Add exit codes helper file (#26)

src/methods/geneformer/config.vsh.yaml

@@ -40,6 +40,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/read_anndata_partial.py
+  - path: /src/utils/exit_codes.py
 
 engines:
   - type: docker

src/methods/geneformer/script.py

@@ -24,13 +24,14 @@
 print(">>> Reading input...", flush=True)
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
+from exit_codes import exit_non_applicable
 
 adata = read_anndata(par["input"], X="layers/counts", obs="obs", var="var", uns="uns")
 
 if adata.uns["dataset_organism"] != "homo_sapiens":
-    raise ValueError(
+    exit_non_applicable(
         f"Geneformer can only be used with human data "
-        f"(dataset_organism == '{adata.uns['dataset_organism']}')"
+        f"(dataset_organism == \"{adata.uns['dataset_organism']}\")"
     )
 
 # Set adata.var_names to gene IDs

src/methods/scgpt/config.vsh.yaml

@@ -45,6 +45,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/read_anndata_partial.py
+  - path: /src/utils/exit_codes.py
 
 engines:
   - type: docker

src/methods/scgpt/script.py

@@ -22,17 +22,18 @@
 meta = {"name": "scgpt"}
 ## VIASH END
 
-print(f"====== scGPT version {scgpt.__version__} ======", flush=True)
-
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
+from exit_codes import exit_non_applicable
+
+print(f"====== scGPT version {scgpt.__version__} ======", flush=True)
 
 print("\n>>> Reading input files...", flush=True)
 print(f"Input H5AD file: '{par['input']}'", flush=True)
 adata = read_anndata(par["input"], X="layers/counts", obs="obs", var="var", uns="uns")
 
 if adata.uns["dataset_organism"] != "homo_sapiens":
-    raise ValueError(
+    exit_non_applicable(
         f"scGPT can only be used with human data "
         f"(dataset_organism == \"{adata.uns['dataset_organism']}\")"
     )

src/methods/scimilarity/config.vsh.yaml

@@ -21,6 +21,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/read_anndata_partial.py
+  - path: /src/utils/exit_codes.py
 engines:
   - type: docker
     image: openproblems/base_pytorch_nvidia:1.0.0

src/methods/scimilarity/script.py

@@ -20,12 +20,13 @@
 
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
+from exit_codes import exit_non_applicable
 
 print("Read input", flush=True)
 adata = read_anndata(par["input"], X="layers/counts", obs="obs", var="var", uns="uns")
 
 if adata.uns["dataset_organism"] != "homo_sapiens":
-    raise ValueError(
+    exit_non_applicable(
         f"SCimilarity can only be used with human data "
         f"(dataset_organism == \"{adata.uns['dataset_organism']}\")"
     )

src/methods/scprint/config.vsh.yaml

@@ -54,6 +54,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/read_anndata_partial.py
+  - path: /src/utils/exit_codes.py
 
 engines:
   - type: docker

src/methods/scprint/script.py

@@ -20,6 +20,7 @@
 
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
+from exit_codes import exit_non_applicable
 
 print(f"====== scPRINT version {scprint.__version__} ======", flush=True)
 
@@ -30,7 +31,7 @@
 elif input.uns["dataset_organism"] == "mus_musculus":
     input.obs["organism_ontology_term_id"] = "NCBITaxon:10090"
 else:
-    raise ValueError(
+    exit_non_applicable(
         f"scPRINT requires human or mouse data, not '{input.uns['dataset_organism']}'"
     )
 adata = input.copy()

src/methods/uce/config.vsh.yaml

@@ -28,6 +28,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/read_anndata_partial.py
+  - path: /src/utils/exit_codes.py
 
 engines:
   - type: docker

src/methods/uce/script.py

@@ -46,6 +46,7 @@
 print(">>> Reading input...", flush=True)
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
+from exit_codes import exit_non_applicable
 
 adata = read_anndata(par["input"], X="layers/counts", obs="obs", var="var", uns="uns")
 
@@ -54,7 +55,7 @@
 elif adata.uns["dataset_organism"] == "mus_musculus":
     species = "mouse"
 else:
-    raise ValueError(f"Species '{adata.uns['dataset_organism']}' not yet implemented")
+    exit_non_applicable(f"Species '{adata.uns['dataset_organism']}' not yet implemented")
 
 print("\n>>> Creating working directory...", flush=True)
 work_dir = tempfile.TemporaryDirectory()

src/utils/exit_codes.py

@@ -0,0 +1,6 @@
+import sys
+
+
+def exit_non_applicable(msg):
+    print(f"NON-APPLICABLE ERROR: {msg}", flush=True)
+    sys.exit(99)