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Add templates for displaying EDA phenotype variables as gene record attributes. Uses new WDK META_ATTRIBUTE_COLUMNS_FOR_CROSSTAB macro with two-parameter crosstab to dynamically pivot tall attributevalue data into columns based on attributegraph metadata. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Add template and anchor for categorizing phenotype EDA attributes under Phenomics ontology. Attributes will display in results and download sections of gene record pages. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Add TEMPLATE_ANCHOR comments for phenotypeEdaAttributeRef and phenotypeEdaAttributeQueries to enable template injection. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Create dataset-specific categories under Phenomics, with phenotype variables grouped under their respective datasets. This provides better organization in the gene record page. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Convert profileAttributeQueries and profileAttributeQueriesStrandSpecificRNASeq to use two-parameter crosstab with META_ATTRIBUTE_COLUMNS_FOR_CROSSTAB macro. This fixes the broken column name matching between data and meta queries (was generating pan1/pan2/pan3 but meta query returned pan_12345/pan_67890). Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Add gene_source_id column declaration and selection to fix error: "doesn't return the required primary key column gene_source_id". Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Modified PhenotypeVariables query to use LEFT OUTER JOIN to return all transcript attributes with null values when no matching data exists in EDA tables. Added filter to MetaPhenotypeVariables to exclude attributes where hidden field contains 'variableTree'. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Add the same hidden filter to the crosstab column definition query to ensure the pivot columns match the metadata columns. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Changed from jsonb ? operator to @> containment operator to prevent JDBC from interpreting ? as a parameter placeholder. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…e_id. WIP only numeric for now
Split the phenotypeEdaAttributeQueries template into separate templates for numeric and string data types: - phenotypeEdaAttributeQueriesNumeric: Uses number_value, histogram reporter - phenotypeEdaAttributeQueriesString: Uses string_value, word cloud reporter Updated templates to filter by data_type and apply appropriate reporters. Added both template anchors to transcriptAttributeQueries.xml and updated attribute refs and individuals.txt categories. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Added 'number' as column_type to MetaProfileSamples queries for both regular and strand-specific RNASeq profile attributes to be consistent with phenotype attribute metadata. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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This has been tested in ToxoDB. There is one known bug for Plasmo (maybe Fungi too?) where we need to pass not one but multiple organism abbreviations per dataset. |
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After fixes for profile sample ids.... Builds for PlasmoDB (with the WDK branch) |
Add 5 new templates to inject numeric and string cellular localization attributes with histogram and word cloud reporters. Create EdaCellularLocalizationGraphs queries and tables for gene record display. Rename GenesBySubcellularGeneList to GenesBySubcellularLocalization. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…stel/project_home/ApiCommonModel into meta-attributes
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Injector code for adding attributes dynamically for phenotype and rnaseq datasets. This is related to a PR for WDK