Merge pull request #348 from arayabrain/feature/improve-snakemake-runner

improve snakemake runner
arayabrain · Jun 11, 2024 · e9cf786 · e9cf786
2 parents 9b0e3f1 + c580332
commit e9cf786
Show file tree

Hide file tree

Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/studio/app/Snakefile b/studio/app/Snakefile
@@ -26,6 +26,8 @@ else:
             FILETYPE.MICROSCOPE,
         ]:
             rule:
+                name:
+                    rule_name
                 input:
                     SmkUtils.input(details)
                 output:
@@ -36,6 +38,8 @@ else:
                     f"{DIRPATH.APP_DIR}/common/core/rules/data.py"
         else:
             rule:
+                name:
+                    rule_name
                 input:
                     SmkUtils.input(details)
                 output:

diff --git a/studio/app/common/core/rules/runner.py b/studio/app/common/core/rules/runner.py
@@ -150,6 +150,12 @@ def read_input_info(cls, input_files):
         input_info = {}
         for filepath in input_files:
             load_data = PickleReader.read(filepath)
+
+            # validate load_data content
+            assert (
+                type(load_data) is dict
+            ), f"Invalid node input data content. [{filepath}]"
+
             merged_nwb = cls.deep_merge(
                 load_data.pop("nwbfile", {}), input_info.pop("nwbfile", {})
             )

diff --git a/studio/app/common/core/snakemake/snakemake_rule.py b/studio/app/common/core/snakemake/snakemake_rule.py
@@ -44,14 +44,16 @@ def __init__(
         )
 
     def image(self) -> Rule:
-        return self.builder.set_type("image").build()
+        return self.builder.set_type(FILETYPE.IMAGE).build()
 
-    def csv(self, nodeType="csv") -> Rule:
+    def csv(self, nodeType=FILETYPE.CSV) -> Rule:
         return self.builder.set_type(nodeType).build()
 
     def hdf5(self) -> Rule:
         return (
-            self.builder.set_type("hdf5").set_hdf5Path(self._node.data.hdf5Path).build()
+            self.builder.set_type(FILETYPE.HDF5)
+            .set_hdf5Path(self._node.data.hdf5Path)
+            .build()
         )
 
     def mat(self) -> Rule: