Update spec to 2.8.1 #32
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
arteymix
force-pushed
the
update-spec-to-2.8.1
branch
from
d19a0fa
to
222acdf
Compare
arteymix
commented
Jul 31, 2024
| @@ -36,13 +36,12 @@ class FactorValueValueObject(object): | |||
| 'statements': 'list[StatementValueObject]', | |||
| 'summary': 'str', | |||
| 'factor_id': 'int', | |||
| 'char_id': 'int', | |||
arteymix
commented
Jul 31, 2024
| 'bio_assay_set_id': 'int', | ||
| 'source_experiment': 'int', | ||
| 'experiment_analyzed_id': 'int', | ||
| 'source_experiment_id': 'int', |
There was a problem hiding this comment.
@oganm those were renamed, backward-compatible fields are provided below.
arteymix
commented
Jul 31, 2024
| @@ -6461,7 +6475,7 @@ components: | |||
| \ the exact phrase \"alpha beta gamma\". \ | |||
| \ |\n| Field | `shortName:GSE00001` \ | |||
| \ | Results with short name GSE00001. <details><summary>List of supported\ | |||
| \ fields</summary><h2>ubic.gemma.model.genome.gene.GeneSet</h2><ul><li>description</li><li>name</li><li>characteristics.value</li><li>characteristics.valueUri</li><li>literatureSources.abstractText</li><li>literatureSources.authorList</li><li>literatureSources.fullTextUri</li><li>literatureSources.name</li><li>literatureSources.title</li><li>sourceAccession.accession</li><li>literatureSources.chemicals.name</li><li>literatureSources.chemicals.registryNumber</li><li>literatureSources.keywords.term</li><li>literatureSources.meshTerms.term</li><li>literatureSources.pubAccession.accession</li><li>members.gene.ensemblId</li><li>members.gene.name</li><li>members.gene.ncbiGeneId</li><li>members.gene.officialName</li><li>members.gene.officialSymbol</li><li>members.gene.accessions.accession</li><li>members.gene.aliases.alias</li><li>members.gene.products.name</li><li>members.gene.products.ncbiGi</li><li>members.gene.products.previousNcbiId</li><li>members.gene.products.accessions.accession</li></ul><h2>ubic.gemma.model.expression.experiment.ExpressionExperiment</h2><ul><li>description</li><li>name</li><li>shortName</li><li>accession.accession</li><li>bioAssays.description</li><li>bioAssays.name</li><li>characteristics.value</li><li>characteristics.valueUri</li><li>experimentalDesign.description</li><li>experimentalDesign.name</li><li>otherRelevantPublications.abstractText</li><li>otherRelevantPublications.authorList</li><li>otherRelevantPublications.fullTextUri</li><li>otherRelevantPublications.name</li><li>otherRelevantPublications.title</li><li>primaryPublication.abstractText</li><li>primaryPublication.authorList</li><li>primaryPublication.fullTextUri</li><li>primaryPublication.name</li><li>primaryPublication.title</li><li>bioAssays.accession.accession</li><li>bioAssays.sampleUsed.name</li><li>experimentalDesign.experimentalFactors.description</li><li>experimentalDesign.experimentalFactors.name</li><li>otherRelevantPublications.chemicals.name</li><li>otherRelevantPublications.chemicals.registryNumber</li><li>otherRelevantPublications.keywords.term</li><li>otherRelevantPublications.meshTerms.term</li><li>otherRelevantPublications.pubAccession.accession</li><li>primaryPublication.chemicals.name</li><li>primaryPublication.chemicals.registryNumber</li><li>primaryPublication.keywords.term</li><li>primaryPublication.meshTerms.term</li><li>primaryPublication.pubAccession.accession</li><li>bioAssays.sampleUsed.characteristics.value</li><li>bioAssays.sampleUsed.characteristics.valueUri</li><li>experimentalDesign.experimentalFactors.category.category</li><li>experimentalDesign.experimentalFactors.category.categoryUri</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.object</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.objectUri</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.secondObject</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.secondObjectUri</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.value</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.valueUri</li></ul><h2>ubic.gemma.model.expression.designElement.CompositeSequence</h2><ul><li>description</li><li>name</li><li>biologicalCharacteristic.name</li><li>biologicalCharacteristic.sequenceDatabaseEntry.accession</li></ul><h2>ubic.gemma.model.expression.arrayDesign.ArrayDesign</h2><ul><li>description</li><li>name</li><li>shortName</li><li>alternateNames.name</li><li>externalReferences.accession</li></ul><h2>ubic.gemma.model.genome.Gene</h2><ul><li>ensemblId</li><li>name</li><li>ncbiGeneId</li><li>officialName</li><li>officialSymbol</li><li>accessions.accession</li><li>aliases.alias</li><li>products.name</li><li>products.ncbiGi</li><li>products.previousNcbiId</li><li>products.accessions.accession</li></ul><h2>ubic.gemma.model.genome.biosequence.BioSequence</h2><ul><li>name</li><li>sequenceDatabaseEntry.accession</li></ul></details>\ | |||
| \ fields</summary><h2>ubic.gemma.model.expression.experiment.ExpressionExperiment</h2><ul><li>description</li><li>name</li><li>shortName</li><li>accession.accession</li><li>bioAssays.description</li><li>bioAssays.name</li><li>characteristics.value</li><li>characteristics.valueUri</li><li>experimentalDesign.description</li><li>experimentalDesign.name</li><li>otherRelevantPublications.abstractText</li><li>otherRelevantPublications.authorList</li><li>otherRelevantPublications.fullTextUri</li><li>otherRelevantPublications.name</li><li>otherRelevantPublications.title</li><li>primaryPublication.abstractText</li><li>primaryPublication.authorList</li><li>primaryPublication.fullTextUri</li><li>primaryPublication.name</li><li>primaryPublication.title</li><li>bioAssays.accession.accession</li><li>bioAssays.sampleUsed.name</li><li>experimentalDesign.experimentalFactors.description</li><li>experimentalDesign.experimentalFactors.name</li><li>otherRelevantPublications.chemicals.name</li><li>otherRelevantPublications.chemicals.registryNumber</li><li>otherRelevantPublications.keywords.term</li><li>otherRelevantPublications.meshTerms.term</li><li>otherRelevantPublications.pubAccession.accession</li><li>primaryPublication.chemicals.name</li><li>primaryPublication.chemicals.registryNumber</li><li>primaryPublication.keywords.term</li><li>primaryPublication.meshTerms.term</li><li>primaryPublication.pubAccession.accession</li><li>bioAssays.sampleUsed.characteristics.value</li><li>bioAssays.sampleUsed.characteristics.valueUri</li><li>experimentalDesign.experimentalFactors.category.category</li><li>experimentalDesign.experimentalFactors.category.categoryUri</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.object</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.objectUri</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.secondObject</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.secondObjectUri</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.value</li><li>experimentalDesign.experimentalFactors.factorValues.characteristics.valueUri</li></ul><h2>ubic.gemma.model.genome.gene.GeneSet</h2><ul><li>description</li><li>name</li><li>characteristics.value</li><li>characteristics.valueUri</li><li>literatureSources.abstractText</li><li>literatureSources.authorList</li><li>literatureSources.fullTextUri</li><li>literatureSources.name</li><li>literatureSources.title</li><li>sourceAccession.accession</li><li>literatureSources.chemicals.name</li><li>literatureSources.chemicals.registryNumber</li><li>literatureSources.keywords.term</li><li>literatureSources.meshTerms.term</li><li>literatureSources.pubAccession.accession</li><li>members.gene.ensemblId</li><li>members.gene.name</li><li>members.gene.ncbiGeneId</li><li>members.gene.officialName</li><li>members.gene.officialSymbol</li><li>members.gene.accessions.accession</li><li>members.gene.aliases.alias</li><li>members.gene.products.name</li><li>members.gene.products.ncbiGi</li><li>members.gene.products.previousNcbiId</li><li>members.gene.products.accessions.accession</li></ul><h2>ubic.gemma.model.expression.designElement.CompositeSequence</h2><ul><li>description</li><li>name</li><li>biologicalCharacteristic.name</li><li>biologicalCharacteristic.sequenceDatabaseEntry.accession</li></ul><h2>ubic.gemma.model.expression.arrayDesign.ArrayDesign</h2><ul><li>description</li><li>name</li><li>shortName</li><li>alternateNames.name</li><li>externalReferences.accession</li></ul><h2>ubic.gemma.model.genome.Gene</h2><ul><li>ensemblId</li><li>name</li><li>ncbiGeneId</li><li>officialName</li><li>officialSymbol</li><li>accessions.accession</li><li>aliases.alias</li><li>products.name</li><li>products.ncbiGi</li><li>products.previousNcbiId</li><li>products.accessions.accession</li></ul><h2>ubic.gemma.model.genome.biosequence.BioSequence</h2><ul><li>name</li><li>sequenceDatabaseEntry.accession</li></ul></details>\ | |||
There was a problem hiding this comment.
I'll see if I can order those consistently...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.