Merge pull request #150 from obophenotype/dendrogram_check

#100 github action for cell_set_preferred_alias uniqueness testing added

.github/workflows/dendrogram_check.yaml

@@ -0,0 +1,25 @@
+name: Validate Dendrograms
+
+# Since this validation fails, added as a separate action and disabled. I future can be integrated to main build task.
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    paths:
+      - 'src/dendrograms/**.json'
+      - '.github/workflows/dendrogram_check.yaml'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  validate-dendrograms:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: validate dendrograms
+        run: python ./src/scripts/dendrogram_validator.py

src/scripts/dendrogram_validator.py

@@ -0,0 +1,64 @@
+import logging
+import os
+from dendrogram_tools import dend_json_2_nodes_n_edges
+from abc import ABC, abstractmethod
+from os.path import isfile, join
+
+log = logging.getLogger(__name__)
+
+DENDROGRAM_FOLDER = join(os.path.dirname(os.path.realpath(__file__)), "../dendrograms")
+
+
+class BaseChecker(ABC):
+
+    @abstractmethod
+    def check(self, dend_file, dendrogram):
+        pass
+
+
+class PrefAliasUniquenessChecker(BaseChecker):
+    """
+    cell_set_preferred_alias should be unique within any one dendrogram - ignoring nodes with no
+    cell_set_preferred_alias, no two nodes should have the same one
+    """
+
+    def __init__(self):
+        self.reports = []
+
+    def check(self, dend_file, dendrogram):
+        pref_aliases = list()
+        is_valid = True
+        for o in dendrogram['nodes']:
+            if o['cell_set_preferred_alias']:
+                if o['cell_set_preferred_alias'] not in pref_aliases:
+                    pref_aliases.append(o['cell_set_preferred_alias'])
+                else:
+                    is_valid = False
+                    log.error("cell_set_preferred_alias '{}' is duplicate in {}"
+                              .format(o['cell_set_preferred_alias'], dend_file))
+        return is_valid
+
+
+class ValidationError(Exception):
+
+    def __init__(self, message):
+        Exception.__init__(self)
+        self.message = message
+
+
+def main():
+    log.info("Dendrogram validation started.")
+    files = [f for f in os.listdir(DENDROGRAM_FOLDER) if isfile(join(DENDROGRAM_FOLDER, f))]
+    is_valid = True
+    for file in files:
+        filename, file_extension = os.path.splitext(file)
+        if file_extension == ".json":
+            dend = dend_json_2_nodes_n_edges(join(DENDROGRAM_FOLDER, file))
+            is_valid &= PrefAliasUniquenessChecker().check(filename, dend)
+
+    if not is_valid:
+        raise ValidationError("Dendrogram validation failed and issues logged.")
+
+
+if __name__ == '__main__':
+    main()