From 110bd8df259793612538504403462947781ae8d1 Mon Sep 17 00:00:00 2001
From: Daniel Bolin <axbolin@iu.edu>
Date: Wed, 8 Nov 2023 09:00:18 -0500
Subject: [PATCH] Skip further processing when annotation tool fails

---
 src/algorithm/report.py           | 10 +++-------
 steps/check_annotation_report.cwl | 21 +++++++++++++++++++++
 steps/js/options-util.js          |  2 +-
 steps/run-one.cwl                 | 16 ++++++++++++++--
 4 files changed, 39 insertions(+), 10 deletions(-)
 create mode 100644 steps/check_annotation_report.cwl

diff --git a/src/algorithm/report.py b/src/algorithm/report.py
index 7a435f3..189bfef 100644
--- a/src/algorithm/report.py
+++ b/src/algorithm/report.py
@@ -9,7 +9,6 @@
 from pathlib import Path
 
 import anndata
-import pandas
 
 
 class Status(enum.Enum):
@@ -49,13 +48,10 @@ def save_matrix(self):
         if isinstance(self.data, Path):
             self.data = anndata.read_h5ad(self.data)
 
-        obs = self.data.obs
-        if not self.is_success():
-            # Create an empty observations frame with the same columns as the original
-            obs = pandas.DataFrame(columns=obs.columns)
-        obs['hra_prediction'] = obs[self.prediction_column]
+        if self.is_success():
+            self.data.obs["hra_prediction"] = self.data.obs[self.prediction_column]
 
-        obs.to_csv(self.annotations)
+        self.data.obs.to_csv(self.annotations)
         self.data.write_h5ad(self.matrix)
 
     def save_report(self):
diff --git a/steps/check_annotation_report.cwl b/steps/check_annotation_report.cwl
new file mode 100644
index 0000000..f226ef6
--- /dev/null
+++ b/steps/check_annotation_report.cwl
@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+class: ExpressionTool
+cwlVersion: v1.2
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  report:
+    type: File
+    loadContents: true
+  matrix: File
+
+outputs:
+  matrix_or_null: File?
+
+expression: |
+  ${
+    var isSuccess = /success/g.test(inputs.report.contents);
+    return { matrix_or_null: isSuccess ? inputs.matrix : null };
+  }
diff --git a/steps/js/options-util.js b/steps/js/options-util.js
index 25b40a8..76f1e1a 100644
--- a/steps/js/options-util.js
+++ b/steps/js/options-util.js
@@ -3,7 +3,7 @@ var ALGORITHMS = ["azimuth", "celltypist", "popv"];
 function _find_algorithm(obj) {
   for (var index = 0; index < ALGORITHMS.length; ++index) {
     var name = ALGORITHMS[index];
-    if (typeof obj[name] === "object") {
+    if (typeof obj[name] === "object" && obj[name] !== null) {
       return name;
     }
   }
diff --git a/steps/run-one.cwl b/steps/run-one.cwl
index 544a7ec..1eb1082 100644
--- a/steps/run-one.cwl
+++ b/steps/run-one.cwl
@@ -48,10 +48,18 @@ steps:
       algorithm: algorithm
     out: [annotations, annotated_matrix, report]
 
+  check_result:
+    run: ./check_annotation_report.cwl
+    in:
+      report: annotate/report
+      matrix: annotate/annotated_matrix
+    out: [matrix_or_null]
+
   crosswalk:
     run: ../containers/crosswalking/pipeline.cwl
+    when: $(!!inputs.matrix)
     in:
-      matrix: annotate/annotated_matrix
+      matrix: check_result/matrix_or_null
       options:
         source: algorithm
         valueFrom: $(self.crosswalk || {})
@@ -59,6 +67,7 @@ steps:
 
   gene_expression:
     run: ../containers/gene-expression/pipeline.cwl
+    when: $(!!inputs.matrix)
     in:
       matrix: crosswalk/matrix_with_crosswalking
       options:
@@ -68,6 +77,7 @@ steps:
   
   summarize:
     run: ../containers/extract-summary/pipeline.cwl
+    when: $(!!inputs.matrix)
     in:
       matrix: gene_expression/matrix_with_gene_expr
       options:
@@ -78,7 +88,9 @@ steps:
   collect:
     run: ./collect-files.cwl
     in:
-      files: [summarize/summary, summarize/annotations, annotate/report]
+      files:
+        source: [summarize/summary, summarize/annotations, annotate/report]
+        pickValue: all_non_null
       outputDirectory:
         source: algorithm
         valueFrom: $(selectOutputDirectory(self))