Test output of cmd_input_cmd function

Clinical-Genomics-Lund · Dec 11, 2023 · d1e4fc8 · d1e4fc8
1 parent abbc069
commit d1e4fc8
Show file tree

Hide file tree

Showing 2 changed files with 50 additions and 44 deletions.
diff --git a/tests/fixtures/ecoli/cdm_input.json b/tests/fixtures/ecoli/cdm_input.json
@@ -1,46 +1,46 @@
 [
-    {
-      "software": "quast",
-      "version": null,
-      "result": {
-        "total_length": 5103744,
-        "reference_length": 4641652,
-        "largest_contig": 359420,
-        "n_contigs": 109,
-        "n50": 173071,
-        "assembly_gc": 50.81,
-        "reference_gc": 50.79,
-        "duplication_ratio": 1.001
-      }
-    },
-    {
-      "software": "postalignqc",
-      "version": null,
-      "result": {
-        "ins_size": 375,
-        "ins_size_dev": 328,
-        "mean_cov": 210,
-        "pct_above_x": {
-          "1": 99.8908335372424,
-          "500": 0.0,
-          "250": 8.28531811957226,
-          "10": 99.8664503084393,
-          "1000": 0.0,
-          "30": 99.8493219487695,
-          "100": 99.7996110703293
-        },
-        "mapped_reads": 6078594,
-        "tot_reads": 7579030,
-        "iqr_median": 0.19047619047619,
-        "dup_pct": 0.0,
-        "dup_reads": 0
-      }
-    },
-    {
-      "software": "chewbbaca",
-      "version": null,
-      "result": {
-        "n_missing": 4228
-      }
+  {
+    "software": "postalignqc",
+    "version": null,
+    "result": {
+      "ins_size": 375,
+      "ins_size_dev": 328,
+      "mean_cov": 210,
+      "pct_above_x": {
+        "1": 99.8908335372424,
+        "500": 0.0,
+        "250": 8.28531811957226,
+        "10": 99.8664503084393,
+        "1000": 0.0,
+        "30": 99.8493219487695,
+        "100": 99.7996110703293
+      },
+      "mapped_reads": 6078594,
+      "tot_reads": 7579030,
+      "iqr_median": 0.19047619047619,
+      "dup_pct": 0.0,
+      "dup_reads": 0
     }
+  },
+  {
+    "software": "quast",
+    "version": null,
+    "result": {
+      "total_length": 5103744,
+      "reference_length": 4641652,
+      "largest_contig": 359420,
+      "n_contigs": 109,
+      "n50": 173071,
+      "assembly_gc": 50.81,
+      "reference_gc": 50.79,
+      "duplication_ratio": 1.001
+    }
+  },
+  {
+    "software": "chewbbaca",
+    "version": null,
+    "result": {
+      "n_missing": 4228
+    }
+  }
 ]
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -1,5 +1,6 @@
 """Test PRP cli functions."""
 
+import json
 from click.testing import CliRunner
 
 from prp.cli import create_bonsai_input, create_cdm_input, print_schema
@@ -107,7 +108,7 @@ def test_create_output_ecoli(
         assert result.exit_code == 0
 
 
-def test_cdm_input_cmd(ecoli_quast_path, ecoli_bwa_path, ecoli_chewbbaca_path):
+def test_cdm_input_cmd(ecoli_quast_path, ecoli_bwa_path, ecoli_chewbbaca_path, ecoli_cdm_input):
     """Test command for creating CDM input."""
     runner = CliRunner()
     with runner.isolated_filesystem():
@@ -127,3 +128,8 @@ def test_cdm_input_cmd(ecoli_quast_path, ecoli_bwa_path, ecoli_chewbbaca_path):
 
         # test successful execution of command
         assert result.exit_code == 0
+
+        # test correct output format
+        with open(output_fname) as inpt:
+            cmd_output = json.load(inpt)
+            assert cmd_output == ecoli_cdm_input