Merge pull request #506 from kbase/fix_biolog_data_parser

Fix biolog data parser
kbase · Oct 16, 2023 · 1f94ddd · 1f94ddd
2 parents 5cf038c + 547b3bf
commit 1f94ddd
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Showing 4 changed files with 14 additions and 5 deletions.
diff --git a/src/common/product_models/heatmap_common_models.py b/src/common/product_models/heatmap_common_models.py
@@ -25,6 +25,8 @@
 FIELD_HEATMAP_CATEGORY = "category"
 FIELD_HEATMAP_COLUMNS = "columns"
 FIELD_HEATMAP_CATEGORIES = "categories"
+FIELD_HEATMAP_CELL_DETAIL_ENTRY_VALUE = "val"
+FIELD_HEATMAP_CELL_DETAIL_ENTRY_ID = "id"
 
 
 _FLD_CELL_ID = Field(

diff --git a/src/loaders/compute_tools/microtrait/microtrait.py b/src/loaders/compute_tools/microtrait/microtrait.py
@@ -19,7 +19,9 @@
     FIELD_HEATMAP_DESCR,
     FIELD_HEATMAP_TYPE,
     FIELD_HEATMAP_CATEGORY,
-    ColumnType)
+    FIELD_HEATMAP_CELL_DETAIL_ENTRY_ID,
+    FIELD_HEATMAP_CELL_DETAIL_ENTRY_VALUE,
+    ColumnType,)
 from src.common.storage.field_names import FLD_KBASE_ID
 from src.loaders.common import loader_common_names
 from src.loaders.compute_tools.tool_common import (
@@ -237,8 +239,9 @@ def _run_microtrait(tool_safe_data_id: str, data_id: str, fna_file: Path, genome
 
         trait_counts_df[_DETECTED_GENE_SCORE_COL] = trait_counts_df[
             loader_common_names.UNWRAPPED_GENE_COL].apply(
-            lambda x: {gene: detected_genes_score.get(gene) for gene in str(x).split(';') if
-                       gene in detected_genes_score})
+            lambda x: [{FIELD_HEATMAP_CELL_DETAIL_ENTRY_ID: gene,
+                        FIELD_HEATMAP_CELL_DETAIL_ENTRY_VALUE: detected_genes_score.get(gene)} for gene in
+                       str(x).split(';') if gene in detected_genes_score])
     else:
         raise ValueError('Please set environment variable MT_TRAIT_UNWRAPPED_FILE')
 

diff --git a/src/loaders/compute_tools/microtrait/versions.yaml b/src/loaders/compute_tools/microtrait/versions.yaml
@@ -8,4 +8,8 @@ versions:
   - version: 0.1.2
     date: 2023-08-24
     notes: |
-      - upgrade pydantic to 2.3.0
+      - upgrade pydantic to 2.3.0
+  - version: 0.1.3
+    date: 2023-10-16
+    notes: |
+      - fix cells value data type
diff --git a/src/loaders/genome_collection/parse_PMI_biolog_data.py b/src/loaders/genome_collection/parse_PMI_biolog_data.py
@@ -228,7 +228,7 @@ def generate_pmi_biolog_heatmap_data(
             # append a document for the heatmap cell details
             heatmap_cell_details.append({
                 FIELD_HEATMAP_CELL_ID: cell_uuid,
-                FIELD_HEATMAP_VALUES: dict(),  # 'values' for biolog is always empty
+                FIELD_HEATMAP_VALUES: list(),  # 'values' for biolog is always empty
                 FLD_COLLECTION_ID: kbase_collection,
                 FLD_LOAD_VERSION: load_ver,
                 FLD_ARANGO_KEY: collection_data_id_key(kbase_collection, load_ver, cell_uuid),