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feat: add pdc changelog
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- add PDC model v2.0.2
- update other changelogs with fixed MDF loader bug
- update models & links in docs
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@nelsonwmoore
nelsonwmoore committed May 1, 2024
1 parent 3db0eba commit 086979d
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Showing 23 changed files with 310,730 additions and 410,878 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -160,3 +160,4 @@ cython_debug/
#.idea/
**/liquibase.properties
changelogs/liquibase.properties.backup.01
.vscode
2 changes: 1 addition & 1 deletion changelogs/changelog.ini
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[changelog]
changeset_id = 98482
changeset_id = 125722
354 changes: 177 additions & 177 deletions changelogs/mappings/DSS/dss_map_changelog.xml
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14 changes: 7 additions & 7 deletions changelogs/mdb_setup_changelog.xml
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Expand Up @@ -22,25 +22,25 @@
<neo4j:cypher>create index if not exists for (n:tag) on (n.key, n.value)</neo4j:cypher>
</changeSet>
<changeSet id="8" author="NWM">
<neo4j:cypher>create fulltext index termDefn for (t:term) on each [t.origin_definition]</neo4j:cypher>
<neo4j:cypher>create fulltext index termDefn if not exists for (t:term) on each [t.origin_definition]</neo4j:cypher>
</changeSet>
<changeSet id="9" author="NWM">
<neo4j:cypher>create fulltext index termValue for (t:term) on each [t.value]</neo4j:cypher>
<neo4j:cypher>create fulltext index termValue if not exists for (t:term) on each [t.value]</neo4j:cypher>
</changeSet>
<changeSet id="10" author="NWM">
<neo4j:cypher>create fulltext index termValueDefn for (t:term) on each [t.value, t.origin_defintion]</neo4j:cypher>
<neo4j:cypher>create fulltext index termValueDefn if not exists for (t:term) on each [t.value, t.origin_defintion]</neo4j:cypher>
</changeSet>
<changeSet id="11" author="NWM">
<neo4j:cypher>create fulltext index tagKeyValue for (g:tag) on each [g.key, g.value]</neo4j:cypher>
<neo4j:cypher>create fulltext index tagKeyValue if not exists for (g:tag) on each [g.key, g.value]</neo4j:cypher>
</changeSet>
<changeSet id="12" author="NWM">
<neo4j:cypher>create fulltext index nodeHandle for (n:node) on each [n.handle]</neo4j:cypher>
<neo4j:cypher>create fulltext index nodeHandle if not exists for (n:node) on each [n.handle]</neo4j:cypher>
</changeSet>
<changeSet id="13" author="NWM">
<neo4j:cypher>create fulltext index edgeHandle for (n:relationship) on each [n.handle]</neo4j:cypher>
<neo4j:cypher>create fulltext index edgeHandle if not exists for (n:relationship) on each [n.handle]</neo4j:cypher>
</changeSet>
<changeSet id="14" author="NWM">
<neo4j:cypher>create fulltext index propHandle for (n:property) on each [n.handle]</neo4j:cypher>
<neo4j:cypher>create fulltext index propHandle if not exists for (n:property) on each [n.handle]</neo4j:cypher>
</changeSet>
<changeSet id="15" author="NWM">
<!--Only looks at node's first label-->
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57,007 changes: 19,009 additions & 37,998 deletions changelogs/models/CCDI/ccdi_changelog_1.7.2.xml
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43,100 changes: 14,373 additions & 28,727 deletions ...gelogs/models/CDS/cds_changelog_1.2.0.xml → ...elogs/models/CDS/cds_changelog_v1.3.3.xml
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9,403 changes: 0 additions & 9,403 deletions changelogs/models/CTDC/ctdc_changelog_9880861.xml
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7,053 changes: 7,053 additions & 0 deletions changelogs/models/CTDC/ctdc_changelog_vTBD.xml
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2,879 changes: 0 additions & 2,879 deletions changelogs/models/DSS/dss_changelog_0.0.1.xml
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2,160 changes: 2,160 additions & 0 deletions changelogs/models/DSS/dss_changelog_vTBD.xml
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135,351 changes: 0 additions & 135,351 deletions changelogs/models/GDC/gdc_changelog_cbe1102.xml
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110,283 changes: 110,283 additions & 0 deletions changelogs/models/GDC/gdc_changelog_v3.0.3.xml
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84,051 changes: 0 additions & 84,051 deletions changelogs/models/HTAN/htan_changelog.xml
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85,887 changes: 0 additions & 85,887 deletions changelogs/models/HTAN/htan_changelog_df49c65.xml
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51,693 changes: 51,693 additions & 0 deletions changelogs/models/HTAN/htan_changelog_v24.3.1.xml
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9,423 changes: 0 additions & 9,423 deletions changelogs/models/ICDC/icdc_changelog_dc6d5b0.xml
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7,056 changes: 7,056 additions & 0 deletions changelogs/models/ICDC/icdc_changelog_vTBD.xml
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86,150 changes: 86,150 additions & 0 deletions changelogs/models/PDC/pdc_changelog_v2.0.2.xml
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33 changes: 30 additions & 3 deletions changelogs/models/create_model_node_changelog.xml
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<?xml version='1.0' encoding='UTF-8'?>
<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:neo4j="http://www.liquibase.org/xml/ns/dbchangelog-ext" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-latest.xsd">
<?xml version='1.0' encoding='us-ascii'?>
<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:neo4j="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-latest.xsd">
<changeSet id="17" author="MAJ">
<neo4j:cypher>MERGE (:model {handle: 'CCDI', name: 'CCDI', repository: 'https://github.com/CBIIT/ccdi-model'})</neo4j:cypher>
</changeSet>
<changeSet id="18" author="MAJ">
<neo4j:cypher>MERGE (:model {handle: 'CDS', name: 'CDS', repository: 'https://github.com/CBIIT/cds-model'})</neo4j:cypher>
</changeSet>
<changeSet id="19" author="MAJ">
<neo4j:cypher>MERGE (:model {handle: 'DSS', name: 'DSS', repository: 'https://github.com/CBIIT/dss-model'})</neo4j:cypher>
<neo4j:cypher>MERGE (:model {handle: 'CRDC', name: 'CRDC', repository: 'https://github.com/CBIIT/crdc-model'})</neo4j:cypher>
</changeSet>
<changeSet id="20" author="MAJ">
<neo4j:cypher>MERGE (:model {handle: 'GDC', name: 'GDC', repository: 'https://github.com/CBIIT/gdc-model'})</neo4j:cypher>
Expand All @@ -24,4 +24,31 @@
<changeSet id="24" author="NWM">
<neo4j:cypher>MERGE (:model {handle: 'mCODE', name: 'mCODE', repository: 'https://github.com/CBIIT/mcode-model'})</neo4j:cypher>
</changeSet>
<changeSet id="25" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'CCDI'}) SET m.version = "v1.7.2"</neo4j:cypher>
</changeSet>
<changeSet id="26" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'CDS'}) SET m.version = "v1.3.3"</neo4j:cypher>
</changeSet>
<changeSet id="27" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'CRDC'}) SET m.version = "vTBD"</neo4j:cypher>
</changeSet>
<changeSet id="28" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'GDC'}) SET m.version = "v3.0.3"</neo4j:cypher>
</changeSet>
<changeSet id="29" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'ICDC'}) SET m.version = "vTBD"</neo4j:cypher>
</changeSet>
<changeSet id="30" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'CTDC'}) SET m.version = "vTBD"</neo4j:cypher>
</changeSet>
<changeSet id="31" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'HTAN'}) SET m.version = "v24.3.1"</neo4j:cypher>
</changeSet>
<changeSet id="32" author="NWM">
<neo4j:cypher>MATCH (m:model {handle: 'mCODE'}) SET m.version = "v3.0.0"</neo4j:cypher>
</changeSet>
<changeSet id="33" author="NWM">
<neo4j:cypher>MERGE (:model {handle: 'PDC', name: 'PDC', version: "v2.0.2", repository: 'https://github.com/CBIIT/pdc-model'})</neo4j:cypher>
</changeSet>
</databaseChangeLog>
24 changes: 12 additions & 12 deletions changelogs/models/create_origin_node_changelog.xml
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@@ -1,33 +1,33 @@
<?xml version='1.0' encoding='UTF-8'?>
<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:neo4j="http://www.liquibase.org/xml/ns/dbchangelog-ext" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-latest.xsd">
<changeSet id="25" author="MAJ">
<?xml version='1.0' encoding='us-ascii'?>
<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:neo4j="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-latest.xsd">
<changeSet id="34" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'CCDI', desc:'Childrens Cancer Data Initiative', url: 'https://github.com/CBIIT/ccdi-model'})</neo4j:cypher>
</changeSet>
<changeSet id="26" author="MAJ">
<changeSet id="35" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'CDS', desc:'Cancer Data Service', url: 'https://github.com/CBIIT/cds-model'})</neo4j:cypher>
</changeSet>
<changeSet id="27" author="MAJ">
<changeSet id="36" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'DSS', desc:'Data Standards Services', url: 'https://github.com/CBIIT/dss-model'})</neo4j:cypher>
</changeSet>
<changeSet id="28" author="MAJ">
<changeSet id="37" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'GDC', desc:'Genomic Data Commons', url: 'https://github.com/CBIIT/gdc-model'})</neo4j:cypher>
</changeSet>
<changeSet id="29" author="MAJ">
<changeSet id="38" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'NCIt', desc:'NCI Thesaurus', url: 'https://ncit.nci.nih.gov'})</neo4j:cypher>
</changeSet>
<changeSet id="30" author="MAJ">
<changeSet id="39" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'caDSR', desc:'Cancer Data Standards Repository', url: 'https://cadsr.cancer.gov'})</neo4j:cypher>
</changeSet>
<changeSet id="31" author="MAJ">
<changeSet id="40" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'MeSH', desc: 'Medical Subject Headings (NLM)', url:'https://www.ncbi.nlm.nih.gov/mesh'})</neo4j:cypher>
</changeSet>
<changeSet id="32" author="MAJ">
<changeSet id="41" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'PubMedCentral', desc: 'PubMed Central', url:'https://www.ncbi.nlm.nih.gov/pmc/'})</neo4j:cypher>
</changeSet>
<changeSet id="33" author="MAJ">
<changeSet id="42" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'OBI', desc: 'Ontology of Biomedical Investigations', url:'https://www.ebi.ac.uk/ols/ontologies/obi'})</neo4j:cypher>
</changeSet>
<changeSet id="34" author="MAJ">
<changeSet id="43" author="MAJ">
<neo4j:cypher>MERGE (:origin {name: 'HTAN', desc: 'Human Tumor Atlas Network', url:'https://humantumoratlas.org/'})</neo4j:cypher>
</changeSet>
</databaseChangeLog>
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