[#58] get data from biolink

scripts/configuration-generator.py

@@ -0,0 +1,41 @@
+#!/usr/bin/python
+
+# grab the curie mapping
+# scan the current directory for the tsvs
+# output an owlsim config file
+
+import yaml
+import urllib2
+import fnmatch
+import os
+
+def main():
+
+    # Getting tsv file path
+    tsvs = []
+    for root, _, filenames in os.walk('.'):
+        for filename in fnmatch.filter(filenames, '*.tsv'):
+            tsvs.append(os.path.abspath(os.path.join(root, filename))) # Check that: it looks insane to get the absolute path...
+
+    dataTsvs = [filename for filename in tsvs if not filename.endswith('label.tsv')]
+    labelTsvs = [filename for filename in tsvs if filename.endswith('label.tsv')]
+
+    # Note: the yaml dump is buggy with the empty string key, so I'm just appending the raw string and add indentation manually
+    curies = urllib2.urlopen("https://raw.githubusercontent.com/monarch-initiative/dipper/master/dipper/curie_map.yaml").read()
+
+    data = dict(
+        ontologyUris = ['http://purl.obolibrary.org/obo/upheno/monarch.owl'],
+        ontologyDataUris = [],
+        dataTsvs = dataTsvs,
+        labelTsvs = labelTsvs
+    )
+
+    print("Generating owlsim configuration")
+    with open('configuration.yaml', 'w') as outfile:
+        yaml.dump(data, outfile, default_flow_style=False)
+        outfile.write("curies:\n")
+        outfile.write('  '.join(curies.splitlines(True)))
+
+
+if __name__ == "__main__":
+    main()