Merge branch 'dev'

cwl/updateCaseList.cwl

@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand: ['bash', 'run.sh']
+requirements:
+  InlineJavascriptRequirement: {}
+  DockerRequirement:
+    dockerPull: mskcc/helix:21.4.2
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: run.sh
+        entry: |-
+          set -eu
+          # get a comma-delim string of the sample names
+          samples_arg="${ return inputs.sample_ids.join(',') ; }"
+          input_file="${ return inputs.case_list.path ; }"
+          output_file="${ return inputs.output_filename }"
+
+          updateCaseList "\${input_file}" "\${samples_arg}" > "\${output_file}"
+
+inputs:
+  sample_ids: string[]
+  case_list: File
+  output_filename:
+    type: string
+    default: "cases.txt"
+outputs:
+  output_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_filename)

tests/test_updateCaseList_cwl.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+"""
+import os
+import sys
+import unittest
+
+THIS_DIR = os.path.dirname(os.path.realpath(__file__))
+PARENT_DIR = os.path.dirname(THIS_DIR)
+sys.path.insert(0, PARENT_DIR)
+from pluto.tools import PlutoTestCase
+from pluto.serializer import OFile
+sys.path.pop(0)
+
+
+class TestUpdateCaseList(PlutoTestCase):
+    cwl_file = 'updateCaseList.cwl'
+
+    def test_update_caselist_1(self):
+        """
+        """
+        case_list_str = """case_list_category: all_cases_in_study
+stable_id: pi_123_all
+case_list_name: All Tumors
+case_list_description: All tumor samples
+cancer_study_identifier: pi_123
+case_list_ids: Sample1\tSample2"""
+        input_file = os.path.join(self.tmpdir, "cases.txt")
+        with open(input_file, "w") as fout:
+            fout.write(case_list_str)
+
+        self.input = {
+            "case_list": {"class": "File", "path": input_file},
+            "sample_ids": ["Sample3", "Sample4"],
+            "output_filename": "cases_all.txt"
+        }
+        output_json, output_dir = self.run_cwl()
+
+        output_file = os.path.join(output_dir, 'cases_all.txt')
+
+        expected_output = {
+            "output_file": OFile(name = 'cases_all.txt', size = 208, hash = '59aa4b6b6695b7adfd4493390edd4038808a018f', dir = output_dir)
+        }
+
+        self.assertCWLDictEqual(output_json, expected_output)
+
+        with open(output_file) as fin:
+            text = fin.read()
+
+        expected_text = """case_list_category: all_cases_in_study
+stable_id: pi_123_all
+case_list_name: All Tumors
+case_list_description: All tumor samples
+cancer_study_identifier: pi_123
+case_list_ids: Sample1\tSample2\tSample3\tSample4
+"""
+        self.assertEqual(text, expected_text)
+
+
+
+
+if __name__ == "__main__":
+    unittest.main()