From 345ff50a8af85b70404a652f63529e77020cdba0 Mon Sep 17 00:00:00 2001
From: Daniel Bolin <axbolin@iu.edu>
Date: Fri, 8 Mar 2024 14:53:01 -0500
Subject: [PATCH] Raise error in gene-expression if there are to few cells for
 gene ranking

---
 containers/gene-expression/context/main.py | 30 +++++++++++++++++++---
 containers/gene-expression/pipeline.cwl    |  6 ++++-
 steps/run-one.cwl                          | 23 +++++++++++++++--
 3 files changed, 52 insertions(+), 7 deletions(-)

diff --git a/containers/gene-expression/context/main.py b/containers/gene-expression/context/main.py
index 5f5b6f8..fa8ee9e 100644
--- a/containers/gene-expression/context/main.py
+++ b/containers/gene-expression/context/main.py
@@ -1,5 +1,6 @@
 import argparse
 import json
+import traceback
 import typing as t
 from pathlib import Path
 
@@ -121,6 +122,9 @@ def get_gene_expr(
     matrix.raw = matrix  # for getting gene names as output for sc.tl.rank_genes_groups
     filtered_matrix = filter_matrix(matrix, clid_column)
     filtered_matrix = add_ensemble_data(filtered_matrix, ensemble)
+    if len(filtered_matrix.obs[clid_column].unique()) <= 1:
+        raise ValueError("Data has too few unique cells for `rank_genes_groups`")
+
     sc.tl.rank_genes_groups(filtered_matrix, groupby=clid_column, n_genes=10)
     ct_marker_genes_df = format_marker_genes_df(
         pd.DataFrame(filtered_matrix.uns["rank_genes_groups"]["names"]),
@@ -156,10 +160,22 @@ def main(args: argparse.Namespace):
             CLI arguments, must contain "matrix", "clid_column",
             "gene_expr_column", and "output_matrix"
     """
-    matrix = get_gene_expr(
-        args.matrix, args.ensemble_lookup, args.clid_column, args.gene_expr_column
-    )
-    matrix.write_h5ad(args.output_matrix)
+    try:
+        matrix = get_gene_expr(
+            args.matrix, args.ensemble_lookup, args.clid_column, args.gene_expr_column
+        )
+        matrix.write_h5ad(args.output_matrix)
+    except Exception as error:
+        with open(args.output_report, "w") as file:
+            json.dump(
+                {
+                    "status": "failure",
+                    "cause": repr(error),
+                    "traceback": traceback.format_tb(error.__traceback__),
+                },
+                file,
+                indent=4,
+            )
 
 
 def _get_arg_parser() -> argparse.ArgumentParser:
@@ -180,6 +196,12 @@ def _get_arg_parser() -> argparse.ArgumentParser:
         default="matrix_with_gene_expr.h5ad",
         help="matrix with gene expressions output path",
     )
+    parser.add_argument(
+        "--output-report",
+        type=Path,
+        default="report.json",
+        help="Report file path in case of errors",
+    )
 
     return parser
 
diff --git a/containers/gene-expression/pipeline.cwl b/containers/gene-expression/pipeline.cwl
index 807793c..fdd5d2e 100644
--- a/containers/gene-expression/pipeline.cwl
+++ b/containers/gene-expression/pipeline.cwl
@@ -23,6 +23,10 @@ inputs:
 
 outputs:
   matrix_with_gene_expr:
-    type: File
+    type: File?
     outputBinding:
       glob: matrix_with_gene_expr.h5ad
+  report:
+    type: File?
+    outputBinding:
+      glob: report.json
diff --git a/steps/run-one.cwl b/steps/run-one.cwl
index 50511b0..a92ffad 100644
--- a/steps/run-one.cwl
+++ b/steps/run-one.cwl
@@ -72,7 +72,7 @@ steps:
       options:
         source: algorithm
         valueFrom: $(self.geneExpression || {})
-    out: [matrix_with_gene_expr]
+    out: [matrix_with_gene_expr, report]
   
   summarize:
     run: ../containers/extract-summary/pipeline.cwl
@@ -84,11 +84,30 @@ steps:
         valueFrom: $(self.summarize || {})
     out: [summary, annotations]
 
+  selectReport:
+    run:
+      class: ExpressionTool
+      requirements:
+        InlineJavascriptRequirement: {}
+
+      inputs:
+        reports: File[]
+      outputs:
+        report: File
+
+      expression: |
+        ${ return { report: inputs.reports[inputs.reports.length - 1] }; }
+    in:
+      reports:
+        source: [annotate/report, gene_expression/report]
+        pickValue: all_non_null
+    out: [report]
+
   collect:
     run: ./collect-files.cwl
     in:
       files:
-        source: [summarize/summary, summarize/annotations, annotate/report]
+        source: [summarize/summary, summarize/annotations, selectReport/report]
         pickValue: all_non_null
       outputDirectory:
         source: algorithm