diff --git a/complex-go-export/pom.xml b/complex-go-export/pom.xml index ee2287dce..fc5b60f49 100644 --- a/complex-go-export/pom.xml +++ b/complex-go-export/pom.xml @@ -5,7 +5,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT complex-go-export diff --git a/complex-pdb-export/pom.xml b/complex-pdb-export/pom.xml index d016a72e8..9183add84 100644 --- a/complex-pdb-export/pom.xml +++ b/complex-pdb-export/pom.xml @@ -5,7 +5,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT complex-pdb-export diff --git a/complex-tab-export/pom.xml b/complex-tab-export/pom.xml index 177f8e586..dc85acedb 100644 --- a/complex-tab-export/pom.xml +++ b/complex-tab-export/pom.xml @@ -5,7 +5,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT diff --git a/complex-uniprot-dr-export/pom.xml b/complex-uniprot-dr-export/pom.xml index 2f856cc92..e91f8c8fe 100644 --- a/complex-uniprot-dr-export/pom.xml +++ b/complex-uniprot-dr-export/pom.xml @@ -5,7 +5,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT complex-uniprot-dr-export diff --git a/cttv-exporter/pom.xml b/cttv-exporter/pom.xml index 79324b587..493bc1af9 100644 --- a/cttv-exporter/pom.xml +++ b/cttv-exporter/pom.xml @@ -3,7 +3,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/imex-id-update/pom.xml b/imex-id-update/pom.xml index db7459438..dcc17ff2d 100755 --- a/imex-id-update/pom.xml +++ b/imex-id-update/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT uk.ac.ebi.intact.dataexchange.imex diff --git a/intact-cvutils/pom.xml b/intact-cvutils/pom.xml index 87f67fce4..fbe4a64cd 100644 --- a/intact-cvutils/pom.xml +++ b/intact-cvutils/pom.xml @@ -3,7 +3,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/intact-db-importer/pom.xml b/intact-db-importer/pom.xml index c8f39ae26..92f07fd90 100644 --- a/intact-db-importer/pom.xml +++ b/intact-db-importer/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-db-importer diff --git a/intact-enricher/pom.xml b/intact-enricher/pom.xml index 0cb4bfcf3..1fc4320de 100644 --- a/intact-enricher/pom.xml +++ b/intact-enricher/pom.xml @@ -4,7 +4,7 @@ intact-dataexchange-master uk.ac.ebi.intact.dataexchange - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/intact-mi-cluster-score/pom.xml b/intact-mi-cluster-score/pom.xml index d88af8727..f1f76fdd6 100644 --- a/intact-mi-cluster-score/pom.xml +++ b/intact-mi-cluster-score/pom.xml @@ -4,7 +4,7 @@ intact-dataexchange-master uk.ac.ebi.intact.dataexchange - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-mi-cluster-score diff --git a/intact-mutation-export/pom.xml b/intact-mutation-export/pom.xml index 4668f9e57..55e877a14 100644 --- a/intact-mutation-export/pom.xml +++ b/intact-mutation-export/pom.xml @@ -3,7 +3,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/intact-orthology-import/pom.xml b/intact-orthology-import/pom.xml index ff10e1961..d92b3adcb 100644 --- a/intact-orthology-import/pom.xml +++ b/intact-orthology-import/pom.xml @@ -8,7 +8,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-orthology-import diff --git a/intact-pdbe-import/pom.xml b/intact-pdbe-import/pom.xml index fbf09bcf4..bcb3f5b78 100644 --- a/intact-pdbe-import/pom.xml +++ b/intact-pdbe-import/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/intact-tasks/pom.xml b/intact-tasks/pom.xml index 0634e4a85..7ab4e5554 100644 --- a/intact-tasks/pom.xml +++ b/intact-tasks/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationFileEntry.java b/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationFileEntry.java index 41cd90fc2..cccf3a60f 100644 --- a/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationFileEntry.java +++ b/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationFileEntry.java @@ -1,6 +1,7 @@ package uk.ac.ebi.intact.task.mitab.pmid; import java.util.Date; +import java.util.List; /** * The publication entry is an mitab inputstream with a few information about the publication. A publicationEntry only contains interactions of a same publication. @@ -29,8 +30,14 @@ public class PublicationFileEntry implements Comparable{ private boolean isNegative; private String publicationDate; - - public PublicationFileEntry(Date createdDate, String pubId, StringBuffer mitab, boolean isNegative, String publicationDate){ + private List datasets; + + public PublicationFileEntry(Date createdDate, + String pubId, + StringBuffer mitab, + boolean isNegative, + String publicationDate, + List datasets) { super(); this.createdDate = createdDate; this.entryName = pubId; @@ -42,6 +49,7 @@ public PublicationFileEntry(Date createdDate, String pubId, StringBuffer mitab, } this.isNegative = isNegative; this.publicationDate = publicationDate; + this.datasets = datasets; } public Date getCreatedDate() { @@ -72,6 +80,14 @@ public void setPublicationDate(String publicationDate) { this.publicationDate = publicationDate; } + public List getDatasets() { + return datasets; + } + + public void setDatasets(List datasets) { + this.datasets = datasets; + } + @Override public int compareTo(PublicationFileEntry o) { final int BEFORE = -1; diff --git a/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationMitabItemProcessor.java b/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationMitabItemProcessor.java index 003dc8ab6..165359337 100644 --- a/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationMitabItemProcessor.java +++ b/intact-tasks/src/main/java/uk/ac/ebi/intact/task/mitab/pmid/PublicationMitabItemProcessor.java @@ -29,8 +29,6 @@ import uk.ac.ebi.intact.task.mitab.InteractionExpansionCompositeProcessor; import uk.ac.ebi.intact.task.util.FileNameGenerator; -import java.text.DateFormat; -import java.text.SimpleDateFormat; import java.util.*; import java.util.regex.Pattern; @@ -134,8 +132,9 @@ public SortedSet process(Publication item) throws Exceptio } String publicationDate = null; + List datasets = new ArrayList<>(); Collection pubAnnotations = AnnotatedObjectUtils.getPublicAnnotations(publication); - for (Annotation annot : pubAnnotations){ + for (Annotation annot : pubAnnotations) { if (annot.getCvTopic() != null){ // date if (CvTopic.PUBLICATION_YEAR_MI_REF.equals(annot.getCvTopic().getIdentifier())) { @@ -143,16 +142,20 @@ public SortedSet process(Publication item) throws Exceptio publicationDate = annot.getAnnotationText(); } } + // dataset + if (CvTopic.DATASET_MI_REF.equals(annot.getCvTopic().getIdentifier())) { + datasets.add(annot.getAnnotationText()); + } } } if (this.currentNegativeStringBuilder.length() > 0){ createPublicationEntry( - publicationEntries, publication.getCreated(), publication.getShortLabel(), this.currentNegativeStringBuilder, true, publicationDate); + publicationEntries, publication.getCreated(), publication.getShortLabel(), this.currentNegativeStringBuilder, true, publicationDate, datasets); } if (this.currentStringBuilder.length() > 0){ createPublicationEntry( - publicationEntries, publication.getCreated(), publication.getShortLabel(), this.currentStringBuilder, false, publicationDate); + publicationEntries, publication.getCreated(), publication.getShortLabel(), this.currentStringBuilder, false, publicationDate, datasets); } IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().clear(); @@ -228,7 +231,8 @@ private void createPublicationEntry(Set publicationEntries String publicationName, StringBuffer mitab, boolean isNegative, - String publicationDate) { + String publicationDate, + List datasets) { log.info("create publication entry : " + publicationName); // create a publication name @@ -236,7 +240,7 @@ private void createPublicationEntry(Set publicationEntries String entryName = publicationNameGenerator.createPublicationName(publicationName, null, isNegative); // create a publication entry - PublicationFileEntry publicationEntry = new PublicationFileEntry(date, entryName, mitab, isNegative, publicationDate); + PublicationFileEntry publicationEntry = new PublicationFileEntry(date, entryName, mitab, isNegative, publicationDate, datasets); // add the publication entry to the list of publication entries publicationEntries.add(publicationEntry); diff --git a/intact-tasks/src/test/java/uk/ac/ebi/intact/task/pmid/PublicationMitabItemWriterTest.java b/intact-tasks/src/test/java/uk/ac/ebi/intact/task/pmid/PublicationMitabItemWriterTest.java index 8f3262d2d..7d02da08d 100644 --- a/intact-tasks/src/test/java/uk/ac/ebi/intact/task/pmid/PublicationMitabItemWriterTest.java +++ b/intact-tasks/src/test/java/uk/ac/ebi/intact/task/pmid/PublicationMitabItemWriterTest.java @@ -137,11 +137,11 @@ public void test_write_publications() throws Exception { PublicationFileEntry oldEntryWithNoPublicationDate = pubWithNoPublicationDateEntries.iterator().next(); PublicationFileEntry newEntryWithNoPublicationDate = new PublicationFileEntry( - dateFormatForEntry.parse(secondCreatedDate), "12345_10", oldEntryWithNoPublicationDate.getBinaryInteractions(), false, null); + dateFormatForEntry.parse(secondCreatedDate), "12345_10", oldEntryWithNoPublicationDate.getBinaryInteractions(), false, null, new ArrayList<>()); pubWithNoPublicationDateEntries2.add(newEntryWithNoPublicationDate); PublicationFileEntry oldEntryWithPublicationDate = pubWithPublicationDateEntries.iterator().next(); PublicationFileEntry newEntryWithPublicationDate = new PublicationFileEntry( - dateFormatForEntry.parse(secondCreatedDate), "98765_10", oldEntryWithPublicationDate.getBinaryInteractions(), false, secondPublicationDate); + dateFormatForEntry.parse(secondCreatedDate), "98765_10", oldEntryWithPublicationDate.getBinaryInteractions(), false, secondPublicationDate, new ArrayList<>()); pubWithPublicationDateEntries2.add(newEntryWithPublicationDate); DateFormat format = new SimpleDateFormat("yyyy"); diff --git a/intact-uniprot-export/pom.xml b/intact-uniprot-export/pom.xml index 4b8731580..99d11bb26 100644 --- a/intact-uniprot-export/pom.xml +++ b/intact-uniprot-export/pom.xml @@ -3,7 +3,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/pom.xml b/pom.xml index 9f6dfbb39..f574d939b 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master pom - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT IntAct Data Exchange Data Exchange Master POM diff --git a/psimi/intact-psimi-exporter/pom.xml b/psimi/intact-psimi-exporter/pom.xml index e3ded35b2..43f4e2ea8 100644 --- a/psimi/intact-psimi-exporter/pom.xml +++ b/psimi/intact-psimi-exporter/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-psimi-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-psimi-exporter diff --git a/psimi/pom.xml b/psimi/pom.xml index 5663f78cc..a9969f538 100644 --- a/psimi/pom.xml +++ b/psimi/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psimitab/intact-calimocho-converters/pom.xml b/psimi/psimitab/intact-calimocho-converters/pom.xml index 9a10354f5..258b63291 100644 --- a/psimi/psimitab/intact-calimocho-converters/pom.xml +++ b/psimi/psimitab/intact-calimocho-converters/pom.xml @@ -4,7 +4,7 @@ psimitab-master uk.ac.ebi.intact.dataexchange.psimi - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-calimocho-converters diff --git a/psimi/psimitab/intact-jami-mitab/pom.xml b/psimi/psimitab/intact-jami-mitab/pom.xml index d600dcf50..5d6184913 100644 --- a/psimi/psimitab/intact-jami-mitab/pom.xml +++ b/psimi/psimitab/intact-jami-mitab/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange.psimi psimitab-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-jami-mitab diff --git a/psimi/psimitab/intact-psimitab-converters/pom.xml b/psimi/psimitab/intact-psimitab-converters/pom.xml index 639da1468..4d59d44bb 100755 --- a/psimi/psimitab/intact-psimitab-converters/pom.xml +++ b/psimi/psimitab/intact-psimitab-converters/pom.xml @@ -3,7 +3,7 @@ psimitab-master uk.ac.ebi.intact.dataexchange.psimi - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psimitab/intact-solr-home/pom.xml b/psimi/psimitab/intact-solr-home/pom.xml index 70d92f92b..9a7349d0d 100644 --- a/psimi/psimitab/intact-solr-home/pom.xml +++ b/psimi/psimitab/intact-solr-home/pom.xml @@ -3,7 +3,7 @@ psimitab-master uk.ac.ebi.intact.dataexchange.psimi - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psimitab/intact-solr/pom.xml b/psimi/psimitab/intact-solr/pom.xml index e5ab81cde..5d1770816 100644 --- a/psimi/psimitab/intact-solr/pom.xml +++ b/psimi/psimitab/intact-solr/pom.xml @@ -6,7 +6,7 @@ psimitab-master uk.ac.ebi.intact.dataexchange.psimi - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psimitab/pom.xml b/psimi/psimitab/pom.xml index 1c6be957e..f9af932d7 100644 --- a/psimi/psimitab/pom.xml +++ b/psimi/psimitab/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-psimi-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psixml/intact-jami-xml/pom.xml b/psimi/psixml/intact-jami-xml/pom.xml index 9c33a49b7..1102d0c76 100644 --- a/psimi/psixml/intact-jami-xml/pom.xml +++ b/psimi/psixml/intact-jami-xml/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-psixml - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-jami-xml diff --git a/psimi/psixml/intact-psixml-converters/pom.xml b/psimi/psixml/intact-psixml-converters/pom.xml index 492417902..10c6dbeb7 100644 --- a/psimi/psixml/intact-psixml-converters/pom.xml +++ b/psimi/psixml/intact-psixml-converters/pom.xml @@ -4,7 +4,7 @@ intact-psixml uk.ac.ebi.intact.dataexchange.psimi - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psixml/intact-psixml-dbimporter/pom.xml b/psimi/psixml/intact-psixml-dbimporter/pom.xml index 977d5a259..ca63fe8d9 100644 --- a/psimi/psixml/intact-psixml-dbimporter/pom.xml +++ b/psimi/psixml/intact-psixml-dbimporter/pom.xml @@ -6,7 +6,7 @@ intact-psixml uk.ac.ebi.intact.dataexchange.psimi - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT intact-psixml-dbimporter diff --git a/psimi/psixml/intact-psixml-exchange/pom.xml b/psimi/psixml/intact-psixml-exchange/pom.xml index d5e00573c..33d1ee9c6 100644 --- a/psimi/psixml/intact-psixml-exchange/pom.xml +++ b/psimi/psixml/intact-psixml-exchange/pom.xml @@ -3,7 +3,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-psixml - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/psimi/psixml/pom.xml b/psimi/psixml/pom.xml index 7ae8dff8f..924ef84d7 100644 --- a/psimi/psixml/pom.xml +++ b/psimi/psixml/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange.psimi intact-psimi-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT 4.0.0 diff --git a/structured-abstract/pom.xml b/structured-abstract/pom.xml index 2005f81e8..7be30db66 100644 --- a/structured-abstract/pom.xml +++ b/structured-abstract/pom.xml @@ -4,7 +4,7 @@ uk.ac.ebi.intact.dataexchange intact-dataexchange-master - 4.2.0-SNAPSHOT + 4.3.0-SNAPSHOT structured-abstract