Provide override option when import generic assay data (for review) #3
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pvannierop
reviewed
Dec 16, 2019
| @@ -100,7 +100,7 @@ public void run() { | |||
| importer.importData(); | |||
| } else if (geneticProfile.getGeneticAlterationType() == GeneticAlterationType.GENERIC_ASSAY) { | |||
| // add all missing `genetic_entities` for this assay to the database | |||
| ImportGenericAssayEntity.importData(dataFile, geneticProfile.getGeneticAlterationType(), geneticProfile.getOtherMetaDataField("generic_entity_meta_properties")); | |||
| ImportGenericAssayEntity.importData(dataFile, geneticProfile.getGeneticAlterationType(), geneticProfile.getOtherMetaDataField("generic_entity_meta_properties"), true); | |||
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Why do we always overwrite the entities when importing profiles? Should this not be linked to the CLI variable?
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Previously, SV genetic profile was automatically generated for fusion files, but this could result in adding multiple genetic profiles with same names causing an exception Added unit tests for "split" fusions file
…ticprofile Add a check for existing "SV Genetic Profile" during import
Extend valid mRNA expression profile ids
Filter enrichments with no mapped gene object
update references to tcga provisional
CoExpression: fix error while querying for geneset molecular profile
Add case list sample counts api in study view
Update example_commands.md
…er-from-docs Remove skin.custom_header from docs
add v3.3.0 news item
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* Update Deployment-Procedure.md
Temporary fix for error in mutation enrichments
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Fix cBioPortal#7442. Publish docker images for each tag on github Note that we can't reuse the existing master image as proposed in the issue, because the version in the pom is determined on the fly from git i.e. the latest master version shows a different version in the api/info response than a proper tagged version even though the code might be completely the same otherwise.
…-action-docker Publish tags to docker hub
…y are shared with other studies
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Provide override option when import generic assay data
related document updated here.
Changes in this pr:
updateInfo) when import generic assay data.