Merge pull request hms-dbmi-cellenics#518 from biomage-org/add-suppor…

…t-for-parse Add support for parse
biomage-org · Dec 21, 2023 · ded3d54 · ded3d54
2 parents cb5a71c + 542217d
commit ded3d54
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diff --git a/src/api.v2/helpers/s3/signedUrl.js b/src/api.v2/helpers/s3/signedUrl.js
@@ -106,6 +106,9 @@ const fileNameToReturn = {
   rhapsody: 'expression_data.st.gz',
   seurat: 'r.rds',
   '10x_h5': 'matrix.h5.gz',
+  featuresParse: 'all_genes.csv.gz',
+  barcodesParse: 'cell_metadata.csv.gz',
+  matrixParse: 'DGE.mtx.gz',
 };
 
 const getSampleFileDownloadUrl = async (experimentId, sampleId, fileType) => {

diff --git a/src/specs/models/samples-bodies/CreateSamples.v2.yaml b/src/specs/models/samples-bodies/CreateSamples.v2.yaml
@@ -14,6 +14,7 @@ items:
             - pattern: ^rhapsody$
             - pattern: ^10x_h5$
             - pattern: ^seurat$
+            - pattern: ^parse$
     options:
       type: object
 

diff --git a/src/sql/migrations/20231218171424_add_parse_technology.js b/src/sql/migrations/20231218171424_add_parse_technology.js
@@ -0,0 +1,15 @@
+/**
+ * @param { import("knex").Knex } knex
+ * @returns { Promise<void> }
+ */
+exports.up = async (knex) => {
+  await knex.raw("ALTER TYPE sample_technology ADD VALUE 'parse';");
+  await knex.raw("ALTER TYPE sample_file_type ADD VALUE 'matrixParse';");
+  await knex.raw("ALTER TYPE sample_file_type ADD VALUE 'barcodesParse';");
+  await knex.raw("ALTER TYPE sample_file_type ADD VALUE 'featuresParse';");
+};
+
+/**
+ * @returns { Promise < void> }
+*/
+exports.down = async () => { };