====>" + getOntologyTermName()+", iri ===> "+iri); if (iri!=null) { ontologyTermIRI = iri; diff --git a/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClient4Test.java b/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClient4Test.java index 581b4336..7033136a 100644 --- a/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClient4Test.java +++ b/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClient4Test.java @@ -18,7 +18,7 @@ public class BioPortalClient4Test { private BioPortal4Client client = new BioPortal4Client(); private String testOntologySource = "EFO"; private String testTermAccession = "http://www.ebi.ac.uk/efo/EFO_0000428"; - private String testSearchTerm = "dose"; + private String testSearchTerm = "assay"; private String ontologyId = "http://data.bioontology.org/ontologies/EFO"; private String obiOntologyId = "http://data.bioontology.org/ontologies/OBI"; @@ -51,9 +51,8 @@ public void getTermsByPartialNameFromSource1Test() { System.out.println("_____Testing getTermsByPartialNameFromSource()____"); long startTime = System.currentTimeMillis(); - Map> result = client.getTermsByPartialNameFromSource("dose", obiOntologyId, false); - System.out.println("Took " + (System.currentTimeMillis() - startTime) + "ms to do query 'dose' in OBI."); - + Map> result = client.getTermsByPartialNameFromSource(testSearchTerm, obiOntologyId, false); + System.out.println("Took " + (System.currentTimeMillis() - startTime) + "ms to do query '" + testSearchTerm +"' in OBI."); for (OntologySourceRefObject source : result.keySet()) { System.out.println(source.getSourceName() + " (" + source.getSourceVersion() + ")"); @@ -62,7 +61,6 @@ public void getTermsByPartialNameFromSource1Test() { System.out.println("\t" + term.getOntologyTermName() + " (" + term.getOntologyTermAccession() + ")"); } } - } @Test diff --git a/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClientTest.java b/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClientTest.java deleted file mode 100644 index 2757f8c4..00000000 --- a/src/test/java/org/isatools/isacreator/ontologymanager/BioPortalClientTest.java +++ /dev/null @@ -1,255 +0,0 @@ -/** - ISAcreator is a component of the ISA software suite (http://www.isa-tools.org) - - License: - ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL) - - EXHIBIT A. CPAL version 1.0 - �The contents of this file are subject to the CPAL version 1.0 (the �License�); - you may not use this file except in compliance with the License. You may obtain a - copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html. - The License is based on the Mozilla Public License version 1.1 but Sections - 14 and 15 have been added to cover use of software over a computer network and - provide for limited attribution for the Original Developer. In addition, Exhibit - A has been modified to be consistent with Exhibit B. - - Software distributed under the License is distributed on an �AS IS� basis, - WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for - the specific language governing rights and limitations under the License. - - The Original Code is ISAcreator. - The Original Developer is the Initial Developer. The Initial Developer of the - Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com; - Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com; - http://www.isa-tools.org). All portions of the code written by the ISA Team are - Copyright (c) 2007-2011 ISA Team. All Rights Reserved. - - EXHIBIT B. Attribution Information - Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team - Attribution Phrase: Developed by the ISA Team - Attribution URL: http://www.isa-tools.org - Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png - Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL. - - Sponsors: - The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone). - */ - -package org.isatools.isacreator.ontologymanager; - -import org.isatools.isacreator.configuration.Ontology; -import org.isatools.isacreator.ontologymanager.common.OntologyTerm; -import org.junit.Test; - -import java.util.List; -import java.util.Map; - -import static org.junit.Assert.assertTrue; - -/** - * Created by the ISA team - * - * @author Eamonn Maguire (eamonnmag@gmail.com) - *

- * Date: Dec 15, 2010 - * Time: 1:52:52 PM - */ -public class BioPortalClientTest { - - private static BioPortalClient client = new BioPortalClient(); - public static String testOntologyID = "1136"; - public static String testTermAccession = "efo:EFO_0000428"; - public static String testOntologyVersion = "45781"; - public static String testSearchTerm = "dose"; - - public static String obiID = "1123"; - public static String obiVersion = "47893"; - - @Test - public void getAllOntologies() { - System.out.println("_____Testing getAllOntologies()____"); - - List ontologies = client.getAllOntologies(); - - assertTrue("Oh no! No returned ontologies (empty result)! ", ontologies.size() > 0); - - System.out.println("Found " + ontologies.size() + " ontologies \n"); - for (Ontology ontology : ontologies) { - System.out.println(ontology.getOntologyID() + " - " + ontology.getOntologyAbbreviation() + " -> " + ontology.getOntologyDisplayLabel() - + " -> " + ontology.getOntologyVersion() + " - " + ontology.getHomepage() + " " + ontology.getContactName()); - } - } - - @Test - public void getTermInformation() { - System.out.println("_____Testing getTermInformation()____"); - - OntologyTerm term = client.getTermInformation(testTermAccession, testOntologyVersion); - - assertTrue("No metadata found for " + testOntologyID, term != null); - - System.out.println("Found " + term.getComments().size() + " properties for " + term.getOntologyTermName()); - - System.out.println("Comments " + term.getComments()); - - System.out.println("Ontology PURL "+term.getOntologyTermURI()); - - } - - - @Test - public void getOBITermInformation() { - System.out.println("_____Testing getTermInformation()____"); - - OntologyTerm term = client.getTermInformation("obo:OBI_0500006", obiVersion); - - assert(term!=null); - - System.out.println("Found " + term.getComments().size() + " properties for " + term.getOntologyTermName()); - - System.out.println("Comments " + term.getComments()); - - System.out.println("Ontology PURL "+term.getOntologyTermURI()); - - } - - - @Test - public void getTermMetadata() { - System.out.println("_____Testing getTermMetadata()____"); - - Map map = client.getTermMetadata(testTermAccession, testOntologyVersion); - - assertTrue("No metadata found for " + testOntologyID, map != null); - - System.out.println("Map " + map); - - } - - - @Test - public void getOntologyById() { - System.out.println("_____Testing getOntologyById()____"); - - Ontology ontology = client.getOntologyById(testOntologyID); - - assertTrue("No ontology found for " + testOntologyID, ontology != null); - - System.out.println("Ontology found -> " + ontology.toString() + "\n"); - } - - @Test - public void getLatestOntologyVersion() { - System.out.println("_____Testing getLatestOntologyVersion()____"); - - String ontologyVersion = client.getLatestOntologyVersion(testOntologyID); - - assertTrue("Latest ontology version not found for " + testOntologyID, ontologyVersion != null); - - System.out.println("Latest ontology version found for " + testOntologyID + " -> " + ontologyVersion + "\n"); - } - - @Test - public void getTermsByPartialNameFromSource() { - System.out.println("_____Testing getTermsByPartialNameFromSource()____"); - - Map> result = client.getTermsByPartialNameFromSource(testSearchTerm, "all", false); - - assertTrue("No results found for " + testSearchTerm + " in " + testOntologyID, result.size() > 0); - - for (OntologySourceRefObject source : result.keySet()) { - System.out.println(source.getSourceName() + " (" + source.getSourceVersion() + ")"); - - for (OntologyTerm term : result.get(source)) { - System.out.println("\t" + term.getOntologyTermName() + " (" + term.getOntologyTermAccession() + ")"); - } - } - - System.out.println("Found " + result.values().size() + " matches...\n"); - } - - @Test - public void getOntologyRoots() { - System.out.println("_____Testing getOntologyRoots()____"); - Map ontologyRoots = client.getOntologyRoots(testOntologyVersion); - - assertTrue("No ontology roots found for " + testOntologyVersion, ontologyRoots.size() > 0); - - - System.out.println("Found " + ontologyRoots.size() + " roots for " + testOntologyVersion); - } - - @Test - public void getTermParents() { - System.out.println("_____Testing getTermChildrenOrParents()____"); - - Map parentTerms = client.getAllTermParents(testTermAccession, testOntologyVersion); - - assertTrue("No parents roots found for " + testTermAccession, parentTerms.size() > 0); - - for (OntologyTerm term : parentTerms.values()) { - System.out.println(term); - } - - System.out.println("Found " + parentTerms.size() + " parents for 45781"); - } - - @Test - public void downloadOntologyTest() { - System.out.println("_____Testing downloadOntology()____"); - - //obi version - client.downloadOntology("47893"); - } - - @Test - public void downloadOntologyTest2() { - System.out.println("_____Testing downloadOntology()____"); - - //a previous obi version - client.downloadOntology("47203"); - } - - @Test - public void downloadLatestVersionOntologyTest(){ - System.out.println("_____Testing downloadLatestVersionOntology()____"); - - //obi - client.downloadLatestVersionOntology("1127"); - } - - @Test - public void getRDFTermTest(){ - System.out.println("_____Testing getRDFTerm()____"); - - //obi - //client.getRDFTerm("47893", "obo:OBI_0000634"); - client.getRDFTerm("47893", "obo:OBI_0000634"); - } - - @Test - public void getTermIRITest(){ - System.out.println("_____Testing getTermIRI()____"); - - - String termAccession = "obo:OBI_0000634"; - //obi - //client.getRDFTerm("47893", "obo:OBI_0000634"); - String url = client.getTermIRI("47893", termAccession); - - System.out.println("URL for term "+termAccession+ " is "+ url ); - } - - //@Test - public void getTermIRITest2(){ - System.out.println("_____Testing getTermIRI()____"); - - String termAccession = "PATO:0000011"; - - String url = client.getTermIRI("49640", termAccession); - - System.out.println("URL for term "+termAccession+ " is "+ url ); - } - - -} From b236600f80b58b909db7d832ac11723d914564eb Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Mon, 10 Mar 2014 14:18:12 +0000 Subject: [PATCH 06/16] More commits for the annotator client. --- .../logic/impl/AnnotatorSearchClient.java | 3 ++- .../BioPortalSearchResultHandler.java | 16 +++------------- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/ontologiser/logic/impl/AnnotatorSearchClient.java b/src/main/java/org/isatools/isacreator/ontologiser/logic/impl/AnnotatorSearchClient.java index acb6a8f7..797b5f94 100644 --- a/src/main/java/org/isatools/isacreator/ontologiser/logic/impl/AnnotatorSearchClient.java +++ b/src/main/java/org/isatools/isacreator/ontologiser/logic/impl/AnnotatorSearchClient.java @@ -29,7 +29,7 @@ public class AnnotatorSearchClient { public static final String BASE_QUERY_URL = "http://data.bioontology.org/annotator"; public Map> searchForTerms(Set terms) { - return searchForTerms(terms, AcceptedOntologies.getAllowedOntologyAcronyms(new HashSet()), true); + return searchForTerms(terms, "", true); } public Map> searchForTerms(Set terms, String ontologiesToSearchOn, boolean wholeWordOnly) { @@ -44,6 +44,7 @@ public Map> searchForTerms(Set term method.addParameter("ontologies", ontologiesToSearchOn); method.addParameter("text", flattenedTerms); + method.addParameter("include", "prefLabel"); method.addParameter("apikey", "fd88ee35-6995-475d-b15a-85f1b9dd7a42"); try { diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java index da8ae576..d18bb475 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java @@ -65,9 +65,7 @@ public Map> getSearchResults(String term, String onto if (!result.containsKey(ontologyId)) { result.put(ontologyId, new ArrayList()); } - OntologyTerm ontologyTerm = createOntologyTerm(resultItem); - result.get(ontologyId).add(ontologyTerm); } @@ -124,8 +122,7 @@ private String querySearchEndpoint(String term, String ontologyIds, String subtr method.addParameter("apikey", API_KEY); - method.addParameter("pagesize", "500"); -// method.addParameter("no_links", "true"); + method.addParameter("pagesize", "100"); method.addParameter("no_context", "true"); if (exactMatch){ @@ -138,14 +135,10 @@ private String querySearchEndpoint(String term, String ontologyIds, String subtr System.err.println("Problem encountered setting host configuration for search"); } -// System.out.println(method.getURI().toString()); -// for(NameValuePair pair : method.getParameters()) { -// System.out.println(pair.getName() + "=" + pair.getValue()); -// } - + long startTime = System.currentTimeMillis(); int statusCode = client.executeMethod(method); if (statusCode != -1) { - + System.out.println("It took " + (System.currentTimeMillis() - startTime) + "ms to do that query..."); String contents = method.getResponseBodyAsString(); method.releaseConnection(); return contents; @@ -209,7 +202,6 @@ public String queryOntologyEndpoint() { System.err.println("Problem encountered setting host configuration for ontology search"); } - int statusCode = client.executeMethod(method); if (statusCode != -1) { String contents = method.getResponseBodyAsString(); @@ -301,8 +293,6 @@ public Map getOntologyRoots(String ontologyAbbreviation) { JsonArray rootArray = rdr.readArray(); for (JsonObject annotationItem : rootArray.getValuesAs(JsonObject.class)) { - - OntologySourceRefObject osro = getOntologySourceRefObject(extractOntologyId(annotationItem)); OntologyTerm ontologyTerm = createOntologyTerm(annotationItem); From e431010c5796f466fb3189a165e3c77663228ce8 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Mon, 10 Mar 2014 17:08:01 +0000 Subject: [PATCH 07/16] Upgraded JSON parser. Much faster now (2 seconds instead of 40 :-o) --- pom.xml | 6 + .../launch/ISAcreatorApplication.java | 2 - .../WSOntologyTreeCreator.java | 9 -- .../BioPortalAnnotatorResultHandler.java | 40 +++--- .../BioPortalSearchResultHandler.java | 129 +++++++++--------- 5 files changed, 86 insertions(+), 100 deletions(-) diff --git a/pom.xml b/pom.xml index fdc6a9d6..53fdfbdf 100644 --- a/pom.xml +++ b/pom.xml @@ -305,6 +305,12 @@ beta-20080629 + + net.minidev + json-smart + 2.0-RC3 + + commons-lang commons-lang diff --git a/src/main/java/org/isatools/isacreator/launch/ISAcreatorApplication.java b/src/main/java/org/isatools/isacreator/launch/ISAcreatorApplication.java index 40f03d89..b72a0ba8 100644 --- a/src/main/java/org/isatools/isacreator/launch/ISAcreatorApplication.java +++ b/src/main/java/org/isatools/isacreator/launch/ISAcreatorApplication.java @@ -32,8 +32,6 @@ public class ISAcreatorApplication { private static final Logger log = Logger.getLogger(ISAcreatorApplication.class); - private static Framework m_framework = null; - /** * Enables the bundle to run as a stand-alone application. When this * static {@code main()} method is invoked, the application creates diff --git a/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java b/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java index cf6c16ce..3c1d5a31 100644 --- a/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java +++ b/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java @@ -111,14 +111,8 @@ private void initiateOntologyVisualization() { try { browser.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (String ontology : ontologies.keySet()) { - System.out.println("Adding " + ontology + " to tree"); - RecommendedOntology recommendedOntology = ontologies.get(ontology); - System.out.println("initialising ontology visualisation for " + recommendedOntology.getOntology().getOntologyDisplayLabel()); - System.out.println("Ontology version is: " + recommendedOntology.getOntology().getOntologyVersion()); - System.out.println("Ontology ID: " + recommendedOntology.getOntology().getOntologyID()); - System.out.println("Ontology Abbreviation: " + recommendedOntology.getOntology().getOntologyAbbreviation()); // if ontology has no branch specified, query the whole ontology. Map rootTerms; @@ -127,15 +121,12 @@ private void initiateOntologyVisualization() { if (recommendedOntology.getBranchToSearchUnder() != null) { nodeLabel += " under " + recommendedOntology.getBranchToSearchUnder().getBranchName(); - String branchIdentifier = recommendedOntology.getBranchToSearchUnder().getBranchIdentifier(); if (StringProcessing.isURL(branchIdentifier)) { branchIdentifier = OntologyUtils.getModifiedBranchIdentifier(branchIdentifier, "#"); } - System.out.println("Going to search for " + branchIdentifier + " in " + recommendedOntology.getOntology().getOntologyDisplayLabel()); - rootTerms = bioportalClient.getTermChildren(branchIdentifier, recommendedOntology.getOntology().getOntologyAbbreviation()); } else { diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java index 1f301f06..3d52dbab 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java @@ -1,13 +1,14 @@ package org.isatools.isacreator.ontologymanager.bioportal.jsonresulthandlers; +import net.minidev.json.JSONArray; +import net.minidev.json.JSONObject; +import net.minidev.json.JSONValue; import org.isatools.isacreator.ontologymanager.OntologyManager; import org.isatools.isacreator.ontologymanager.OntologySourceRefObject; import org.isatools.isacreator.ontologymanager.bioportal.io.AcceptedOntologies; import org.isatools.isacreator.ontologymanager.bioportal.model.AnnotatorResult; import org.isatools.isacreator.ontologymanager.common.OntologyTerm; -import javax.json.*; -import java.io.StringReader; import java.util.HashMap; import java.util.Map; import java.util.Set; @@ -31,16 +32,11 @@ public Map> getSearchResults(String queryCo Map> result = new HashMap>(); // for each token, we wan to find the matches and add them to the list - StringReader reader = new StringReader(queryContents); + JSONArray obj = (JSONArray) JSONValue.parse(queryContents); - System.out.println(queryContents); - JsonReader rdr = Json.createReader(reader); + for (Object annotationItem : obj) { - JsonArray obj = rdr.readArray(); - - for (JsonObject annotationItem : obj.getValuesAs(JsonObject.class)) { - - AnnotatorResult annotatorResult = extractAnnotatorResult(annotationItem); + AnnotatorResult annotatorResult = extractAnnotatorResult((JSONObject)annotationItem); if (annotatorResult != null) { @@ -63,25 +59,27 @@ public Map> getSearchResults(String queryCo return result; } - private AnnotatorResult extractAnnotatorResult(JsonObject resultItem) { - JsonObject annotatedClass = resultItem.getJsonObject("annotatedClass"); - JsonObject links = annotatedClass.getJsonObject("links"); + private AnnotatorResult extractAnnotatorResult(JSONObject resultItem) { + JSONObject annotatedClass = (JSONObject)resultItem.get("annotatedClass"); + JSONObject links = (JSONObject) annotatedClass.get("links"); - String ontologyId = links.getJsonString("ontology").toString(); + String ontologyId = links.get("ontology").toString(); OntologySourceRefObject sourceRefObject = OntologyManager.getOntologySourceReferenceObjectByAbbreviation(ontologyId); - OntologyTerm ontologyTerm = new OntologyTerm(annotatedClass.getString("prefLabel"), annotatedClass.getString("@id"), annotatedClass.getString("@id"), sourceRefObject); + OntologyTerm ontologyTerm = new OntologyTerm( + annotatedClass.get("prefLabel").toString(), annotatedClass.get("@id").toString(), annotatedClass.get("@id").toString(), sourceRefObject); - JsonNumber from = null, to = null; + int from = -1, to = -1; - for (JsonObject annotation : resultItem.getJsonArray("annotations").getValuesAs(JsonObject.class)) { - from = annotation.getJsonNumber("from"); - to = annotation.getJsonNumber("to"); + for (Object annotation : (JSONArray)resultItem.get("annotations")) { + JSONObject annotationObject = (JSONObject) annotation; + from = Integer.valueOf(annotationObject.get("from").toString()); + to = Integer.valueOf(annotationObject.get("to").toString()); } - if (from != null && to != null) { + if (from != -1 && to != -1) { return new AnnotatorResult(ontologyTerm, AcceptedOntologies.getAcceptedOntologies().get(ontologyId), 1, - from.intValue(), to.intValue()); + from, to); } return null; diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java index d18bb475..1cbe0078 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalSearchResultHandler.java @@ -1,5 +1,8 @@ package org.isatools.isacreator.ontologymanager.bioportal.jsonresulthandlers; +import net.minidev.json.JSONArray; +import net.minidev.json.JSONObject; +import net.minidev.json.JSONValue; import org.apache.commons.collections15.map.ListOrderedMap; import org.apache.commons.httpclient.HostConfiguration; import org.apache.commons.httpclient.HttpClient; @@ -13,8 +16,6 @@ import org.isatools.isacreator.ontologymanager.bioportal.io.AcceptedOntologies; import org.isatools.isacreator.ontologymanager.common.OntologyTerm; -import javax.json.*; -import java.io.StringReader; import java.io.UnsupportedEncodingException; import java.net.URLEncoder; import java.util.ArrayList; @@ -30,7 +31,7 @@ public class BioPortalSearchResultHandler { public Map> getSearchResults(String term, String ontologyIds, String subtree) { - return getSearchResults(term, ontologyIds, subtree, false); + return getSearchResults(term, ontologyIds, subtree, false); } /** @@ -48,18 +49,16 @@ public Map> getSearchResults(String term, String onto String content = querySearchEndpoint(term, ontologyIds, subtree, exactMatch); - StringReader reader = new StringReader(content); + JSONObject obj = (JSONObject) JSONValue.parse(content); - JsonReader rdr = Json.createReader(reader); + JSONArray results = (JSONArray) obj.get("collection"); - JsonObject obj = rdr.readObject(); - JsonArray results = obj.getJsonArray("collection"); - - if (results==null) + if (results == null) return result; - for (JsonObject resultItem : results.getValuesAs(JsonObject.class)) { + for (Object result1 : results) { + JSONObject resultItem = (JSONObject) result1; String ontologyId = extractOntologyId(resultItem); if (!result.containsKey(ontologyId)) { @@ -73,24 +72,24 @@ public Map> getSearchResults(String term, String onto return result; } - private String extractOntologyId(JsonObject ontologyItemJsonDictionary) { - JsonObject links = ontologyItemJsonDictionary.getJsonObject("links"); - return links.getJsonString("ontology").toString(); + private String extractOntologyId(JSONObject ontologyItemJsonDictionary) { + JSONObject links = (JSONObject) ontologyItemJsonDictionary.get("links"); + return links.get("ontology").toString(); } - private void extractDefinitionFromOntologyTerm(JsonObject ontologyItemJsonDictionary, OntologyTerm ontologyTerm) { - JsonArray definitions = ontologyItemJsonDictionary.getJsonArray("definition"); + private void extractDefinitionFromOntologyTerm(JSONObject ontologyItemJsonDictionary, OntologyTerm ontologyTerm) { + JSONArray definitions = (JSONArray) ontologyItemJsonDictionary.get("definition"); if (definitions != null && definitions.size() > 0) { ontologyTerm.addToComments("definition", definitions.get(0).toString()); } } - private void extractSynonymsFromOntologyTerm(JsonObject ontologyItemJsonDictionary, OntologyTerm ontologyTerm) { - JsonArray synonyms = ontologyItemJsonDictionary.getJsonArray("synonyms"); + private void extractSynonymsFromOntologyTerm(JSONObject ontologyItemJsonDictionary, OntologyTerm ontologyTerm) { + JSONArray synonyms = (JSONArray) ontologyItemJsonDictionary.get("synonyms"); if (synonyms != null && synonyms.size() > 0) { StringBuilder synonymList = new StringBuilder(); int count = 0; - for (JsonValue value : synonyms.getValuesAs(JsonValue.class)) { + for (Object value : synonyms) { synonymList.append(value.toString()); if (count != synonyms.size() - 1) { synonymList.append(","); @@ -102,7 +101,6 @@ private void extractSynonymsFromOntologyTerm(JsonObject ontologyItemJsonDictiona } - private String querySearchEndpoint(String term, String ontologyIds, String subtree, boolean exactMatch) { try { HttpClient client = new HttpClient(); @@ -114,9 +112,9 @@ private String querySearchEndpoint(String term, String ontologyIds, String subtr if (StringUtils.trimToNull(subtree) != null) { method.addParameter("subtree", subtree); - if (ontologyIds!=null) + if (ontologyIds != null) method.addParameter("ontology", ontologyIds); - } else if(!ontologyIds.equals("all")) { + } else if (!ontologyIds.equals("all")) { method.addParameter("ontologies", ontologyIds); } @@ -125,7 +123,7 @@ private String querySearchEndpoint(String term, String ontologyIds, String subtr method.addParameter("pagesize", "100"); method.addParameter("no_context", "true"); - if (exactMatch){ + if (exactMatch) { method.addParameter("exact_match", "true"); } @@ -154,35 +152,32 @@ public Map getAllOntologies() { Map result = new HashMap(); String content = queryOntologyEndpoint(); + JSONArray obj = (JSONArray) JSONValue.parse(content); - StringReader reader = new StringReader(content); - JsonReader rdr = Json.createReader(reader); - JsonArray array = rdr.readArray(); - - for (JsonObject resultItem : array.getValuesAs(JsonObject.class)) { - addOntology(result, resultItem); + for (Object resultItem : obj) { + addOntology(result, (JSONObject) resultItem); } return result; } - private void addOntology(Map result, JsonObject resultItem) { - JsonObject ontology = resultItem.getJsonObject("ontology"); - JsonValue summaryOnly = ontology.get("summaryOnly"); - if (summaryOnly != null) { - Ontology newOntology = new Ontology(ontology.getString("@id"), "version", ontology.getString("acronym"), ontology.getString("name")); + private void addOntology(Map result, JSONObject resultItem) { + JSONObject ontology = (JSONObject) resultItem.get("ontology"); + boolean summaryOnly = Boolean.valueOf(ontology.get("summaryOnly") != null ? ontology.get("summaryOnly").toString() : "false"); + if (!summaryOnly) { + Ontology newOntology = new Ontology(ontology.get("@id").toString(), "version", ontology.get("acronym").toString(), ontology.get("name").toString()); if (!newOntology.getOntologyAbbreviation().contains("test") && !newOntology.getOntologyDisplayLabel().contains("test")) { - String version = resultItem.get("version").toString(); - JsonNumber submissionId = resultItem.getJsonNumber("submissionId"); - String homepage = resultItem.get("homepage").toString(); + String version = resultItem.get("version") != null ? resultItem.get("version").toString() : ""; + String submissionId = resultItem.get("submissionId") != null ? resultItem.get("submissionId").toString() : ""; + String homepage = resultItem.get("homepage") != null ? resultItem.get("homepage").toString() : ""; newOntology.setHomePage(homepage); newOntology.setOntologyVersion(version); - newOntology.setSubmissionId(submissionId.toString()); + newOntology.setSubmissionId(submissionId); - result.put(resultItem.getString("@id"), newOntology); + result.put(resultItem.get("@id").toString(), newOntology); } } @@ -219,7 +214,7 @@ private void setHostConfiguration(HttpClient client) { HostConfiguration configuration = new HostConfiguration(); configuration.setHost("http://data.bioontology.org"); String proxyPort = System.getProperty("http.proxyPort"); - if (proxyPort ==null) + if (proxyPort == null) return; configuration.setProxy(System.getProperty("http.proxyHost"), Integer.valueOf(System.getProperty("http.proxyPort"))); client.setHostConfiguration(configuration); @@ -228,20 +223,22 @@ private void setHostConfiguration(HttpClient client) { public OntologyTerm getTermMetadata(String termId, String ontologyId) { String content = queryTermMetadataEndpoint(termId, ontologyId); - StringReader reader = new StringReader(content); - JsonReader rdr = Json.createReader(reader); - JsonObject obj = rdr.readObject(); + JSONObject obj = (JSONObject) JSONValue.parse(content); + // if we have a nice error free page, continue if (!obj.containsKey("errors")) { OntologySourceRefObject osro = getOntologySourceRefObject(ontologyId); - OntologyTerm ontologyTerm = new OntologyTerm(obj.getString("prefLabel"), obj.getString("@id"), obj.getString("@id"), osro); + OntologyTerm ontologyTerm = new OntologyTerm( + obj.get("prefLabel").toString(), + obj.get("@id").toString(), + obj.get("@id").toString(), osro); ontologyTerm.addToComments("Service Provider", OntologyManager.BIO_PORTAL); extractDefinitionFromOntologyTerm(obj, ontologyTerm); extractSynonymsFromOntologyTerm(obj, ontologyTerm); - System.out.println(ontologyTerm.getOntologyTermName() + " - " + ontologyTerm.getOntologyTermAccession() + " - " + ontologyTerm.getOntologyTermURI() ); + System.out.println(ontologyTerm.getOntologyTermName() + " - " + ontologyTerm.getOntologyTermAccession() + " - " + ontologyTerm.getOntologyTermURI()); return ontologyTerm; } else { @@ -288,14 +285,15 @@ public Map getOntologyRoots(String ontologyAbbreviation) { String queryContents = generalQueryEndpoint(BioPortal4Client.REST_URL + "ontologies/" + ontologyAbbreviation + "/classes/roots?apikey=" + API_KEY); System.out.println(BioPortal4Client.REST_URL + "ontologies/" + ontologyAbbreviation + "/classes/roots?apikey=" + API_KEY); - StringReader reader = new StringReader(queryContents); - JsonReader rdr = Json.createReader(reader); - JsonArray rootArray = rdr.readArray(); - for (JsonObject annotationItem : rootArray.getValuesAs(JsonObject.class)) { - OntologySourceRefObject osro = getOntologySourceRefObject(extractOntologyId(annotationItem)); + JSONArray ontologyTerms = (JSONArray) JSONValue.parse(queryContents); + + + for (Object annotationItem : ontologyTerms) { + JSONObject annotationObject = (JSONObject) annotationItem; + OntologySourceRefObject osro = getOntologySourceRefObject(extractOntologyId(annotationObject)); - OntologyTerm ontologyTerm = createOntologyTerm(annotationItem); + OntologyTerm ontologyTerm = createOntologyTerm(annotationObject); ontologyTerm.setOntologySourceInformation(osro); roots.put(ontologyTerm.getOntologyTermAccession(), ontologyTerm); @@ -304,17 +302,17 @@ public Map getOntologyRoots(String ontologyAbbreviation) { return roots; } - private OntologyTerm createOntologyTerm(JsonObject annotationItem) { + private OntologyTerm createOntologyTerm(JSONObject annotationItem) { - OntologyTerm ontologyTerm = new OntologyTerm(annotationItem.getString("prefLabel"), annotationItem.getString("@id"), annotationItem.getString("@id"), null); + OntologyTerm ontologyTerm = new OntologyTerm(annotationItem.get("prefLabel").toString(), annotationItem.get("@id").toString(), annotationItem.get("@id").toString(), null); ontologyTerm.addToComments("Service Provider", OntologyManager.BIO_PORTAL); extractDefinitionFromOntologyTerm(annotationItem, ontologyTerm); extractSynonymsFromOntologyTerm(annotationItem, ontologyTerm); String ontologyId = extractOntologyId(annotationItem); - if (ontologyId!=null){ - String ontologyAbbreviation = ontologyId.substring(ontologyId.lastIndexOf('/')+1); + if (ontologyId != null) { + String ontologyAbbreviation = ontologyId.substring(ontologyId.lastIndexOf('/') + 1); OntologySourceRefObject sourceRefObject = OntologyManager.getOntologySourceReferenceObjectByAbbreviation(ontologyAbbreviation); - if (sourceRefObject!=null) + if (sourceRefObject != null) ontologyTerm.setOntologySourceInformation(sourceRefObject); } return ontologyTerm; @@ -371,25 +369,23 @@ public Map getTermChildrenOrParents(String termAccession, String queryContents = generalQueryEndpoint(BioPortal4Client.REST_URL + "ontologies/" + ontologyAbbreviation + "/classes/" + URLEncoder.encode(termAccession, "UTF-8") + "/" + parentsOrChildren + "?apikey=" + API_KEY); - StringReader reader = new StringReader(queryContents); - JsonReader rdr = Json.createReader(reader); - System.out.println(queryContents); - JsonStructure topLevelStructure = rdr.read(); - JsonArray rootArray; + Object obj = JSONValue.parse(queryContents); + JSONArray rootArray; - if (topLevelStructure instanceof JsonObject) { + if (obj instanceof JSONObject) { // the children result returns a dictionary, or JsonStructure, so we have to go down one level to get // the collection of results. - rootArray = ((JsonObject) topLevelStructure).getJsonArray("collection"); + rootArray = (JSONArray) ((JSONObject) obj).get("collection"); } else { // the parents result returns an array directly, so we can just use it immediately. - rootArray = (JsonArray) topLevelStructure; + rootArray = (JSONArray) obj; } - for (JsonObject annotationItem : rootArray.getValuesAs(JsonObject.class)) { + for (Object arrayValue: rootArray) { + JSONObject annotationItem = (JSONObject) arrayValue; OntologySourceRefObject osro = getOntologySourceRefObject(extractOntologyId(annotationItem)); OntologyTerm ontologyTerm = createOntologyTerm(annotationItem); @@ -399,13 +395,10 @@ public Map getTermChildrenOrParents(String termAccession, } return parents; + } catch (UnsupportedEncodingException e) { e.printStackTrace(); } - return null; - } - - } From 3cadb2564a0854f5b6b8ff57cfbdf3eb20bb1338 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Mon, 10 Mar 2014 17:08:30 +0000 Subject: [PATCH 08/16] Updated release version to 1.7.7 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 53fdfbdf..9b3f6e2d 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.isatools ISAcreator bundle - 1.7.6 + 1.7.7 ISAcreator http://www.isa-tools.org From f192d8997354c6f7067f800551e92f973a7f326e Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Tue, 11 Mar 2014 10:50:42 +0000 Subject: [PATCH 09/16] Fixed issue with selecting ontology from the tree view. --- .../ontologybrowsingutils/WSOntologyTreeCreator.java | 10 ---------- .../ontologymanager/utils/OntologyUtils.java | 6 ++++-- .../ontologyselectiontool/OntologySelectionTool.java | 3 --- 3 files changed, 4 insertions(+), 15 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java b/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java index 3c1d5a31..bf7a7e2f 100644 --- a/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java +++ b/src/main/java/org/isatools/isacreator/ontologybrowsingutils/WSOntologyTreeCreator.java @@ -82,32 +82,24 @@ public WSOntologyTreeCreator(Container browser, JTree tree) { this.browser = browser; this.tree = tree; observers = new ArrayList(); - bioportalClient = new BioPortal4Client(); } public DefaultMutableTreeNode createTree(Map ontologies) throws FileNotFoundException { this.ontologies = ontologies; - rootNode = new DefaultMutableTreeNode(ontologies.size() + " recommended ontologies"); treeModel = new DefaultTreeModel(rootNode); treeModel.addTreeModelListener(this); - tree.setModel(treeModel); tree.addTreeExpansionListener(this); tree.addTreeSelectionListener(this); - - initiateOntologyVisualization(); return rootNode; } private void initiateOntologyVisualization() { - - // instead of visualising just one ontology, we need to visualise all that have been selected to browse on, if they have branches // specified...or maybe should allow to browse the whole ontology as well. - try { browser.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); for (String ontology : ontologies.keySet()) { @@ -182,8 +174,6 @@ private void preloadNextOntologyLevel(String termAccession, DefaultMutableTreeNo browser.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); Ontology ontology = extractOntologyFromNode(parentTerm); - - Map termChildren = bioportalClient.getTermChildren(termAccession, ontology.getOntologyAbbreviation()); // add the level of non visible nodes diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/utils/OntologyUtils.java b/src/main/java/org/isatools/isacreator/ontologymanager/utils/OntologyUtils.java index 034c37b2..84b18072 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/utils/OntologyUtils.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/utils/OntologyUtils.java @@ -55,7 +55,9 @@ public static OntologySourceRefObject convertOntologyToOntologySourceReferenceOb } public static OntologyTerm convertOntologyBranchToOntologyTerm(OntologyBranch branch, OntologySourceRefObject ontologySource) { - OntologyTerm historyObject = new OntologyTerm(branch.getBranchName(),branch.getBranchIdentifier(), null, ontologySource); - return historyObject; + System.out.println(branch.getBranchIdentifier()); + System.out.println("Source Name = " + ontologySource.getSourceName()); + System.out.println("Source Description = " + ontologySource.getSourceDescription()); + return new OntologyTerm(branch.getBranchName(),branch.getBranchIdentifier(), branch.getBranchIdentifier(), ontologySource); } } diff --git a/src/main/java/org/isatools/isacreator/ontologyselectiontool/OntologySelectionTool.java b/src/main/java/org/isatools/isacreator/ontologyselectiontool/OntologySelectionTool.java index de080e4e..06bbc852 100755 --- a/src/main/java/org/isatools/isacreator/ontologyselectiontool/OntologySelectionTool.java +++ b/src/main/java/org/isatools/isacreator/ontologyselectiontool/OntologySelectionTool.java @@ -1102,14 +1102,11 @@ public void mousePressed(MouseEvent event) { OntologyTerm ontologyTerm = (OntologyTerm) selectedNode.getUserObject(); if (event.getClickCount() == 1) { - addTerm(ontologyTerm); } - boolean sourceIsInPlugins = OntologySearchPluginRegistry.isOntologySourceAbbreviationDefinedInPlugins(ontologyTerm.getOntologySource()); viewTermDefinition.setContent(createOntologyBranch(ontologyTerm), ontologySource.getSourceFile(), sourceIsInPlugins ? null : bioportalClient == null ? new BioPortal4Client() : bioportalClient); - } } else if (tree == browseRecommendedOntologyTree) { From 936a5040c162e6e51734fc79cd17d98655c46209 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Tue, 11 Mar 2014 11:51:11 +0000 Subject: [PATCH 10/16] Archive output appears to be fixed. Needs testing by @proccaserra :) --- .../isatools/isacreator/archiveoutput/ArchiveOutputUtil.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java b/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java index 1abfbf8e..38ebc7f4 100755 --- a/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java +++ b/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java @@ -217,7 +217,8 @@ public void setupProgressBar() { private JLayeredPane getAssayByRef(String assayRef) { for (ISASection isaSection : ApplicationManager.getIsaSectionToDataEntryForm().keySet()) { - if (isaSection.getFieldValues().get(Assay.ASSAY_REFERENCE).equals(assayRef)) { + System.out.println(isaSection); + if (isaSection.getFieldValues().get(Assay.ASSAY_REFERENCE) != null && isaSection.getFieldValues().get(Assay.ASSAY_REFERENCE).equals(assayRef)) { return ApplicationManager.getUserInterfaceForISASection(isaSection); } } From 43392597c10b781a168c301a5f7fd11e73861ebe Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Tue, 11 Mar 2014 14:25:19 +0000 Subject: [PATCH 11/16] Fixed IO tests. --- .../isatools/isacreator/gui/ISAcreator.java | 2 - .../isatools/isacreator/io/CommonTestIO.java | 13 + .../io/exportisa/OutputISAFilesTest.java | 7 +- .../ISAtabFilesImporterFromGUITest.java | 8 +- .../io/importisa/ISAtabFilesImporterTest.java | 5 +- .../io/importisa/InvestigationImportTest.java | 6 +- .../test-data/BII-I-1/a_metabolome.txt | 224 ++++++------ .../test-data/BII-I-1/a_microarray.txt | 30 +- .../test-data/BII-I-1/a_proteome.txt | 38 +- .../test-data/BII-I-1/a_transcriptome.txt | 98 +++--- .../test-data/BII-I-1/i_investigation.txt | 19 +- .../resources/test-data/BII-I-1/s_BII-S-1.txt | 330 +++++++++--------- .../resources/test-data/BII-I-1/s_BII-S-2.txt | 30 +- 13 files changed, 414 insertions(+), 396 deletions(-) create mode 100644 src/test/java/org/isatools/isacreator/io/CommonTestIO.java diff --git a/src/main/java/org/isatools/isacreator/gui/ISAcreator.java b/src/main/java/org/isatools/isacreator/gui/ISAcreator.java index ccdef14b..c61291a4 100755 --- a/src/main/java/org/isatools/isacreator/gui/ISAcreator.java +++ b/src/main/java/org/isatools/isacreator/gui/ISAcreator.java @@ -103,8 +103,6 @@ public class ISAcreator extends AnimatableJFrame implements WindowFocusListener private static Logger log = Logger.getLogger(ISAcreator.class); - public static final String CONFIG_DIR = "/Configurations/isaconfig-default_v2013-02-13/"; - public static String DEFAULT_ISATAB_SAVE_DIRECTORY = "isatab files"; public static String DEFAULT_CONFIGURATIONS_DIRECTORY = "Configurations"; public static String DEFAULT_USER_PROFILE_DIRECTORY = ""; diff --git a/src/test/java/org/isatools/isacreator/io/CommonTestIO.java b/src/test/java/org/isatools/isacreator/io/CommonTestIO.java new file mode 100644 index 00000000..5bd6fa5a --- /dev/null +++ b/src/test/java/org/isatools/isacreator/io/CommonTestIO.java @@ -0,0 +1,13 @@ +package org.isatools.isacreator.io; + +/** + * Created with IntelliJ IDEA. + * User: eamonnmaguire + * Date: 11/03/2014 + * Time: 14:11 + * To change this template use File | Settings | File Templates. + */ +public interface CommonTestIO { + + public static final String DEFAULT_CONFIG_DIR = "/src/main/resources/Configurations/isaconfig-default_v2014-01-16/"; +} diff --git a/src/test/java/org/isatools/isacreator/io/exportisa/OutputISAFilesTest.java b/src/test/java/org/isatools/isacreator/io/exportisa/OutputISAFilesTest.java index 815a0564..18ca4ca7 100644 --- a/src/test/java/org/isatools/isacreator/io/exportisa/OutputISAFilesTest.java +++ b/src/test/java/org/isatools/isacreator/io/exportisa/OutputISAFilesTest.java @@ -1,7 +1,7 @@ package org.isatools.isacreator.io.exportisa; import org.apache.log4j.Logger; -import org.isatools.isacreator.gui.ISAcreator; +import org.isatools.isacreator.io.CommonTestIO; import org.isatools.isacreator.io.importisa.ISAtabFilesImporter; import org.isatools.isacreator.model.Investigation; import org.junit.After; @@ -19,7 +19,7 @@ * * @author Alejandra Gonzalez-Beltran */ -public class OutputISAFilesTest { +public class OutputISAFilesTest implements CommonTestIO { private String configDir = null; private static Logger log = Logger.getLogger(OutputISAFilesTest.class); @@ -42,9 +42,8 @@ public void setUp() { } } - configDir = baseDir + ISAcreator.CONFIG_DIR; + configDir = baseDir + DEFAULT_CONFIG_DIR; - log.debug("configDir=" + configDir); importer = new ISAtabFilesImporter(configDir); exporter = new OutputISAFiles(); isatabParentDir = baseDir + "/src/test/resources/test-data/BII-I-1"; diff --git a/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterFromGUITest.java b/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterFromGUITest.java index d363a030..6e44aea4 100644 --- a/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterFromGUITest.java +++ b/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterFromGUITest.java @@ -3,6 +3,7 @@ import org.isatools.isacreator.gui.ISAcreator; import org.isatools.isacreator.gui.io.importisa.ISAtabFilesImporterFromGUI; import org.isatools.isacreator.gui.modeselection.Mode; +import org.isatools.isacreator.io.CommonTestIO; import org.isatools.isacreator.launch.ISAcreatorGUIProperties; import org.junit.After; import org.junit.Before; @@ -16,7 +17,7 @@ * * @author Alejandra Gonzalez-Beltran */ -public class ISAtabFilesImporterFromGUITest { +public class ISAtabFilesImporterFromGUITest implements CommonTestIO { private String baseDir = null, isatabParentDir = null; private ISAcreator isacreator = null; @@ -26,7 +27,10 @@ public class ISAtabFilesImporterFromGUITest { public void setUp() { ISAcreatorGUIProperties.setProperties(); baseDir = System.getProperty("basedir"); - isacreator = new ISAcreator(Mode.NORMAL_MODE, null, baseDir + ISAcreator.CONFIG_DIR); + + String configDir = baseDir + DEFAULT_CONFIG_DIR; + + isacreator = new ISAcreator(Mode.NORMAL_MODE, null, configDir); importer = new ISAtabFilesImporterFromGUI(isacreator); } diff --git a/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterTest.java b/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterTest.java index 19231dbf..9ca7e238 100644 --- a/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterTest.java +++ b/src/test/java/org/isatools/isacreator/io/importisa/ISAtabFilesImporterTest.java @@ -3,6 +3,7 @@ import org.apache.log4j.Logger; import org.isatools.errorreporter.model.ErrorMessage; import org.isatools.errorreporter.model.ISAFileErrorReport; +import org.isatools.isacreator.io.CommonTestIO; import org.isatools.isacreator.model.Investigation; import org.isatools.isacreator.ontologymanager.OntologyManager; import org.junit.After; @@ -26,7 +27,7 @@ * * @author Alejandra Gonzalez-Beltran */ -public class ISAtabFilesImporterTest { +public class ISAtabFilesImporterTest implements CommonTestIO { private String configDir = null; private static Logger log = Logger.getLogger(ISAtabFilesImporterTest.class); @@ -47,7 +48,7 @@ public void setUp() { } } - configDir = baseDir + "/Configurations/isaconfig-default_v2013-02-13/"; + configDir = baseDir + DEFAULT_CONFIG_DIR; log.debug("configDir=" + configDir); importer = new ISAtabFilesImporter(configDir); diff --git a/src/test/java/org/isatools/isacreator/io/importisa/InvestigationImportTest.java b/src/test/java/org/isatools/isacreator/io/importisa/InvestigationImportTest.java index d483ada1..31e149a1 100644 --- a/src/test/java/org/isatools/isacreator/io/importisa/InvestigationImportTest.java +++ b/src/test/java/org/isatools/isacreator/io/importisa/InvestigationImportTest.java @@ -39,7 +39,9 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi import org.apache.commons.collections15.OrderedMap; import org.isatools.errorreporter.model.ErrorMessage; +import org.isatools.isacreator.io.CommonTestIO; import org.isatools.isacreator.io.importisa.investigationproperties.InvestigationFileSection; +import org.isatools.isacreator.managers.ConfigurationManager; import org.isatools.isacreator.model.Investigation; import org.isatools.isacreator.model.Publication; import org.junit.Test; @@ -51,7 +53,7 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi import static junit.framework.Assert.assertTrue; -public class InvestigationImportTest { +public class InvestigationImportTest implements CommonTestIO { @Test public void loadInvestigationFile() { @@ -60,6 +62,8 @@ public void loadInvestigationFile() { File testInvestigationFile = new File(baseDir + "/target/test-classes/test-data/BII-I-1/i_investigation.txt"); + ConfigurationManager.loadConfigurations(baseDir + DEFAULT_CONFIG_DIR); + System.out.println("__TESTING loadInvestigationFile() on " + testInvestigationFile.getName()); InvestigationImport importer = new InvestigationImport(); diff --git a/src/test/resources/test-data/BII-I-1/a_metabolome.txt b/src/test/resources/test-data/BII-I-1/a_metabolome.txt index 4f9465c9..cb5b3d64 100644 --- a/src/test/resources/test-data/BII-I-1/a_metabolome.txt +++ b/src/test/resources/test-data/BII-I-1/a_metabolome.txt @@ -1,112 +1,112 @@ -"Sample Name" "Material Type" "Term Source REF" "Term Accession Number" "Protocol REF" "Parameter Value[standard volume]" "Unit" "Term Source REF" "Term Accession Number" "Parameter Value[sample volume]" "Unit" "Term Source REF" "Term Accession Number" "Extract Name" "MS Assay Name" "Raw Spectral Data File" "Comment[Data Repository]" "Comment[Data Record Accession]" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"C-0.1-aliquot1" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "S-0.2-aliquot8" "JIC36_Sulphate_0.20_Internal_1_3" "JIC36_Sulphate_0.20_Internal_1_3.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hour" "" "" -"P-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot8" "JIC20_Phosphate_0.07_Internal_1_1" "JIC20_Phosphate_0.07_Internal_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" -"P-0.07-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.07-aliquot9" "JIC21_Phosphate_0.07_Internal_2_1" "JIC21_Phosphate_0.07_Internal_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.07" "l/hr" "" "" -"P-0.1-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot8" "JIC22_Phosphate_0.10_Internal_1_1" "JIC22_Phosphate_0.10_Internal_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" -"P-0.1-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot9" "JIC23_Phosphate_0.10_Internal_2_1" "JIC23_Phosphate_0.10_Internal_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" -"P-0.1-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.1-aliquot10" "JIC24_Phosphate_0.10_Internal_3_1" "JIC24_Phosphate_0.10_Internal_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" -"P-0.2-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot8" "JIC25_Phosphate_0.20_Internal_1_1" "JIC25_Phosphate_0.20_Internal_1_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" -"P-0.2-aliquot9" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot9" "JIC26_Phosphate_0.20_Internal_2_1" "JIC26_Phosphate_0.20_Internal_2_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" -"P-0.2-aliquot10" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "P-0.2-aliquot10" "JIC27_Phosphate_0.20_Internal_3_1" "JIC27_Phosphate_0.20_Internal_3_1.txt" "" "" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" -"N-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot8" "JIC10_Nitrogen_0.07_Internal_1_1" "JIC10_Nitrogen_0.07_Internal_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" -"N-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.07-aliquot8" "JIC10_Nitrogen_0.07_Internal_1_2" "JIC10_Nitrogen_0.07_Internal_1_2.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.07" "l/hr" "" "" -"N-0.07-aliquot8" "intracellular" "CL" "http://purl.obolibrary.org/obo/GO_0005622" "metabolite extraction" "4" "microliter" "UO" 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"http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot5" "JIC70_Nitrogen_0.20_External_1_1" "JIC70_Nitrogen_0.20_External_1_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" -"N-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot6" "JIC71_Nitrogen_0.20_External_2_1" "JIC71_Nitrogen_0.20_External_2_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" -"N-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "N-0.2-aliquot7" "JIC72_Nitrogen_0.20_External_3_1" "JIC72_Nitrogen_0.20_External_3_1.txt" "" "" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" -"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_1" "JIC55_Carbon_0.07_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_2" "JIC55_Carbon_0.07_External_1_2.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot5" "JIC55_Carbon_0.07_External_1_3" "JIC55_Carbon_0.07_External_1_3.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot6" "JIC56_Carbon_0.07_External_2_1" "JIC56_Carbon_0.07_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.07-aliquot7" "JIC57_Carbon_0.07_External_3_1" "JIC57_Carbon_0.07_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.1-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot5" "JIC58_Carbon_0.10_External_1_1" "JIC58_Carbon_0.10_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" -"C-0.1-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot6" "JIC59_Carbon_0.10_External_2_1" "JIC59_Carbon_0.10_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" -"C-0.1-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.1-aliquot7" "JIC60_Carbon_0.10_External_3_1" "JIC60_Carbon_0.10_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" -"C-0.2-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot5" "JIC61_Carbon_0.20_External_1_1" "JIC61_Carbon_0.20_External_1_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" -"C-0.2-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot6" "JIC62_Carbon_0.20_External_2_1" "JIC62_Carbon_0.20_External_2_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" -"C-0.2-aliquot7" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "C-0.2-aliquot7" "JIC63_Carbon_0.20_External_3_1" "JIC63_Carbon_0.20_External_3_1.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" -"G-0.07-aliquot1" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.07-aliquot1" "JIC100_GlucoseO2_0.07_External_1_1" "JIC100_GlucoseO2_0.07_External_1_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.07" "l/hr" "" "" -"G-0.07-aliquot1" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.07-aliquot1" "JIC100_GlucoseO2_0.07_External_1_2" "JIC100_GlucoseO2_0.07_External_1_2.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.07" "l/hr" "" "" -"G-0.07-aliquot2" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.07-aliquot2" "JIC101_GlucoseO2_0.07_External_2_1" "JIC101_GlucoseO2_0.07_External_2_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.07" "l/hr" "" "" -"G-0.07-aliquot3" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.07-aliquot3" "JIC102_GlucoseO2_0.07_External_3_1" "JIC102_GlucoseO2_0.07_External_3_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.07" "l/hr" "" "" -"G-0.1-aliquot1" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.1-aliquot1" "JIC103_GlucoseO2_0.10_External_1_1" "JIC103_GlucoseO2_0.10_External_1_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.1" "l/hr" "" "" -"G-0.1-aliquot2" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.1-aliquot2" "JIC104_GlucoseO2_0.10_External_2_1" "JIC104_GlucoseO2_0.10_External_2_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.1" "l/hr" "" "" -"G-0.1-aliquot3" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.1-aliquot3" "JIC105_GlucoseO2_0.10_External_3_1" "JIC105_GlucoseO2_0.10_External_3_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.1" "l/hr" "" "" -"G-0.2-aliquot1" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.2-aliquot1" "JIC106_GlucoseO2_0.20_External_1_1" "JIC106_GlucoseO2_0.20_External_1_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.2" "l/hr" "" "" -"G-0.2-aliquot2" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.2-aliquot2" "JIC107_GlucoseO2_0.20_External_2_1" "JIC107_GlucoseO2_0.20_External_2_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.2" "l/hr" "" "" -"G-0.2-aliquot3" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "G-0.2-aliquot3" "JIC108_GlucoseO2_0.20_External_3_1" "JIC108_GlucoseO2_0.20_External_3_1.txt" "" "" "glucose" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_17234" "0.2" "l/hr" "" "" -"E-0.07-aliquot4" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.07-aliquot4" "JIC91_Ethanol_0.07_External_1_1" "JIC91_Ethanol_0.07_External_1_1.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.07" "l/hr" "" "" -"E-0.07-aliquot4" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.07-aliquot4" "JIC91_Ethanol_0.07_External_1_2" "JIC91_Ethanol_0.07_External_1_2.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.07" "l/hr" "" "" -"E-0.07-aliquot4" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.07-aliquot4" "JIC91_Ethanol_0.07_External_1_3" "JIC91_Ethanol_0.07_External_1_3.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.07" "l/hr" "" "" -"E-0.07-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.07-aliquot5" "JIC92_Ethanol_0.07_External_2_1" "JIC92_Ethanol_0.07_External_2_1.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.07" "l/hr" "" "" -"E-0.07-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.07-aliquot6" "JIC93_Ethanol_0.07_External_3_1" "JIC93_Ethanol_0.07_External_3_1.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.07" "l/hr" "" "" -"E-0.1-aliquot4" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.1-aliquot4" "JIC94_Ethanol_0.10_External_1_1" "JIC94_Ethanol_0.10_External_1_1.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.1" "l/hr" "" "" -"E-0.1-aliquot5" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.1-aliquot5" "JIC95_Ethanol_0.10_External_2_1" "JIC95_Ethanol_0.10_External_2_1.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.1" "l/hr" "" "" -"E-0.1-aliquot6" "extracellular region part" "CL" "http://purl.obolibrary.org/obo/GO_0044421" "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101" "E-0.1-aliquot6" "JIC96_Ethanol_0.10_External_3_1" "JIC96_Ethanol_0.10_External_3_1.txt" "" "" "ethanol" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_16236" "0.1" "l/hr" "" "" +Sample Name Material Type Protocol REF Parameter Value[standard volume] Unit Parameter Value[sample volume] Unit Extract Name MS Assay Name Raw Spectral Data File Comment[Data Repository] Comment[Data Record Accession] Factor Value[limiting nutrient] Factor Value[rate] Unit +C-0.1-aliquot1 intracellular metabolite extraction 4 microliter 200 microliter S-0.2-aliquot8 JIC36_Sulphate_0.20_Internal_1_3 JIC36_Sulphate_0.20_Internal_1_3.txt elemental sulfur 0.1 l/hour +P-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter P-0.07-aliquot8 JIC20_Phosphate_0.07_Internal_1_1 JIC20_Phosphate_0.07_Internal_1_1.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter P-0.07-aliquot9 JIC21_Phosphate_0.07_Internal_2_1 JIC21_Phosphate_0.07_Internal_2_1.txt elemental phosphorus 0.07 l/hr +P-0.1-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter P-0.1-aliquot8 JIC22_Phosphate_0.10_Internal_1_1 JIC22_Phosphate_0.10_Internal_1_1.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter P-0.1-aliquot9 JIC23_Phosphate_0.10_Internal_2_1 JIC23_Phosphate_0.10_Internal_2_1.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter P-0.1-aliquot10 JIC24_Phosphate_0.10_Internal_3_1 JIC24_Phosphate_0.10_Internal_3_1.txt elemental phosphorus 0.1 l/hr +P-0.2-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter P-0.2-aliquot8 JIC25_Phosphate_0.20_Internal_1_1 JIC25_Phosphate_0.20_Internal_1_1.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter P-0.2-aliquot9 JIC26_Phosphate_0.20_Internal_2_1 JIC26_Phosphate_0.20_Internal_2_1.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter P-0.2-aliquot10 JIC27_Phosphate_0.20_Internal_3_1 JIC27_Phosphate_0.20_Internal_3_1.txt elemental phosphorus 0.2 l/hr +N-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter N-0.07-aliquot8 JIC10_Nitrogen_0.07_Internal_1_1 JIC10_Nitrogen_0.07_Internal_1_1.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter N-0.07-aliquot8 JIC10_Nitrogen_0.07_Internal_1_2 JIC10_Nitrogen_0.07_Internal_1_2.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter N-0.07-aliquot8 JIC10_Nitrogen_0.07_Internal_1_3 JIC10_Nitrogen_0.07_Internal_1_3.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter N-0.07-aliquot9 JIC11_Nitrogen_0.07_Internal_2_1 JIC11_Nitrogen_0.07_Internal_2_1.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter N-0.07-aliquot10 JIC12_Nitrogen_0.07_Internal_3_1 JIC12_Nitrogen_0.07_Internal_3_1.txt elemental nitrogen 0.07 l/hr +N-0.1-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter N-0.1-aliquot8 JIC13_Nitrogen_0.10_Internal_1_1 JIC13_Nitrogen_0.10_Internal_1_1.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter N-0.1-aliquot9 JIC14_Nitrogen_0.10_Internal_2_1 JIC14_Nitrogen_0.10_Internal_2_1.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter N-0.1-aliquot10 JIC15_Nitrogen_0.10_Internal_3_1 JIC15_Nitrogen_0.10_Internal_3_1.txt elemental nitrogen 0.1 l/hr +N-0.2-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter N-0.2-aliquot8 JIC16_Nitrogen_0.20_Internal_1_1 JIC16_Nitrogen_0.20_Internal_1_1.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter N-0.2-aliquot9 JIC17_Nitrogen_0.20_Internal_2_1 JIC17_Nitrogen_0.20_Internal_2_1.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter N-0.2-aliquot10 JIC18_Nitrogen_0.20_Internal_3_1 JIC18_Nitrogen_0.20_Internal_3_1.txt elemental nitrogen 0.2 l/hr +C-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter C-0.07-aliquot8 JIC1_Carbon_0.07_Internal_1_1 JIC1_Carbon_0.07_Internal_1_1.txt elemental carbon 0.07 l/hr +C-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter C-0.07-aliquot8 JIC1_Carbon_0.07_Internal_1_2 JIC1_Carbon_0.07_Internal_1_2.txt elemental carbon 0.07 l/hr +C-0.07-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter C-0.07-aliquot8 JIC1_Carbon_0.07_Internal_1_3 JIC1_Carbon_0.07_Internal_1_3.txt elemental carbon 0.07 l/hr +C-0.07-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter C-0.07-aliquot9 JIC2_Carbon_0.07_Internal_2_1 JIC2_Carbon_0.07_Internal_2_1.txt elemental carbon 0.07 l/hr +C-0.07-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter C-0.07-aliquot10 JIC3_Carbon_0.07_Internal_3_1 JIC3_Carbon_0.07_Internal_3_1.txt elemental carbon 0.07 l/hr +C-0.1-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter C-0.1-aliquot8 JIC4_Carbon_0.10_Internal_1_1 JIC4_Carbon_0.10_Internal_1_1.txt elemental carbon 0.1 l/hr +C-0.1-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter C-0.1-aliquot9 JIC5_Carbon_0.10_Internal_2_1 JIC5_Carbon_0.10_Internal_2_1.txt elemental carbon 0.1 l/hr +C-0.1-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter C-0.1-aliquot10 JIC6_Carbon_0.10_Internal_3_1 JIC6_Carbon_0.10_Internal_3_1.txt elemental carbon 0.1 l/hr +C-0.2-aliquot8 intracellular metabolite extraction 4 microliter 200 microliter C-0.2-aliquot8 JIC7_Carbon_0.20_Internal_1_1 JIC7_Carbon_0.20_Internal_1_1.txt elemental carbon 0.2 l/hr +C-0.2-aliquot9 intracellular metabolite extraction 4 microliter 200 microliter C-0.2-aliquot9 JIC8_Carbon_0.20_Internal_2_1 JIC8_Carbon_0.20_Internal_2_1.txt elemental carbon 0.2 l/hr +C-0.2-aliquot10 intracellular metabolite extraction 4 microliter 200 microliter C-0.2-aliquot10 JIC9_Carbon_0.20_Internal_3_1 JIC9_Carbon_0.20_Internal_3_1.txt elemental carbon 0.2 l/hr +G-0.07-aliquot4 intracellular metabolite extraction 4 microliter 200 microliter G-0.07-aliquot4 JIC46_GlucoseO2_0.07_Internal_1_1 JIC46_GlucoseO2_0.07_Internal_1_1.txt glucose 0.07 l/hr +G-0.07-aliquot4 intracellular metabolite extraction 4 microliter 200 microliter G-0.07-aliquot4 JIC46_GlucoseO2_0.07_Internal_1_2 JIC46_GlucoseO2_0.07_Internal_1_2.txt glucose 0.07 l/hr +G-0.07-aliquot4 intracellular metabolite extraction 4 microliter 200 microliter G-0.07-aliquot4 JIC46_GlucoseO2_0.07_Internal_1_3 JIC46_GlucoseO2_0.07_Internal_1_3.txt glucose 0.07 l/hr +G-0.07-aliquot5 intracellular metabolite extraction 4 microliter 200 microliter G-0.07-aliquot5 JIC47_GlucoseO2_0.07_Internal_2_1 JIC47_GlucoseO2_0.07_Internal_2_1.txt glucose 0.07 l/hr +G-0.07-aliquot6 intracellular metabolite extraction 4 microliter 200 microliter G-0.07-aliquot6 JIC48_GlucoseO2_0.07_Internal_3_1 JIC48_GlucoseO2_0.07_Internal_3_1.txt glucose 0.07 l/hr +G-0.1-aliquot4 intracellular metabolite extraction 4 microliter 200 microliter G-0.1-aliquot4 JIC49_GlucoseO2_0.10_Internal_1_1 JIC49_GlucoseO2_0.10_Internal_1_1.txt glucose 0.1 l/hr +G-0.1-aliquot5 intracellular metabolite extraction 4 microliter 200 microliter G-0.1-aliquot5 JIC50_GlucoseO2_0.10_Internal_2_1 JIC50_GlucoseO2_0.10_Internal_2_1.txt glucose 0.1 l/hr +G-0.1-aliquot6 intracellular metabolite extraction 4 microliter 200 microliter G-0.1-aliquot6 JIC51_GlucoseO2_0.10_Internal_3_1 JIC51_GlucoseO2_0.10_Internal_3_1.txt glucose 0.1 l/hr +G-0.2-aliquot4 intracellular metabolite extraction 4 microliter 200 microliter G-0.2-aliquot4 JIC52_GlucoseO2_0.20_Internal_1_1 JIC52_GlucoseO2_0.20_Internal_1_1.txt glucose 0.2 l/hr +G-0.2-aliquot5 intracellular metabolite extraction 4 microliter 200 microliter G-0.2-aliquot5 JIC53_GlucoseO2_0.20_Internal_2_1 JIC53_GlucoseO2_0.20_Internal_2_1.txt glucose 0.2 l/hr +G-0.2-aliquot6 intracellular metabolite extraction 4 microliter 200 microliter G-0.2-aliquot6 JIC54_GlucoseO2_0.20_Internal_3_1 JIC54_GlucoseO2_0.20_Internal_3_1.txt glucose 0.2 l/hr +E-0.07-aliquot1 intracellular metabolite extraction 4 microliter 200 microliter E-0.07-aliquot1 JIC37_Ethanol_0.07_Internal_1_1 JIC37_Ethanol_0.07_Internal_1_1.txt ethanol 0.07 l/hr +E-0.07-aliquot1 intracellular metabolite extraction 4 microliter 200 microliter E-0.07-aliquot1 JIC37_Ethanol_0.07_Internal_1_2 JIC37_Ethanol_0.07_Internal_1_2.txt ethanol 0.07 l/hr +E-0.07-aliquot1 intracellular metabolite extraction 4 microliter 200 microliter E-0.07-aliquot1 JIC37_Ethanol_0.07_Internal_1_3 JIC37_Ethanol_0.07_Internal_1_3.txt ethanol 0.07 l/hr +E-0.07-aliquot2 intracellular metabolite extraction 4 microliter 200 microliter E-0.07-aliquot2 JIC38_Ethanol_0.07_Internal_2_1 JIC38_Ethanol_0.07_Internal_2_1.txt ethanol 0.07 l/hr +E-0.07-aliquot3 intracellular metabolite extraction 4 microliter 200 microliter E-0.07-aliquot3 JIC39_Ethanol_0.07_Internal_3_1 JIC39_Ethanol_0.07_Internal_3_1.txt ethanol 0.07 l/hr +E-0.1-aliquot1 intracellular metabolite extraction 4 microliter 200 microliter E-0.1-aliquot1 JIC40_Ethanol_0.10_Internal_1_1 JIC40_Ethanol_0.10_Internal_1_1.txt ethanol 0.1 l/hr +E-0.1-aliquot2 intracellular metabolite extraction 4 microliter 200 microliter E-0.1-aliquot2 JIC41_Ethanol_0.10_Internal_2_1 JIC41_Ethanol_0.10_Internal_2_1.txt ethanol 0.1 l/hr +E-0.1-aliquot3 intracellular metabolite extraction 4 microliter 200 microliter E-0.1-aliquot3 JIC42_Ethanol_0.10_Internal_3_1 JIC42_Ethanol_0.10_Internal_3_1.txt ethanol 0.1 l/hr +S-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.07-aliquot5 JIC82_Sulphate_0.07_External_1_1 JIC82_Sulphate_0.07_External_1_1.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.07-aliquot6 JIC83_Sulphate_0.07_External_2_1 JIC83_Sulphate_0.07_External_2_1.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.07-aliquot7 JIC84_Sulphate_0.07_External_3_1 JIC84_Sulphate_0.07_External_3_1.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.07-aliquot5 JIC82_Sulphate_0.07_External_1_2 JIC82_Sulphate_0.07_External_1_2.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.07-aliquot5 JIC82_Sulphate_0.07_External_1_3 JIC82_Sulphate_0.07_External_1_3.txt elemental sulfur 0.07 l/hr +S-0.1-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.1-aliquot5 JIC85_Sulphate_0.10_External_1_1 JIC85_Sulphate_0.10_External_1_1.txt elemental sulfur 0.1 l/hr +S-0.1-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.1-aliquot6 JIC86_Sulphate_0.10_External_2_1 JIC86_Sulphate_0.10_External_2_1.txt elemental sulfur 0.1 l/hr +S-0.2-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.2-aliquot5 JIC88_Sulphate_0.20_External_1_1 JIC88_Sulphate_0.20_External_1_1.txt elemental sulfur 0.2 l/hr +S-0.2-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.2-aliquot6 JIC89_Sulphate_0.20_External_2_1 JIC89_Sulphate_0.20_External_2_1.txt elemental sulfur 0.2 l/hr +S-0.2-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter S-0.2-aliquot7 JIC90_Sulphate_0.20_External_3_1 JIC90_Sulphate_0.20_External_3_1.txt elemental sulfur 0.2 l/hr +P-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.07-aliquot5 JIC73_Phosphate_0.07_External_1_1 JIC73_Phosphate_0.07_External_1_1.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.07-aliquot6 JIC73_Phosphate_0.07_External_1_2 JIC73_Phosphate_0.07_External_1_2.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.07-aliquot7 JIC73_Phosphate_0.07_External_1_3 JIC73_Phosphate_0.07_External_1_3.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.07-aliquot5 JIC74_Phosphate_0.07_External_2_1 JIC74_Phosphate_0.07_External_2_1.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.07-aliquot5 JIC75_Phosphate_0.07_External_3_1 JIC75_Phosphate_0.07_External_3_1.txt elemental phosphorus 0.07 l/hr +P-0.1-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.1-aliquot5 JIC76_Phosphate_0.10_External_1_1 JIC76_Phosphate_0.10_External_1_1.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.1-aliquot6 JIC77_Phosphate_0.10_External_2_1 JIC77_Phosphate_0.10_External_2_1.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.1-aliquot7 JIC78_Phosphate_0.10_External_3_1 JIC78_Phosphate_0.10_External_3_1.txt elemental phosphorus 0.1 l/hr +P-0.2-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.2-aliquot5 JIC79_Phosphate_0.20_External_1_1 JIC79_Phosphate_0.20_External_1_1.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.2-aliquot6 JIC80_Phosphate_0.20_External_2_1 JIC80_Phosphate_0.20_External_2_1.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter P-0.2-aliquot7 JIC81_Phosphate_0.20_External_3_1 JIC81_Phosphate_0.20_External_3_1.txt elemental phosphorus 0.2 l/hr +N-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.07-aliquot5 JIC64_Nitrogen_0.07_External_1_1 JIC64_Nitrogen_0.07_External_1_1.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.07-aliquot5 JIC64_Nitrogen_0.07_External_1_2 JIC64_Nitrogen_0.07_External_1_2.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.07-aliquot5 JIC64_Nitrogen_0.07_External_1_3 JIC64_Nitrogen_0.07_External_1_3.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.07-aliquot6 JIC65_Nitrogen_0.07_External_2_1 JIC65_Nitrogen_0.07_External_2_1.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.07-aliquot7 JIC66_Nitrogen_0.07_External_3_1 JIC66_Nitrogen_0.07_External_3_1.txt elemental nitrogen 0.07 l/hr +N-0.1-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.1-aliquot5 JIC67_Nitrogen_0.10_External_1_1 JIC67_Nitrogen_0.10_External_1_1.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.1-aliquot6 JIC68_Nitrogen_0.10_External_2_1 JIC68_Nitrogen_0.10_External_2_1.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.1-aliquot7 JIC69_Nitrogen_0.10_External_3_1 JIC69_Nitrogen_0.10_External_3_1.txt elemental nitrogen 0.1 l/hr +N-0.2-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.2-aliquot5 JIC70_Nitrogen_0.20_External_1_1 JIC70_Nitrogen_0.20_External_1_1.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.2-aliquot6 JIC71_Nitrogen_0.20_External_2_1 JIC71_Nitrogen_0.20_External_2_1.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter N-0.2-aliquot7 JIC72_Nitrogen_0.20_External_3_1 JIC72_Nitrogen_0.20_External_3_1.txt elemental nitrogen 0.2 l/hr +C-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.07-aliquot5 JIC55_Carbon_0.07_External_1_1 JIC55_Carbon_0.07_External_1_1.txt elemental carbon 0.07 l/hr +C-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.07-aliquot5 JIC55_Carbon_0.07_External_1_2 JIC55_Carbon_0.07_External_1_2.txt elemental carbon 0.07 l/hr +C-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.07-aliquot5 JIC55_Carbon_0.07_External_1_3 JIC55_Carbon_0.07_External_1_3.txt elemental carbon 0.07 l/hr +C-0.07-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.07-aliquot6 JIC56_Carbon_0.07_External_2_1 JIC56_Carbon_0.07_External_2_1.txt elemental carbon 0.07 l/hr +C-0.07-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.07-aliquot7 JIC57_Carbon_0.07_External_3_1 JIC57_Carbon_0.07_External_3_1.txt elemental carbon 0.07 l/hr +C-0.1-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.1-aliquot5 JIC58_Carbon_0.10_External_1_1 JIC58_Carbon_0.10_External_1_1.txt elemental carbon 0.1 l/hr +C-0.1-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.1-aliquot6 JIC59_Carbon_0.10_External_2_1 JIC59_Carbon_0.10_External_2_1.txt elemental carbon 0.1 l/hr +C-0.1-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.1-aliquot7 JIC60_Carbon_0.10_External_3_1 JIC60_Carbon_0.10_External_3_1.txt elemental carbon 0.1 l/hr +C-0.2-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.2-aliquot5 JIC61_Carbon_0.20_External_1_1 JIC61_Carbon_0.20_External_1_1.txt elemental carbon 0.2 l/hr +C-0.2-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.2-aliquot6 JIC62_Carbon_0.20_External_2_1 JIC62_Carbon_0.20_External_2_1.txt elemental carbon 0.2 l/hr +C-0.2-aliquot7 extracellular region part metabolite extraction 20 microliter 1000 microliter C-0.2-aliquot7 JIC63_Carbon_0.20_External_3_1 JIC63_Carbon_0.20_External_3_1.txt elemental carbon 0.2 l/hr +G-0.07-aliquot1 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.07-aliquot1 JIC100_GlucoseO2_0.07_External_1_1 JIC100_GlucoseO2_0.07_External_1_1.txt glucose 0.07 l/hr +G-0.07-aliquot1 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.07-aliquot1 JIC100_GlucoseO2_0.07_External_1_2 JIC100_GlucoseO2_0.07_External_1_2.txt glucose 0.07 l/hr +G-0.07-aliquot2 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.07-aliquot2 JIC101_GlucoseO2_0.07_External_2_1 JIC101_GlucoseO2_0.07_External_2_1.txt glucose 0.07 l/hr +G-0.07-aliquot3 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.07-aliquot3 JIC102_GlucoseO2_0.07_External_3_1 JIC102_GlucoseO2_0.07_External_3_1.txt glucose 0.07 l/hr +G-0.1-aliquot1 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.1-aliquot1 JIC103_GlucoseO2_0.10_External_1_1 JIC103_GlucoseO2_0.10_External_1_1.txt glucose 0.1 l/hr +G-0.1-aliquot2 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.1-aliquot2 JIC104_GlucoseO2_0.10_External_2_1 JIC104_GlucoseO2_0.10_External_2_1.txt glucose 0.1 l/hr +G-0.1-aliquot3 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.1-aliquot3 JIC105_GlucoseO2_0.10_External_3_1 JIC105_GlucoseO2_0.10_External_3_1.txt glucose 0.1 l/hr +G-0.2-aliquot1 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.2-aliquot1 JIC106_GlucoseO2_0.20_External_1_1 JIC106_GlucoseO2_0.20_External_1_1.txt glucose 0.2 l/hr +G-0.2-aliquot2 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.2-aliquot2 JIC107_GlucoseO2_0.20_External_2_1 JIC107_GlucoseO2_0.20_External_2_1.txt glucose 0.2 l/hr +G-0.2-aliquot3 extracellular region part metabolite extraction 20 microliter 1000 microliter G-0.2-aliquot3 JIC108_GlucoseO2_0.20_External_3_1 JIC108_GlucoseO2_0.20_External_3_1.txt glucose 0.2 l/hr +E-0.07-aliquot4 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.07-aliquot4 JIC91_Ethanol_0.07_External_1_1 JIC91_Ethanol_0.07_External_1_1.txt ethanol 0.07 l/hr +E-0.07-aliquot4 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.07-aliquot4 JIC91_Ethanol_0.07_External_1_2 JIC91_Ethanol_0.07_External_1_2.txt ethanol 0.07 l/hr +E-0.07-aliquot4 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.07-aliquot4 JIC91_Ethanol_0.07_External_1_3 JIC91_Ethanol_0.07_External_1_3.txt ethanol 0.07 l/hr +E-0.07-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.07-aliquot5 JIC92_Ethanol_0.07_External_2_1 JIC92_Ethanol_0.07_External_2_1.txt ethanol 0.07 l/hr +E-0.07-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.07-aliquot6 JIC93_Ethanol_0.07_External_3_1 JIC93_Ethanol_0.07_External_3_1.txt ethanol 0.07 l/hr +E-0.1-aliquot4 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.1-aliquot4 JIC94_Ethanol_0.10_External_1_1 JIC94_Ethanol_0.10_External_1_1.txt ethanol 0.1 l/hr +E-0.1-aliquot5 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.1-aliquot5 JIC95_Ethanol_0.10_External_2_1 JIC95_Ethanol_0.10_External_2_1.txt ethanol 0.1 l/hr +E-0.1-aliquot6 extracellular region part metabolite extraction 20 microliter 1000 microliter E-0.1-aliquot6 JIC96_Ethanol_0.10_External_3_1 JIC96_Ethanol_0.10_External_3_1.txt ethanol 0.1 l/hr diff --git a/src/test/resources/test-data/BII-I-1/a_microarray.txt b/src/test/resources/test-data/BII-I-1/a_microarray.txt index 23a36f92..0c0544e5 100644 --- a/src/test/resources/test-data/BII-I-1/a_microarray.txt +++ b/src/test/resources/test-data/BII-I-1/a_microarray.txt @@ -1,15 +1,15 @@ -"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "Protocol REF" "Hybridization Assay Name" "Comment[ArrayExpress Accession]" "Comment[ArrayExpress Raw Data URL]" "Comment[ArrayExpress Processed Data URL]" "Array Design REF" "Scan Name" "Array Data File" "Comment[Data Repository]" "Comment[Data Record Accession]" "Data Transformation Name" "Derived Array Data File" "Factor Value[dose]" "Unit" "Term Source REF" "Term Accession Number" "Factor Value[exposure time]" "Unit" "Term Source REF" "Term Accession Number" "Factor Value[compound]" "Term Source REF" "Term Accession Number" -"NZ_0hrs_Grow1_Sample_1" "mRNA extraction" "NZ_0hrs_Sample_1_Extract" "biotin labeling" "NZ_0hrs_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_0hrs_Sample_1_Labelled_Hyb1" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_0hrs_Sample_1_Labelled_Hyb1_Scan1" "E-MAXD-4-raw-data-426648549.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "0" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "" "" "" -"NZ_1hrs_Grow1_Drug_Sample_1" "mRNA extraction" "NZ_1hrs_Drug_Sample_1_Extract" "biotin labeling" "NZ_1hrs_Drug_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_1hrs_Drug_Sample_1_Labelled_Hyb3" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_1hrs_Drug_Sample_1_Labelled_Hyb3_Scan3" "E-MAXD-4-raw-data-426648567.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_2hrs_Grow1_Drug_Sample_1" "mRNA extraction" "NZ_2hrs_Drug_Sample_1_Extract" "biotin labeling" "NZ_2hrs_Drug_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Drug_Sample_1_Labelled_Hyb7" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Drug_Sample_1_Labelled_Hyb7_Scan7" "E-MAXD-4-raw-data-426648585.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_4hrs_Grow1_Drug_Sample_1" "mRNA extraction" "NZ_4hrs_Drug_Sample_1_Extract" "biotin labeling" "NZ_4hrs_Drug_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Drug_Sample_1_Labelled_Hyb11" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Drug_Sample_1_Labelled_Hyb11_Scan11" "E-MAXD-4-raw-data-426648603.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_2hrs_Grow1_Vehicle_Sample_1" "mRNA extraction" "NZ_2hrs_Vehicle_Sample_1_Extract" "biotin labeling" "NZ_2hrs_Vehicle_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Vehicle_Sample_1_Labelled_Hyb9" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Vehicle_Sample_1_Labelled_Hyb9_Scan9" "E-MAXD-4-raw-data-426648639.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_4hrs_Grow1_Vehicle_Sample_1" "mRNA extraction" "NZ_4hrs_Vehicle_Sample_1_Extract" "biotin labeling" "NZ_4hrs_Vehicle_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Vehicle_Sample_1_Labelled_Hyb13" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Vehicle_Sample_1_Labelled_Hyb13_Scan13" "E-MAXD-4-raw-data-426648657.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_1hrs_Grow1_Vehicle_Sample_1" "mRNA extraction" "NZ_1hrs_Vehicle_Sample_1_Extract" "biotin labeling" "NZ_1hrs_Vehicle_Sample_1_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_1hrs_Vehicle_Sample_1_Labelled_Hyb5" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_1hrs_Vehicle_Sample_1_Labelled_Hyb5_Scan5" "E-MAXD-4-raw-data-426648621.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_0hrs_Grow2_Sample_2" "mRNA extraction" "NZ_0hrs_Sample_2_Extract" "biotin labeling" "NZ_0hrs_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_0hrs_Sample_2_Labelled_Hyb2" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_0hrs_Sample_2_Labelled_Hyb2_Scan2" "E-MAXD-4-raw-data-426648675.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "0" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "" "" "" -"NZ_1hrs_Grow2_Drug_Sample_2" "mRNA extraction" "NZ_1hrs_Drug_Sample_2_Extract" "biotin labeling" "NZ_1hrs_Drug_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_1hrs_Drug_Sample_2_Labelled_Hyb4" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_1hrs_Drug_Sample_2_Labelled_Hyb4_Scan4" "E-MAXD-4-raw-data-426648693.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_4hrs_Grow2_Drug_Sample_2" "mRNA extraction" "NZ_4hrs_Drug_Sample_2_Extract" "biotin labeling" "NZ_4hrs_Drug_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Drug_Sample_2_Labelled_Hyb12" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Drug_Sample_2_Labelled_Hyb12_Scan12" "E-MAXD-4-raw-data-426648729.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_2hrs_Grow2_Drug_Sample_2" "mRNA extraction" "NZ_2hrs_Drug_Sample_2_Extract" "biotin labeling" "NZ_2hrs_Drug_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Drug_Sample_2_Labelled_Hyb8" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Drug_Sample_2_Labelled_Hyb8_Scan8" "E-MAXD-4-raw-data-426648711.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_1hrs_Grow2_Vehicle_Sample_2" "mRNA extraction" "NZ_1hrs_Vehicle_Sample_2_Extract" "biotin labeling" "NZ_1hrs_Vehicle_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_1hrs_Vehicle_Sample_2_Labelled_Hyb6" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_1hrs_Vehicle_Sample_2_Labelled_Hyb6_Scan6" "E-MAXD-4-raw-data-426648747.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_2hrs_Grow2_Vehicle_Sample_2" "mRNA extraction" "NZ_2hrs_Vehicle_Sample_2_Extract" "biotin labeling" "NZ_2hrs_Vehicle_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_2hrs_Vehicle_Sample_2_Labelled_Hyb10" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_2hrs_Vehicle_Sample_2_Labelled_Hyb10_Scan10" "E-MAXD-4-raw-data-426648765.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_4hrs_Grow2_Vehicle_Sample_2" "mRNA extraction" "NZ_4hrs_Vehicle_Sample_2_Extract" "biotin labeling" "NZ_4hrs_Vehicle_Sample_2_Labelled" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14" "E-MEXP-115" "E-MEXP-115" "E-MEXP-115" "A-AFFY-27" "NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14_Scan14" "E-MAXD-4-raw-data-426648783.txt" "" "" "data processing" "E-MAXD-4-processed-data-1342566476.txt" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" +Sample Name Protocol REF Extract Name Protocol REF Labeled Extract Name Label Protocol REF Hybridization Assay Name Comment[ArrayExpress Accession] Comment[ArrayExpress Raw Data URL] Comment[ArrayExpress Processed Data URL] Array Design REF Scan Name Array Data File Comment[Data Repository] Comment[Data Record Accession] Data Transformation Name Derived Array Data File Factor Value[dose] Unit Factor Value[exposure time] Unit Factor Value[compound] +NZ_0hrs_Grow1_Sample_1 mRNA extraction NZ_0hrs_Sample_1_Extract biotin labeling NZ_0hrs_Sample_1_Labelled biotin EukGE-WS4 NZ_0hrs_Sample_1_Labelled_Hyb1 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_0hrs_Sample_1_Labelled_Hyb1_Scan1 E-MAXD-4-raw-data-426648549.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 0 hour +NZ_1hrs_Grow1_Drug_Sample_1 mRNA extraction NZ_1hrs_Drug_Sample_1_Extract biotin labeling NZ_1hrs_Drug_Sample_1_Labelled biotin EukGE-WS4 NZ_1hrs_Drug_Sample_1_Labelled_Hyb3 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_1hrs_Drug_Sample_1_Labelled_Hyb3_Scan3 E-MAXD-4-raw-data-426648567.txt data processing E-MAXD-4-processed-data-1342566476.txt 200 nanogram per milliliter 1 hour sirolimus +NZ_2hrs_Grow1_Drug_Sample_1 mRNA extraction NZ_2hrs_Drug_Sample_1_Extract biotin labeling NZ_2hrs_Drug_Sample_1_Labelled biotin EukGE-WS4 NZ_2hrs_Drug_Sample_1_Labelled_Hyb7 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_2hrs_Drug_Sample_1_Labelled_Hyb7_Scan7 E-MAXD-4-raw-data-426648585.txt data processing E-MAXD-4-processed-data-1342566476.txt 200 nanogram per milliliter 2 hour sirolimus +NZ_4hrs_Grow1_Drug_Sample_1 mRNA extraction NZ_4hrs_Drug_Sample_1_Extract biotin labeling NZ_4hrs_Drug_Sample_1_Labelled biotin EukGE-WS4 NZ_4hrs_Drug_Sample_1_Labelled_Hyb11 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_4hrs_Drug_Sample_1_Labelled_Hyb11_Scan11 E-MAXD-4-raw-data-426648603.txt data processing E-MAXD-4-processed-data-1342566476.txt 200 nanogram per milliliter 4 hour sirolimus +NZ_2hrs_Grow1_Vehicle_Sample_1 mRNA extraction NZ_2hrs_Vehicle_Sample_1_Extract biotin labeling NZ_2hrs_Vehicle_Sample_1_Labelled biotin EukGE-WS4 NZ_2hrs_Vehicle_Sample_1_Labelled_Hyb9 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_2hrs_Vehicle_Sample_1_Labelled_Hyb9_Scan9 E-MAXD-4-raw-data-426648639.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 2 hour drug vehicle (90% ethanol/10% tween-20) +NZ_4hrs_Grow1_Vehicle_Sample_1 mRNA extraction NZ_4hrs_Vehicle_Sample_1_Extract biotin labeling NZ_4hrs_Vehicle_Sample_1_Labelled biotin EukGE-WS4 NZ_4hrs_Vehicle_Sample_1_Labelled_Hyb13 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_4hrs_Vehicle_Sample_1_Labelled_Hyb13_Scan13 E-MAXD-4-raw-data-426648657.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 4 hour drug vehicle (90% ethanol/10% tween-20) +NZ_1hrs_Grow1_Vehicle_Sample_1 mRNA extraction NZ_1hrs_Vehicle_Sample_1_Extract biotin labeling NZ_1hrs_Vehicle_Sample_1_Labelled biotin EukGE-WS4 NZ_1hrs_Vehicle_Sample_1_Labelled_Hyb5 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_1hrs_Vehicle_Sample_1_Labelled_Hyb5_Scan5 E-MAXD-4-raw-data-426648621.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 1 hour drug vehicle (90% ethanol/10% tween-20) +NZ_0hrs_Grow2_Sample_2 mRNA extraction NZ_0hrs_Sample_2_Extract biotin labeling NZ_0hrs_Sample_2_Labelled biotin EukGE-WS4 NZ_0hrs_Sample_2_Labelled_Hyb2 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_0hrs_Sample_2_Labelled_Hyb2_Scan2 E-MAXD-4-raw-data-426648675.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 0 hour +NZ_1hrs_Grow2_Drug_Sample_2 mRNA extraction NZ_1hrs_Drug_Sample_2_Extract biotin labeling NZ_1hrs_Drug_Sample_2_Labelled biotin EukGE-WS4 NZ_1hrs_Drug_Sample_2_Labelled_Hyb4 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_1hrs_Drug_Sample_2_Labelled_Hyb4_Scan4 E-MAXD-4-raw-data-426648693.txt data processing E-MAXD-4-processed-data-1342566476.txt 200 nanogram per milliliter 1 hour sirolimus +NZ_4hrs_Grow2_Drug_Sample_2 mRNA extraction NZ_4hrs_Drug_Sample_2_Extract biotin labeling NZ_4hrs_Drug_Sample_2_Labelled biotin EukGE-WS4 NZ_4hrs_Drug_Sample_2_Labelled_Hyb12 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_4hrs_Drug_Sample_2_Labelled_Hyb12_Scan12 E-MAXD-4-raw-data-426648729.txt data processing E-MAXD-4-processed-data-1342566476.txt 200 nanogram per milliliter 4 hour sirolimus +NZ_2hrs_Grow2_Drug_Sample_2 mRNA extraction NZ_2hrs_Drug_Sample_2_Extract biotin labeling NZ_2hrs_Drug_Sample_2_Labelled biotin EukGE-WS4 NZ_2hrs_Drug_Sample_2_Labelled_Hyb8 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_2hrs_Drug_Sample_2_Labelled_Hyb8_Scan8 E-MAXD-4-raw-data-426648711.txt data processing E-MAXD-4-processed-data-1342566476.txt 200 nanogram per milliliter 2 hour sirolimus +NZ_1hrs_Grow2_Vehicle_Sample_2 mRNA extraction NZ_1hrs_Vehicle_Sample_2_Extract biotin labeling NZ_1hrs_Vehicle_Sample_2_Labelled biotin EukGE-WS4 NZ_1hrs_Vehicle_Sample_2_Labelled_Hyb6 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_1hrs_Vehicle_Sample_2_Labelled_Hyb6_Scan6 E-MAXD-4-raw-data-426648747.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 1 hour drug vehicle (90% ethanol/10% tween-20) +NZ_2hrs_Grow2_Vehicle_Sample_2 mRNA extraction NZ_2hrs_Vehicle_Sample_2_Extract biotin labeling NZ_2hrs_Vehicle_Sample_2_Labelled biotin EukGE-WS4 NZ_2hrs_Vehicle_Sample_2_Labelled_Hyb10 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_2hrs_Vehicle_Sample_2_Labelled_Hyb10_Scan10 E-MAXD-4-raw-data-426648765.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 2 hour drug vehicle (90% ethanol/10% tween-20) +NZ_4hrs_Grow2_Vehicle_Sample_2 mRNA extraction NZ_4hrs_Vehicle_Sample_2_Extract biotin labeling NZ_4hrs_Vehicle_Sample_2_Labelled biotin EukGE-WS4 NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14 E-MEXP-115 E-MEXP-115 E-MEXP-115 A-AFFY-27 NZ_4hrs_Vehicle_Sample_2_Labelled_Hyb14_Scan14 E-MAXD-4-raw-data-426648783.txt data processing E-MAXD-4-processed-data-1342566476.txt 0 nanogram per milliliter 4 hour drug vehicle (90% ethanol/10% tween-20) diff --git a/src/test/resources/test-data/BII-I-1/a_proteome.txt b/src/test/resources/test-data/BII-I-1/a_proteome.txt index a6894d46..25f7b9dc 100644 --- a/src/test/resources/test-data/BII-I-1/a_proteome.txt +++ b/src/test/resources/test-data/BII-I-1/a_proteome.txt @@ -1,19 +1,19 @@ -"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "MS Assay Name" "Comment[PRIDE Accession]" "Comment[PRIDE Processed Data Accession]" "Raw Spectral Data File" "Comment[Data Record Accession]" "Comment[Data Repository]" "Normalization Name" "Protein Assignment File" "Peptide Assignment File" "Post Translational Modification Assignment File" "Data Transformation Name" "Derived Spectral Data File" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"S-0.1-aliquot11" "protein extraction" "S-0.1" "ITRAQ labeling" "JC_S-0.1" "iTRAQ reagent 117" "" "" "8761" "8761" "8761" "spectrum.mzdata" "" "" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.1" "l/hr" "" "" -"C-0.1-aliquot11" "protein extraction" "C-0.1" "ITRAQ labeling" "JC_C-0.1" "iTRAQ reagent 116" "" "" "8761" "8761" "8761" "spectrum.mzdata" "" "" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" -"N-0.1-aliquot11" "protein extraction" "N-0.1" "ITRAQ labeling" "JC_N-0.1" "iTRAQ reagent 115" "" "" "8761" "8761" "8761" "spectrum.mzdata" "" "" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.1" "l/hr" "" "" -"S-0.1-aliquot11" "protein extraction" "S-0.1" "ITRAQ labeling" "Pool1" "iTRAQ reagent 114" "" "" "8761" "8761" "8761" "spectrum.mzdata" "" "" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "" "" "" "" "l/hr" "" "" -"C-0.1-aliquot11" "protein extraction" "C-0.1" "ITRAQ labeling" "Pool1" "iTRAQ reagent 114" "" "" "8761" "8761" "8761" "spectrum.mzdata" "" "" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "" "" "" "" "l/hr" "" "" -"N-0.1-aliquot11" "protein extraction" "N-0.1" "ITRAQ labeling" "Pool1" "iTRAQ reagent 114" "" "" "8761" "8761" "8761" "spectrum.mzdata" "" "" "norm1" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation1" "PRIDE_Exp_Complete_Ac_8761.xml" "" "" "" "" "l/hr" "" "" -"C-0.2-aliquot11" "protein extraction" "C-0.2" "ITRAQ labeling" "JC_C-0.2" "iTRAQ reagent 117" "" "" "8762" "8762" "8762" "spectrum.mzdata" "" "" "norm2" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation2" "PRIDE_Exp_Complete_Ac_8762.xml" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.2" "l/hr" "" "" -"N-0.2-aliquot11" "protein extraction" "N-0.2" "ITRAQ labeling" "JC_N-0.2" "iTRAQ reagent 116" "" "" "8762" "8762" "8762" "spectrum.mzdata" "" "" "norm2" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation2" "PRIDE_Exp_Complete_Ac_8762.xml" "elemental nitrogen" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33267" "0.2" "l/hr" "" "" -"P-0.1-aliquot11" "protein extraction" "P-0.1" "ITRAQ labeling" "JC_P-0.1" "iTRAQ reagent 115" "" "" "8762" "8762" "8762" "spectrum.mzdata" "" "" "norm2" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation2" "PRIDE_Exp_Complete_Ac_8762.xml" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.1" "l/hr" "" "" -"C-0.2-aliquot11" "protein extraction" "C-0.2" "ITRAQ labeling" "Pool2" "iTRAQ reagent 114" "" "" "8762" "8762" "8762" "spectrum.mzdata" "" "" "norm2" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation2" "PRIDE_Exp_Complete_Ac_8762.xml" "" "" "" "" "l/hr" "" "" -"N-0.2-aliquot11" "protein extraction" "N-0.2" "ITRAQ labeling" "Pool2" "iTRAQ reagent 114" "" "" "8762" "8762" "8762" "spectrum.mzdata" "" "" "norm2" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation2" "PRIDE_Exp_Complete_Ac_8762.xml" "" "" "" "" "l/hr" "" "" -"P-0.1-aliquot11" "protein extraction" "P-0.1" "ITRAQ labeling" "Pool2" "iTRAQ reagent 114" "" "" "8762" "8762" "8762" "spectrum.mzdata" "" "" "norm2" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation2" "PRIDE_Exp_Complete_Ac_8762.xml" "" "" "" "" "l/hr" "" "" -"P-0.2-aliquot11" "protein extraction" "P-0.2" "ITRAQ labeling" "JC_P-0.2" "iTRAQ reagent 116" "" "" "8763" "8763" "8763" "spectrum.mzdata" "" "" "norm3" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation3" "PRIDE_Exp_Complete_Ac_8763.xml" "elemental phosphorus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33464" "0.2" "l/hr" "" "" -"S-0.2-aliquot11" "protein extraction" "S-0.2" "ITRAQ labeling" "JC_S-0.2" "iTRAQ reagent 115" "" "" "8763" "8763" "8763" "spectrum.mzdata" "" "" "norm3" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation3" "PRIDE_Exp_Complete_Ac_8763.xml" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" -"P-0.2-aliquot11" "protein extraction" "P-0.2" "ITRAQ labeling" "Pool3" "iTRAQ reagent 117" "" "" "8763" "8763" "8763" "spectrum.mzdata" "" "" "norm3" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation3" "PRIDE_Exp_Complete_Ac_8763.xml" "" "" "" "" "l/hr" "" "" -"S-0.2-aliquot11" "protein extraction" "S-0.2" "ITRAQ labeling" "Pool3" "iTRAQ reagent 117" "" "" "8763" "8763" "8763" "spectrum.mzdata" "" "" "norm3" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation3" "PRIDE_Exp_Complete_Ac_8763.xml" "" "" "" "" "l/hr" "" "" -"P-0.2-aliquot11" "protein extraction" "P-0.2" "ITRAQ labeling" "Pool3" "iTRAQ reagent 114" "" "" "8763" "8763" "8763" "spectrum.mzdata" "" "" "norm3" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation3" "PRIDE_Exp_Complete_Ac_8763.xml" "" "" "" "" "l/hr" "" "" -"S-0.2-aliquot11" "protein extraction" "S-0.2" "ITRAQ labeling" "Pool3" "iTRAQ reagent 114" "" "" "8763" "8763" "8763" "spectrum.mzdata" "" "" "norm3" "proteins.csv" "peptides.csv" "ptms.csv" "datatransformation3" "PRIDE_Exp_Complete_Ac_8763.xml" "" "" "" "" "l/hr" "" "" +Sample Name Protocol REF Extract Name Protocol REF Labeled Extract Name Label MS Assay Name Comment[PRIDE Accession] Comment[PRIDE Processed Data Accession] Raw Spectral Data File Comment[Data Record Accession] Comment[Data Repository] Normalization Name Protein Assignment File Peptide Assignment File Post Translational Modification Assignment File Data Transformation Name Derived Spectral Data File Factor Value[limiting nutrient] Factor Value[rate] Unit +S-0.1-aliquot11 protein extraction S-0.1 ITRAQ labeling JC_S-0.1 iTRAQ reagent 117 8761 8761 8761 spectrum.mzdata norm1 proteins.csv peptides.csv ptms.csv datatransformation1 PRIDE_Exp_Complete_Ac_8761.xml elemental sulfur 0.1 l/hr +C-0.1-aliquot11 protein extraction C-0.1 ITRAQ labeling JC_C-0.1 iTRAQ reagent 116 8761 8761 8761 spectrum.mzdata norm1 proteins.csv peptides.csv ptms.csv datatransformation1 PRIDE_Exp_Complete_Ac_8761.xml elemental carbon 0.1 l/hr +N-0.1-aliquot11 protein extraction N-0.1 ITRAQ labeling JC_N-0.1 iTRAQ reagent 115 8761 8761 8761 spectrum.mzdata norm1 proteins.csv peptides.csv ptms.csv datatransformation1 PRIDE_Exp_Complete_Ac_8761.xml elemental nitrogen 0.1 l/hr +S-0.1-aliquot11 protein extraction S-0.1 ITRAQ labeling Pool1 iTRAQ reagent 114 8761 8761 8761 spectrum.mzdata norm1 proteins.csv peptides.csv ptms.csv datatransformation1 PRIDE_Exp_Complete_Ac_8761.xml l/hr +C-0.1-aliquot11 protein extraction C-0.1 ITRAQ labeling Pool1 iTRAQ reagent 114 8761 8761 8761 spectrum.mzdata norm1 proteins.csv peptides.csv ptms.csv datatransformation1 PRIDE_Exp_Complete_Ac_8761.xml l/hr +N-0.1-aliquot11 protein extraction N-0.1 ITRAQ labeling Pool1 iTRAQ reagent 114 8761 8761 8761 spectrum.mzdata norm1 proteins.csv peptides.csv ptms.csv datatransformation1 PRIDE_Exp_Complete_Ac_8761.xml l/hr +C-0.2-aliquot11 protein extraction C-0.2 ITRAQ labeling JC_C-0.2 iTRAQ reagent 117 8762 8762 8762 spectrum.mzdata norm2 proteins.csv peptides.csv ptms.csv datatransformation2 PRIDE_Exp_Complete_Ac_8762.xml elemental carbon 0.2 l/hr +N-0.2-aliquot11 protein extraction N-0.2 ITRAQ labeling JC_N-0.2 iTRAQ reagent 116 8762 8762 8762 spectrum.mzdata norm2 proteins.csv peptides.csv ptms.csv datatransformation2 PRIDE_Exp_Complete_Ac_8762.xml elemental nitrogen 0.2 l/hr +P-0.1-aliquot11 protein extraction P-0.1 ITRAQ labeling JC_P-0.1 iTRAQ reagent 115 8762 8762 8762 spectrum.mzdata norm2 proteins.csv peptides.csv ptms.csv datatransformation2 PRIDE_Exp_Complete_Ac_8762.xml elemental phosphorus 0.1 l/hr +C-0.2-aliquot11 protein extraction C-0.2 ITRAQ labeling Pool2 iTRAQ reagent 114 8762 8762 8762 spectrum.mzdata norm2 proteins.csv peptides.csv ptms.csv datatransformation2 PRIDE_Exp_Complete_Ac_8762.xml l/hr +N-0.2-aliquot11 protein extraction N-0.2 ITRAQ labeling Pool2 iTRAQ reagent 114 8762 8762 8762 spectrum.mzdata norm2 proteins.csv peptides.csv ptms.csv datatransformation2 PRIDE_Exp_Complete_Ac_8762.xml l/hr +P-0.1-aliquot11 protein extraction P-0.1 ITRAQ labeling Pool2 iTRAQ reagent 114 8762 8762 8762 spectrum.mzdata norm2 proteins.csv peptides.csv ptms.csv datatransformation2 PRIDE_Exp_Complete_Ac_8762.xml l/hr +P-0.2-aliquot11 protein extraction P-0.2 ITRAQ labeling JC_P-0.2 iTRAQ reagent 116 8763 8763 8763 spectrum.mzdata norm3 proteins.csv peptides.csv ptms.csv datatransformation3 PRIDE_Exp_Complete_Ac_8763.xml elemental phosphorus 0.2 l/hr +S-0.2-aliquot11 protein extraction S-0.2 ITRAQ labeling JC_S-0.2 iTRAQ reagent 115 8763 8763 8763 spectrum.mzdata norm3 proteins.csv peptides.csv ptms.csv datatransformation3 PRIDE_Exp_Complete_Ac_8763.xml elemental sulfur 0.2 l/hr +P-0.2-aliquot11 protein extraction P-0.2 ITRAQ labeling Pool3 iTRAQ reagent 117 8763 8763 8763 spectrum.mzdata norm3 proteins.csv peptides.csv ptms.csv datatransformation3 PRIDE_Exp_Complete_Ac_8763.xml l/hr +S-0.2-aliquot11 protein extraction S-0.2 ITRAQ labeling Pool3 iTRAQ reagent 117 8763 8763 8763 spectrum.mzdata norm3 proteins.csv peptides.csv ptms.csv datatransformation3 PRIDE_Exp_Complete_Ac_8763.xml l/hr +P-0.2-aliquot11 protein extraction P-0.2 ITRAQ labeling Pool3 iTRAQ reagent 114 8763 8763 8763 spectrum.mzdata norm3 proteins.csv peptides.csv ptms.csv datatransformation3 PRIDE_Exp_Complete_Ac_8763.xml l/hr +S-0.2-aliquot11 protein extraction S-0.2 ITRAQ labeling Pool3 iTRAQ reagent 114 8763 8763 8763 spectrum.mzdata norm3 proteins.csv peptides.csv ptms.csv datatransformation3 PRIDE_Exp_Complete_Ac_8763.xml l/hr diff --git a/src/test/resources/test-data/BII-I-1/a_transcriptome.txt b/src/test/resources/test-data/BII-I-1/a_transcriptome.txt index 4602ae12..3618d9c5 100644 --- a/src/test/resources/test-data/BII-I-1/a_transcriptome.txt +++ b/src/test/resources/test-data/BII-I-1/a_transcriptome.txt @@ -1,49 +1,49 @@ -"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "Protocol REF" "Hybridization Assay Name" "Array Design REF" "Scan Name" "Array Data File" "Comment[Data Repository]" "Comment[Data Record Accession]" "Normalization Name" "Derived Array Data File" "Comment[Data Record Accession]" "Comment[Data Repository]" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"C-0.07-aliquot1" "mRNA extraction" "C-0.07-aliquot1" "biotin labeling" "C-0.07-aliquot1" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3908" "A-AFFY-27" "SCAN:MEXP:3908" "E-MEXP-115-raw-data-331217737.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot2" "mRNA extraction" "C-0.07-aliquot2" "biotin labeling" "C-0.07-aliquot2" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3909" "A-AFFY-27" "SCAN:MEXP:3909" "E-MEXP-115-raw-data-331217860.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot3" "mRNA extraction" "C-0.07-aliquot3" "biotin labeling" "C-0.07-aliquot3" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3910" "A-AFFY-27" "SCAN:MEXP:3910" "E-MEXP-115-raw-data-331217979.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.07-aliquot4" "mRNA extraction" "C-0.07-aliquot4" "biotin labeling" "C-0.07-aliquot4" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3907" "A-AFFY-27" "SCAN:MEXP:3907" "E-MEXP-115-raw-data-331217580.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.07" "l/hr" "" "" -"C-0.1-aliquot1" "mRNA extraction" "C-0.1-aliquot1" "biotin labeling" "C-0.1-aliquot1" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3912" "A-AFFY-27" "SCAN:MEXP:3912" "E-MEXP-115-raw-data-331218271.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" -"C-0.1-aliquot2" "mRNA extraction" "C-0.1-aliquot2" "biotin labeling" "C-0.1-aliquot2" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3913" "A-AFFY-27" "SCAN:MEXP:3913" "E-MEXP-115-raw-data-331218449.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental carbon" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415" "0.1" "l/hr" "" "" -"C-0.1-aliquot3" "mRNA extraction" "C-0.1-aliquot3" "biotin labeling" "C-0.1-aliquot3" "biotin" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3914" 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"http://purl.obolibrary.org/obo/CHEBI_15956" "EukGE-WS4" "HYB:MEXP:3953" "A-AFFY-27" "SCAN:MEXP:3953" "E-MEXP-115-raw-data-331225235.txt" "" "" "GCRMA normalization" "E-MEXP-115-processed-data-1341986893.txt" "" "" "elemental sulfur" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33403" "0.2" "l/hr" "" "" +Sample Name Protocol REF Extract Name Protocol REF Labeled Extract Name Label Protocol REF Hybridization Assay Name Array Design REF Scan Name Array Data File Comment[Data Repository] Comment[Data Record Accession] Normalization Name Derived Array Data File Comment[Data Record Accession] Comment[Data Repository] Factor Value[limiting nutrient] Factor Value[rate] Unit +C-0.07-aliquot1 mRNA extraction C-0.07-aliquot1 biotin labeling C-0.07-aliquot1 biotin EukGE-WS4 HYB:MEXP:3908 A-AFFY-27 SCAN:MEXP:3908 E-MEXP-115-raw-data-331217737.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.07 l/hr +C-0.07-aliquot2 mRNA extraction C-0.07-aliquot2 biotin labeling C-0.07-aliquot2 biotin EukGE-WS4 HYB:MEXP:3909 A-AFFY-27 SCAN:MEXP:3909 E-MEXP-115-raw-data-331217860.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.07 l/hr +C-0.07-aliquot3 mRNA extraction C-0.07-aliquot3 biotin labeling C-0.07-aliquot3 biotin EukGE-WS4 HYB:MEXP:3910 A-AFFY-27 SCAN:MEXP:3910 E-MEXP-115-raw-data-331217979.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.07 l/hr +C-0.07-aliquot4 mRNA extraction C-0.07-aliquot4 biotin labeling C-0.07-aliquot4 biotin EukGE-WS4 HYB:MEXP:3907 A-AFFY-27 SCAN:MEXP:3907 E-MEXP-115-raw-data-331217580.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.07 l/hr +C-0.1-aliquot1 mRNA extraction C-0.1-aliquot1 biotin labeling C-0.1-aliquot1 biotin EukGE-WS4 HYB:MEXP:3912 A-AFFY-27 SCAN:MEXP:3912 E-MEXP-115-raw-data-331218271.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.1 l/hr +C-0.1-aliquot2 mRNA extraction C-0.1-aliquot2 biotin labeling C-0.1-aliquot2 biotin EukGE-WS4 HYB:MEXP:3913 A-AFFY-27 SCAN:MEXP:3913 E-MEXP-115-raw-data-331218449.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.1 l/hr +C-0.1-aliquot3 mRNA extraction C-0.1-aliquot3 biotin labeling C-0.1-aliquot3 biotin EukGE-WS4 HYB:MEXP:3914 A-AFFY-27 SCAN:MEXP:3914 E-MEXP-115-raw-data-331218681.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.1 l/hr +C-0.1-aliquot4 mRNA extraction C-0.1-aliquot4 biotin labeling C-0.1-aliquot4 biotin EukGE-WS4 HYB:MEXP:3911 A-AFFY-27 SCAN:MEXP:3911 E-MEXP-115-raw-data-331218116.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.1 l/hr +C-0.2-aliquot1 mRNA extraction C-0.2-aliquot1 biotin labeling C-0.2-aliquot1 biotin EukGE-WS4 HYB:MEXP:3916 A-AFFY-27 SCAN:MEXP:3916 E-MEXP-115-raw-data-331219013.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.2 l/hr +C-0.2-aliquot2 mRNA extraction C-0.2-aliquot2 biotin labeling C-0.2-aliquot2 biotin EukGE-WS4 HYB:MEXP:3915 A-AFFY-27 SCAN:MEXP:3915 E-MEXP-115-raw-data-331218842.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.2 l/hr +C-0.2-aliquot3 mRNA extraction C-0.2-aliquot3 biotin labeling C-0.2-aliquot3 biotin EukGE-WS4 HYB:MEXP:3918 A-AFFY-27 SCAN:MEXP:3918 E-MEXP-115-raw-data-331219245.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.2 l/hr +C-0.2-aliquot4 mRNA extraction C-0.2-aliquot4 biotin labeling C-0.2-aliquot4 biotin EukGE-WS4 HYB:MEXP:3917 A-AFFY-27 SCAN:MEXP:3917 E-MEXP-115-raw-data-331219131.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental carbon 0.2 l/hr +N-0.07-aliquot1 mRNA extraction N-0.07-aliquot1 biotin labeling N-0.07-aliquot1 biotin EukGE-WS4 HYB:MEXP:3919 A-AFFY-27 SCAN:MEXP:3919 E-MEXP-115-raw-data-331219361.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot2 mRNA extraction N-0.07-aliquot2 biotin labeling N-0.07-aliquot2 biotin EukGE-WS4 HYB:MEXP:3921 A-AFFY-27 SCAN:MEXP:3921 E-MEXP-115-raw-data-331219634.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot3 mRNA extraction N-0.07-aliquot3 biotin labeling N-0.07-aliquot3 biotin EukGE-WS4 HYB:MEXP:3922 A-AFFY-27 SCAN:MEXP:3922 E-MEXP-115-raw-data-331219767.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.07 l/hr +N-0.07-aliquot4 mRNA extraction N-0.07-aliquot4 biotin labeling N-0.07-aliquot4 biotin EukGE-WS4 HYB:MEXP:3920 A-AFFY-27 SCAN:MEXP:3920 E-MEXP-115-raw-data-331219490.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.07 l/hr +N-0.1-aliquot1 mRNA extraction N-0.1-aliquot1 biotin labeling N-0.1-aliquot1 biotin EukGE-WS4 HYB:MEXP:3926 A-AFFY-27 SCAN:MEXP:3926 E-MEXP-115-raw-data-331220431.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot2 mRNA extraction N-0.1-aliquot2 biotin labeling N-0.1-aliquot2 biotin EukGE-WS4 HYB:MEXP:3923 A-AFFY-27 SCAN:MEXP:3923 E-MEXP-115-raw-data-331219914.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot3 mRNA extraction N-0.1-aliquot3 biotin labeling N-0.1-aliquot3 biotin EukGE-WS4 HYB:MEXP:3925 A-AFFY-27 SCAN:MEXP:3925 E-MEXP-115-raw-data-331220272.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.1 l/hr +N-0.1-aliquot4 mRNA extraction N-0.1-aliquot4 biotin labeling N-0.1-aliquot4 biotin EukGE-WS4 HYB:MEXP:3924 A-AFFY-27 SCAN:MEXP:3924 E-MEXP-115-raw-data-331220090.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.1 l/hr +N-0.2-aliquot1 mRNA extraction N-0.2-aliquot1 biotin labeling N-0.2-aliquot1 biotin EukGE-WS4 HYB:MEXP:3930 A-AFFY-27 SCAN:MEXP:3930 E-MEXP-115-raw-data-331221148.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot2 mRNA extraction N-0.2-aliquot2 biotin labeling N-0.2-aliquot2 biotin EukGE-WS4 HYB:MEXP:3929 A-AFFY-27 SCAN:MEXP:3929 E-MEXP-115-raw-data-331220982.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot3 mRNA extraction N-0.2-aliquot3 biotin labeling N-0.2-aliquot3 biotin EukGE-WS4 HYB:MEXP:3928 A-AFFY-27 SCAN:MEXP:3928 E-MEXP-115-raw-data-331220784.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.2 l/hr +N-0.2-aliquot4 mRNA extraction N-0.2-aliquot4 biotin labeling N-0.2-aliquot4 biotin EukGE-WS4 HYB:MEXP:3927 A-AFFY-27 SCAN:MEXP:3927 E-MEXP-115-raw-data-331220607.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental nitrogen 0.2 l/hr +P-0.07-aliquot1 mRNA extraction P-0.07-aliquot1 biotin labeling P-0.07-aliquot1 biotin EukGE-WS4 HYB:MEXP:3932 A-AFFY-27 SCAN:MEXP:3932 E-MEXP-115-raw-data-331221518.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot2 mRNA extraction P-0.07-aliquot2 biotin labeling P-0.07-aliquot2 biotin EukGE-WS4 HYB:MEXP:3934 A-AFFY-27 SCAN:MEXP:3934 E-MEXP-115-raw-data-331221873.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot3 mRNA extraction P-0.07-aliquot3 biotin labeling P-0.07-aliquot3 biotin EukGE-WS4 HYB:MEXP:3931 A-AFFY-27 SCAN:MEXP:3931 E-MEXP-115-raw-data-331221345.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.07 l/hr +P-0.07-aliquot4 mRNA extraction P-0.07-aliquot4 biotin labeling P-0.07-aliquot4 biotin EukGE-WS4 HYB:MEXP:3933 A-AFFY-27 SCAN:MEXP:3933 E-MEXP-115-raw-data-331221668.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.07 l/hr +P-0.1-aliquot1 mRNA extraction P-0.1-aliquot1 biotin labeling P-0.1-aliquot1 biotin EukGE-WS4 HYB:MEXP:3938 A-AFFY-27 SCAN:MEXP:3938 E-MEXP-115-raw-data-331222534.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot2 mRNA extraction P-0.1-aliquot2 biotin labeling P-0.1-aliquot2 biotin EukGE-WS4 HYB:MEXP:3935 A-AFFY-27 SCAN:MEXP:3935 E-MEXP-115-raw-data-331222054.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot3 mRNA extraction P-0.1-aliquot3 biotin labeling P-0.1-aliquot3 biotin EukGE-WS4 HYB:MEXP:3937 A-AFFY-27 SCAN:MEXP:3937 E-MEXP-115-raw-data-331222380.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.1 l/hr +P-0.1-aliquot4 mRNA extraction P-0.1-aliquot4 biotin labeling P-0.1-aliquot4 biotin EukGE-WS4 HYB:MEXP:3936 A-AFFY-27 SCAN:MEXP:3936 E-MEXP-115-raw-data-331222215.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.1 l/hr +P-0.2-aliquot1 mRNA extraction P-0.2-aliquot1 biotin labeling P-0.2-aliquot1 biotin EukGE-WS4 HYB:MEXP:3940 A-AFFY-27 SCAN:MEXP:3940 E-MEXP-115-raw-data-331222917.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot2 mRNA extraction P-0.2-aliquot2 biotin labeling P-0.2-aliquot2 biotin EukGE-WS4 HYB:MEXP:3941 A-AFFY-27 SCAN:MEXP:3941 E-MEXP-115-raw-data-331223115.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot3 mRNA extraction P-0.2-aliquot3 biotin labeling P-0.2-aliquot3 biotin EukGE-WS4 HYB:MEXP:3942 A-AFFY-27 SCAN:MEXP:3942 E-MEXP-115-raw-data-331223321.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.2 l/hr +P-0.2-aliquot4 mRNA extraction P-0.2-aliquot4 biotin labeling P-0.2-aliquot4 biotin EukGE-WS4 HYB:MEXP:3939 A-AFFY-27 SCAN:MEXP:3939 E-MEXP-115-raw-data-331222701.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental phosphorus 0.2 l/hr +S-0.07-aliquot1 mRNA extraction S-0.07-aliquot1 biotin labeling S-0.07-aliquot1 biotin EukGE-WS4 HYB:MEXP:3944 A-AFFY-27 SCAN:MEXP:3944 E-MEXP-115-raw-data-331223667.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot2 mRNA extraction S-0.07-aliquot2 biotin labeling S-0.07-aliquot2 biotin EukGE-WS4 HYB:MEXP:3945 A-AFFY-27 SCAN:MEXP:3945 E-MEXP-115-raw-data-331223835.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot3 mRNA extraction S-0.07-aliquot3 biotin labeling S-0.07-aliquot3 biotin EukGE-WS4 HYB:MEXP:3946 A-AFFY-27 SCAN:MEXP:3946 E-MEXP-115-raw-data-331223977.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.07 l/hr +S-0.07-aliquot4 mRNA extraction S-0.07-aliquot4 biotin labeling S-0.07-aliquot4 biotin EukGE-WS4 HYB:MEXP:3943 A-AFFY-27 SCAN:MEXP:3943 E-MEXP-115-raw-data-331223501.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.07 l/hr +S-0.1-aliquot1 mRNA extraction S-0.1-aliquot1 biotin labeling S-0.1-aliquot1 biotin EukGE-WS4 HYB:MEXP:3948 A-AFFY-27 SCAN:MEXP:3948 E-MEXP-115-raw-data-331224301.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.1 l/hr +S-0.1-aliquot2 mRNA extraction S-0.1-aliquot2 biotin labeling S-0.1-aliquot2 biotin EukGE-WS4 HYB:MEXP:3947 A-AFFY-27 SCAN:MEXP:3947 E-MEXP-115-raw-data-331224145.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.1 l/hr +S-0.1-aliquot3 mRNA extraction S-0.1-aliquot3 biotin labeling S-0.1-aliquot3 biotin EukGE-WS4 HYB:MEXP:3950 A-AFFY-27 SCAN:MEXP:3950 E-MEXP-115-raw-data-331224703.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.1 l/hr +S-0.1-aliquot4 mRNA extraction S-0.1-aliquot4 biotin labeling S-0.1-aliquot4 biotin EukGE-WS4 HYB:MEXP:3949 A-AFFY-27 SCAN:MEXP:3949 E-MEXP-115-raw-data-331224480.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.1 l/hr +S-0.2-aliquot1 mRNA extraction S-0.2-aliquot1 biotin labeling S-0.2-aliquot1 biotin EukGE-WS4 HYB:MEXP:3951 A-AFFY-27 SCAN:MEXP:3951 E-MEXP-115-raw-data-331224884.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.2 l/hr +S-0.2-aliquot2 mRNA extraction S-0.2-aliquot2 biotin labeling S-0.2-aliquot2 biotin EukGE-WS4 HYB:MEXP:3954 A-AFFY-27 SCAN:MEXP:3954 E-MEXP-115-raw-data-331225401.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.2 l/hr +S-0.2-aliquot3 mRNA extraction S-0.2-aliquot3 biotin labeling S-0.2-aliquot3 biotin EukGE-WS4 HYB:MEXP:3952 A-AFFY-27 SCAN:MEXP:3952 E-MEXP-115-raw-data-331225097.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.2 l/hr +S-0.2-aliquot4 mRNA extraction S-0.2-aliquot4 biotin labeling S-0.2-aliquot4 biotin EukGE-WS4 HYB:MEXP:3953 A-AFFY-27 SCAN:MEXP:3953 E-MEXP-115-raw-data-331225235.txt GCRMA normalization E-MEXP-115-processed-data-1341986893.txt elemental sulfur 0.2 l/hr diff --git a/src/test/resources/test-data/BII-I-1/i_investigation.txt b/src/test/resources/test-data/BII-I-1/i_investigation.txt index 463faf37..d897efd9 100644 --- a/src/test/resources/test-data/BII-I-1/i_investigation.txt +++ b/src/test/resources/test-data/BII-I-1/i_investigation.txt @@ -1,17 +1,16 @@ ONTOLOGY SOURCE REFERENCE -Term Source Name "CHEBI" "CL" "OBI" "NCBITAXON" "OBI_BCGO" "PATO" "UO" -Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/CL" "http://data.bioontology.org/ontologies/OBI" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/OBI_BCGO" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/UO" -Term Source Version "78" "43" "21" "2" "8" "160" "42" -Term Source Description "Chemical Entities of Biological Interest Ontology" "Cell Ontology" "Ontology for Biomedical Investigations" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Beta Cell Genomics Ontology" "Phenotypic Quality Ontology" "Units of Measurement Ontology" +Term Source Name +Term Source File +Term Source Version +Term Source Description INVESTIGATION Investigation Identifier "BII-I-1" Investigation Title "Growth control of the eukaryote cell: a systems biology study in yeast" Investigation Description "Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell." Investigation Submission Date "2007-04-30" Investigation Public Release Date "2009-03-10" -Comment[Created with configuration] "" -Comment[Last Opened With Configuration] "" Comment[Created With Configuration] "" +Comment[Last Opened With Configuration] "" Comment[Owning Organisation URI] "" Comment[Consortium URI] "" Comment[Principal Investigator URI] "" @@ -73,14 +72,14 @@ Study Factor Type "chemical entity" "rate" Study Factor Type Term Accession Number "http://purl.obolibrary.org/obo/CHEBI_24431" "http://purl.obolibrary.org/obo/PATO_0000161" Study Factor Type Term Source REF "CHEBI" "PATO" STUDY ASSAYS -Study Assay File Name "a_proteome.txt" "a_metabolome.txt" "a_transcriptome.txt" -Study Assay Measurement Type "protein expression profiling" "metabolite profiling" "transcription profiling" -Study Assay Measurement Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000615" "http://purl.obolibrary.org/obo/OBI_0000366" "http://purl.obolibrary.org/obo/OBI_0000424" +Study Assay File Name "a_metabolome.txt" "a_proteome.txt" "a_transcriptome.txt" +Study Assay Measurement Type "metabolite profiling" "protein expression profiling" "transcription profiling" +Study Assay Measurement Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000366" "http://purl.obolibrary.org/obo/OBI_0000615" "http://purl.obolibrary.org/obo/OBI_0000424" Study Assay Measurement Type Term Source REF "OBI" "OBI" "OBI" Study Assay Technology Type "mass spectrometry" "mass spectrometry" "DNA microarray" Study Assay Technology Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000470" "http://purl.obolibrary.org/obo/OBI_0000470" "http://purl.obolibrary.org/obo/OBI_0400148" Study Assay Technology Type Term Source REF "OBI" "OBI" "OBI" -Study Assay Technology Platform "iTRAQ" "LC-MS/MS" "Affymetrix" +Study Assay Technology Platform "LC-MS/MS" "iTRAQ" "Affymetrix" STUDY PROTOCOLS Study Protocol Name "growth protocol" "mRNA extraction" "protein extraction" "biotin labeling" "ITRAQ labeling" "EukGE-WS4" "metabolite extraction" Study Protocol Type "growth" "RNA extraction" "extraction" "addition of molecular label" "addition of molecular label" "nucleic acid hybridization" "extraction" diff --git a/src/test/resources/test-data/BII-I-1/s_BII-S-1.txt b/src/test/resources/test-data/BII-I-1/s_BII-S-1.txt index f0b691c1..94f768d5 100644 --- a/src/test/resources/test-data/BII-I-1/s_BII-S-1.txt +++ b/src/test/resources/test-data/BII-I-1/s_BII-S-1.txt @@ -1,165 +1,165 @@ -"Source Name" "Characteristics[organism]" "Term Source REF" "Term Accession Number" "Characteristics[strain]" "Term Source REF" "Term Accession Number" "Characteristics[genotype]" "Term Source REF" "Term Accession Number" "Protocol REF" "Sample Name" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" -"culture1" "Saccharomyces cerevisiae" "NCBITAXON" 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KanMx4/hoD growth protocol C-0.07-aliquot1 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot2 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot3 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot4 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot5 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot6 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot7 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot8 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot9 elemental carbon 0.07 l/hour +culture1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.07-aliquot10 elemental carbon 0.07 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot1 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot2 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot3 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot4 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot5 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot6 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot7 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot8 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot9 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot10 elemental carbon 0.1 l/hour +culture2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.1-aliquot11 elemental carbon 0.1 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot1 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot2 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot3 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot4 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot5 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot6 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot7 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot8 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot9 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot10 elemental carbon 0.2 l/hour +culture3 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol C-0.2-aliquot11 elemental carbon 0.2 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot1 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot2 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot3 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot4 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot5 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot6 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot7 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot8 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot9 elemental nitrogen 0.07 l/hour +culture4 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.07-aliquot10 elemental nitrogen 0.07 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot1 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot2 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot3 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot4 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot5 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot6 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot7 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot8 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot9 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot10 elemental nitrogen 0.1 l/hour +culture5 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.1-aliquot11 elemental nitrogen 0.1 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot1 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot2 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot3 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot4 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot5 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot6 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot7 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot8 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot9 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot10 elemental nitrogen 0.2 l/hour +culture6 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol N-0.2-aliquot11 elemental nitrogen 0.2 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot1 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot2 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot3 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot4 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot5 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot6 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot7 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot8 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot9 elemental phosphorus 0.07 l/hour +culture7 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.07-aliquot10 elemental phosphorus 0.07 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot1 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot2 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot3 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot4 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot5 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot6 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot7 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot8 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot9 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot10 elemental phosphorus 0.1 l/hour +culture8 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.1-aliquot11 elemental phosphorus 0.1 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot1 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot2 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot3 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot4 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot5 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot6 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot7 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot8 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot9 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot10 elemental phosphorus 0.2 l/hour +culture9 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol P-0.2-aliquot11 elemental phosphorus 0.2 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot1 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot2 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot3 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot4 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot5 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot6 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot7 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot8 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot9 elemental sulfur 0.07 l/hour +culture10 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.07-aliquot10 elemental sulfur 0.07 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot1 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot2 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot3 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot4 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot5 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot6 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot7 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot8 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot9 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot10 elemental sulfur 0.1 l/hour +culture11 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.1-aliquot11 elemental sulfur 0.1 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot1 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot2 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot3 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot4 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot5 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot6 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot7 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot8 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot9 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot10 elemental sulfur 0.2 l/hour +culture12 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol S-0.2-aliquot11 elemental sulfur 0.2 l/hour +culture13 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.07-aliquot1 ethanol 0.07 l/hour +culture13 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.07-aliquot2 ethanol 0.07 l/hour +culture13 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.07-aliquot3 ethanol 0.07 l/hour +culture13 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.07-aliquot4 ethanol 0.07 l/hour +culture13 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.07-aliquot5 ethanol 0.07 l/hour +culture13 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.07-aliquot6 ethanol 0.07 l/hour +culture14 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.1-aliquot1 ethanol 0.1 l/hour +culture14 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.1-aliquot2 ethanol 0.1 l/hour +culture14 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.1-aliquot3 ethanol 0.1 l/hour +culture14 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.1-aliquot4 ethanol 0.1 l/hour +culture14 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.1-aliquot5 ethanol 0.1 l/hour +culture14 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.1-aliquot6 ethanol 0.1 l/hour +culture15 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.2-aliquot1 ethanol 0.2 l/hour +culture15 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.2-aliquot2 ethanol 0.2 l/hour +culture15 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.2-aliquot3 ethanol 0.2 l/hour +culture15 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.2-aliquot4 ethanol 0.2 l/hour +culture15 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.2-aliquot5 ethanol 0.2 l/hour +culture15 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol E-0.2-aliquot6 ethanol 0.2 l/hour +culture16 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.07-aliquot1 glucose 0.07 l/hour +culture16 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.07-aliquot2 glucose 0.07 l/hour +culture16 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.07-aliquot3 glucose 0.07 l/hour +culture16 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.07-aliquot4 glucose 0.07 l/hour +culture16 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.07-aliquot5 glucose 0.07 l/hour +culture16 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.07-aliquot6 glucose 0.07 l/hour +culture17 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.1-aliquot1 glucose 0.1 l/hour +culture17 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.1-aliquot2 glucose 0.1 l/hour +culture17 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.1-aliquot3 glucose 0.1 l/hour +culture17 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.1-aliquot4 glucose 0.1 l/hour +culture17 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.1-aliquot5 glucose 0.1 l/hour +culture17 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.1-aliquot6 glucose 0.1 l/hour +culture18 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.2-aliquot1 glucose 0.2 l/hour +culture18 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.2-aliquot2 glucose 0.2 l/hour +culture18 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.2-aliquot3 glucose 0.2 l/hour +culture18 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.2-aliquot4 glucose 0.2 l/hour +culture18 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.2-aliquot5 glucose 0.2 l/hour +culture18 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD growth protocol G-0.2-aliquot6 glucose 0.2 l/hour diff --git a/src/test/resources/test-data/BII-I-1/s_BII-S-2.txt b/src/test/resources/test-data/BII-I-1/s_BII-S-2.txt index 9c366671..36b3b3ef 100644 --- a/src/test/resources/test-data/BII-I-1/s_BII-S-2.txt +++ b/src/test/resources/test-data/BII-I-1/s_BII-S-2.txt @@ -1,15 +1,15 @@ -"Source Name" "Characteristics[organism]" "Term Source REF" "Term Accession Number" "Characteristics[strain]" "Term Source REF" "Term Accession Number" "Characteristics[genotype]" "Term Source REF" "Term Accession Number" "Characteristics[mating type]" "Term Source REF" "Term Accession Number" "Protocol REF" "Sample Name" "Factor Value[dose]" "Unit" "Term Source REF" "Term Accession Number" "Factor Value[exposure time]" "Unit" "Term Source REF" "Term Accession Number" "Factor Value[compound]" "Term Source REF" "Term Accession Number" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_0hrs_Grow1_Sample_1" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "0" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "" "" "" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_1hrs_Grow1_Drug_Sample_1" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_2hrs_Grow1_Drug_Sample_1" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_4hrs_Grow1_Drug_Sample_1" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_2hrs_Grow1_Vehicle_Sample_1" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_4hrs_Grow1_Vehicle_Sample_1" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_0hrs_Grow_1" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_1hrs_Grow1_Vehicle_Sample_1" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_0hrs_Grow2_Sample_2" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "0" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "" "" "" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_1hrs_Grow2_Drug_Sample_2" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_4hrs_Grow2_Drug_Sample_2" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_2hrs_Grow2_Drug_Sample_2" "200" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "sirolimus" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_9168" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_1hrs_Grow2_Vehicle_Sample_2" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "1" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_2hrs_Grow2_Vehicle_Sample_2" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "2" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" -"NZ_0hrs_Grow_2" "Saccharomyces cerevisiae" "NCBITAXON" "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679" "" "" "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD" "" "" "alpha mating type (yeast)" "OBI" "http://purl.obolibrary.org/obo/PATO_0001344" "" "NZ_4hrs_Grow2_Vehicle_Sample_2" "0" "nanogram per milliliter" "UO" "http://purl.obolibrary.org/obo/UO_0000275" "4" "hour" "UO" "http://purl.obolibrary.org/obo/UO_0000032" "drug vehicle (90% ethanol/10% tween-20)" "" "" +Source Name Characteristics[organism] Characteristics[strain] Characteristics[genotype] Characteristics[mating type] Protocol REF Sample Name Factor Value[dose] Unit Factor Value[exposure time] Unit Factor Value[compound] +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_0hrs_Grow1_Sample_1 0 nanogram per milliliter 0 hour +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_1hrs_Grow1_Drug_Sample_1 200 nanogram per milliliter 1 hour sirolimus +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_2hrs_Grow1_Drug_Sample_1 200 nanogram per milliliter 2 hour sirolimus +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_4hrs_Grow1_Drug_Sample_1 200 nanogram per milliliter 4 hour sirolimus +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_2hrs_Grow1_Vehicle_Sample_1 0 nanogram per milliliter 2 hour drug vehicle (90% ethanol/10% tween-20) +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_4hrs_Grow1_Vehicle_Sample_1 0 nanogram per milliliter 4 hour drug vehicle (90% ethanol/10% tween-20) +NZ_0hrs_Grow_1 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_1hrs_Grow1_Vehicle_Sample_1 0 nanogram per milliliter 1 hour drug vehicle (90% ethanol/10% tween-20) +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_0hrs_Grow2_Sample_2 0 nanogram per milliliter 0 hour +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_1hrs_Grow2_Drug_Sample_2 200 nanogram per milliliter 1 hour sirolimus +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_4hrs_Grow2_Drug_Sample_2 200 nanogram per milliliter 4 hour sirolimus +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_2hrs_Grow2_Drug_Sample_2 200 nanogram per milliliter 2 hour sirolimus +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_1hrs_Grow2_Vehicle_Sample_2 0 nanogram per milliliter 1 hour drug vehicle (90% ethanol/10% tween-20) +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_2hrs_Grow2_Vehicle_Sample_2 0 nanogram per milliliter 2 hour drug vehicle (90% ethanol/10% tween-20) +NZ_0hrs_Grow_2 Saccharomyces cerevisiae FY1679 KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD alpha mating type (yeast) NZ_4hrs_Grow2_Vehicle_Sample_2 0 nanogram per milliliter 4 hour drug vehicle (90% ethanol/10% tween-20) From 0719acfe1709177fefddb885e40d37dc502a0ae3 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Tue, 11 Mar 2014 14:30:24 +0000 Subject: [PATCH 12/16] Handling errors a bit better. --- .../archiveoutput/ArchiveOutputUtil.java | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java b/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java index 38ebc7f4..b81e7bd0 100755 --- a/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java +++ b/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java @@ -194,6 +194,10 @@ public void run() { updateArchiveOutputStatusLabel("increase memory!"); // force an immediate garbage collect to remove redundant objects immediately! System.gc(); + } catch (Exception e) { + e.printStackTrace(); + updateArchiveOutputStatusLabel("" + e.getMessage() + ""); + log.error(e.getMessage()); } } @@ -262,7 +266,9 @@ public void zipDir(String sourceDir, File dirToZip, ZipOutputStream zos, byte[] } } } catch (Exception e) { + e.printStackTrace(); log.error(e.getMessage()); + updateArchiveOutputStatusLabel("" + e.getMessage() + ""); } } @@ -361,7 +367,7 @@ public boolean zipDirectoryContents(String archiveName, String directory, statistics.setEndTime(System.currentTimeMillis()); if (missingFiles.size() > 0 || missingData.size() > 0) { - log.info("Archive creation failed, there are " + missingFiles.size() + " missing files referenced in the submission."); + log.error("Archive creation failed, there are " + missingFiles.size() + " missing files referenced in the submission."); updateArchiveOutputStatusLabel("Archive output failed, there are files or data missing."); @@ -371,7 +377,7 @@ public boolean zipDirectoryContents(String archiveName, String directory, firePropertyChange("archiveOutputFailed", false, true); return false; } else { - log.error("Archive output successful!"); + log.info("Archive output successful!"); firePropertyChange("archiveOutputCompleted", false, true); return true; } @@ -381,6 +387,11 @@ public boolean zipDirectoryContents(String archiveName, String directory, e.printStackTrace(); return false; } catch (IOException e) { + log.error("IO Exception - " + e.getMessage()); + e.printStackTrace(); + return false; + } catch (Exception e) { + log.error("Unexpected Exception - " + e.getMessage()); e.printStackTrace(); return false; } finally { From 8ed5dd984d3e636a7cd21c00216fa56e1e6cc7d6 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Tue, 11 Mar 2014 14:59:57 +0000 Subject: [PATCH 13/16] Fixed how relative paths were being handled. #245 --- .../isatools/isacreator/archiveoutput/ArchiveOutputUtil.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java b/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java index b81e7bd0..c7fea785 100755 --- a/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java +++ b/src/main/java/org/isatools/isacreator/archiveoutput/ArchiveOutputUtil.java @@ -334,6 +334,7 @@ public boolean zipDirectoryContents(String archiveName, String directory, for (String containingFile : filesToZip.get(parentISAFile)) { File f = new File(containingFile); + log.info("Going to try and zip " + f.getAbsolutePath()); // this will test if the file being mentioned is in a relative location to the directory, just in case! f = testIfRelativeOrAbsolutePath(f, isaFiles[0].getParentFile()); @@ -407,7 +408,8 @@ public boolean zipDirectoryContents(String archiveName, String directory, private File testIfRelativeOrAbsolutePath(File file, File isaDirectory) { if (!file.exists()) { - return new File(isaDirectory.getAbsolutePath() + File.separator + file.getName()); + + return new File(isaDirectory.getAbsolutePath() + File.separator + file.getPath()); } return file; From 26f5ced5e9892c0f18b6f9b95c06786b19fa9370 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Tue, 11 Mar 2014 17:32:56 +0000 Subject: [PATCH 14/16] fixed problem with mapping object loading in the investigation file with the wrong dispath target. Removed some redundant code from about. --- .../isatools/isacreator/configuration/MappingObject.java | 8 ++++++-- .../java/org/isatools/isacreator/gui/AboutPanel.java | 9 --------- 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/configuration/MappingObject.java b/src/main/java/org/isatools/isacreator/configuration/MappingObject.java index 5179c1d8..e6b3efb6 100755 --- a/src/main/java/org/isatools/isacreator/configuration/MappingObject.java +++ b/src/main/java/org/isatools/isacreator/configuration/MappingObject.java @@ -127,11 +127,15 @@ public void setDispatchTarget(String dispatchTarget) { } public String getDispatchTarget() { - return dispatchTarget == null ? measurementType.equals("[Sample]") ? "" : DispatchTargets.GENERIC.toString() : dispatchTarget; + return dispatchTarget == null ? isSampleOrInvestigation() ? "" : DispatchTargets.GENERIC.toString() : dispatchTarget; } public String getAssayType() { - return assayType == null ? measurementType.equals("[Sample]") ? "" : AssayTypes.GENERIC.toString() : assayType; + return assayType == null ? isSampleOrInvestigation() ? "" : AssayTypes.GENERIC.toString() : assayType; + } + + private boolean isSampleOrInvestigation() { + return measurementType.equals("[Sample]") || measurementType.equals("[investigation]"); } public void setAssayType(String assayType) { diff --git a/src/main/java/org/isatools/isacreator/gui/AboutPanel.java b/src/main/java/org/isatools/isacreator/gui/AboutPanel.java index c256cf87..198a4e1b 100755 --- a/src/main/java/org/isatools/isacreator/gui/AboutPanel.java +++ b/src/main/java/org/isatools/isacreator/gui/AboutPanel.java @@ -83,13 +83,4 @@ public void paint(Graphics graphics) { g2d.drawString(ISAcreatorProperties.getProperty("version"), 130, 120); } - public static void main(String[] args) { - ISAcreatorGUIProperties.setProperties(); - JFrame container = new JFrame(); - container.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - container.setLayout(new BorderLayout()); - container.add(new AboutPanel()); - container.pack(); - container.setVisible(true); - } } From eaeb457de769030c934b9da613f603e0b49f2bb9 Mon Sep 17 00:00:00 2001 From: Michael Heuer Date: Thu, 13 Mar 2014 16:14:39 -0500 Subject: [PATCH 15/16] fix for maven warning, pom.version --> project.version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 9b3f6e2d..37a714c1 100644 --- a/pom.xml +++ b/pom.xml @@ -561,7 +561,7 @@ build - ${pom.version} + ${project.version} false From a58ece0e7e07df1e7cee3ef618ac27876e5e7a37 Mon Sep 17 00:00:00 2001 From: Eamonn Maguire Date: Fri, 4 Apr 2014 16:18:34 +0100 Subject: [PATCH 16/16] Closes #272 --- .../BioPortalAnnotatorResultHandler.java | 32 ++++++++++--------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java index 3d52dbab..05a2babe 100644 --- a/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java +++ b/src/main/java/org/isatools/isacreator/ontologymanager/bioportal/jsonresulthandlers/BioPortalAnnotatorResultHandler.java @@ -36,7 +36,7 @@ public Map> getSearchResults(String queryCo for (Object annotationItem : obj) { - AnnotatorResult annotatorResult = extractAnnotatorResult((JSONObject)annotationItem); + AnnotatorResult annotatorResult = extractAnnotatorResult((JSONObject) annotationItem); if (annotatorResult != null) { @@ -60,28 +60,30 @@ public Map> getSearchResults(String queryCo } private AnnotatorResult extractAnnotatorResult(JSONObject resultItem) { - JSONObject annotatedClass = (JSONObject)resultItem.get("annotatedClass"); + JSONObject annotatedClass = (JSONObject) resultItem.get("annotatedClass"); JSONObject links = (JSONObject) annotatedClass.get("links"); String ontologyId = links.get("ontology").toString(); - OntologySourceRefObject sourceRefObject = OntologyManager.getOntologySourceReferenceObjectByAbbreviation(ontologyId); - OntologyTerm ontologyTerm = new OntologyTerm( - annotatedClass.get("prefLabel").toString(), annotatedClass.get("@id").toString(), annotatedClass.get("@id").toString(), sourceRefObject); + if (AcceptedOntologies.getOntologyAbbreviationFromId(ontologyId) != null) { + OntologySourceRefObject sourceRefObject = OntologyManager.getOntologySourceReferenceObjectByAbbreviation(AcceptedOntologies.getOntologyAbbreviationFromId(ontologyId)); + OntologyTerm ontologyTerm = new OntologyTerm( + annotatedClass.get("prefLabel").toString(), annotatedClass.get("@id").toString(), annotatedClass.get("@id").toString(), sourceRefObject); - int from = -1, to = -1; + int from = -1, to = -1; - for (Object annotation : (JSONArray)resultItem.get("annotations")) { - JSONObject annotationObject = (JSONObject) annotation; - from = Integer.valueOf(annotationObject.get("from").toString()); - to = Integer.valueOf(annotationObject.get("to").toString()); - } + for (Object annotation : (JSONArray) resultItem.get("annotations")) { + JSONObject annotationObject = (JSONObject) annotation; + from = Integer.valueOf(annotationObject.get("from").toString()); + to = Integer.valueOf(annotationObject.get("to").toString()); + } - if (from != -1 && to != -1) { - return new AnnotatorResult(ontologyTerm, AcceptedOntologies.getAcceptedOntologies().get(ontologyId), 1, - from, to); - } + if (from != -1 && to != -1) { + return new AnnotatorResult(ontologyTerm, AcceptedOntologies.getAcceptedOntologies().get(ontologyId), 1, + from, to); + } + } return null; } }