Warn if no input for sprm-to-anndata (#88)

* Warn if no input for sprm-to-anndata * Try using HuBMAP's cwltool * Try 3.8 Co-authored-by: ilan-gold <[email protected]>
hubmapconsortium · Apr 15, 2022 · 6d88b87 · 6d88b87
1 parent fb94da7
commit 6d88b87
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -2,7 +2,7 @@ services:
   - docker
 language: python
 python:
-  - "3.7"
+  - "3.8"
 cache: pip
 script:
   - ./test.sh
diff --git a/containers/sprm-to-anndata/VERSION b/containers/sprm-to-anndata/VERSION
@@ -1 +1 @@
-0.0.8
+0.0.9
diff --git a/containers/sprm-to-anndata/context/main.py b/containers/sprm-to-anndata/context/main.py
@@ -128,7 +128,11 @@ def sprm_to_anndata(img_name, input_dir, output_dir):
 def main(input_dir, output_dir):
     output_dir.mkdir(exist_ok=True)
     # Get all img names by looking for input files of one type.
-    for input_file in input_dir.glob(f"*{POLYGON_FILE_SUFFUX}"):
+    glob = f"*{POLYGON_FILE_SUFFUX}"
+    input_files = list(input_dir.glob(glob))
+    if not input_files:
+        raise Exception(f'No matches for {glob} in {input_dir}')
+    for input_file in input_files:
         img_name = Path(input_file).name.split(".")[0]
         sprm_to_anndata(img_name, input_dir, output_dir)
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,3 @@
 # The runner exposes the CLI and the tool is the actual software.
 cwlref-runner==1.0
-cwltool==1.0.20190831161204
+git+https://github.com/hubmapconsortium/cwltool.git@docker-gpu#egg=cwltool