Merge pull request #52 from brain-bican/docs

jinja documentation fixes

Author: hkir-dev

requirements.txt

@@ -1,3 +1,3 @@
 requests
-cas-tools==0.0.1.dev44
+cas-tools==1.0.8
 jinja2

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="tdta",
-    version="0.1.0.dev22",
+    version="0.1.0.dev23",
     description="The aim of this project is to provide taxonomy development tools custom actions.",
     long_description=README,
     long_description_content_type="text/markdown",

src/tdta/__main__.py

@@ -81,12 +81,12 @@ def create_merge_operation_parser(subparsers):
 
 
 def create_docs_operation_parser(subparsers):
-    parser_export = subparsers.add_parser("docs", add_help=False,
+    parser_docs = subparsers.add_parser("docs", add_help=False,
                                           description="The documentation generation parser",
                                           help="Generates the taxonomy github pages docs.")
-    parser_export.add_argument('-db', '--database', action='store', type=pathlib.Path, required=True,
+    parser_docs.add_argument('-db', '--database', action='store', type=pathlib.Path, required=True,
                                help="Database file path.")
-    parser_export.add_argument('-o', '--output', action='store', type=pathlib.Path, required=True,
+    parser_docs.add_argument('-o', '--output', action='store', type=pathlib.Path, required=True,
                                help="Output file path.")
 
 

src/tdta/tdt_export.py

@@ -185,7 +185,7 @@ def parse_labelset_data(cta, sqlite_db, table_name):
                         auto_fill_object_from_row(automated_annotation, renamed_columns, row)
                         labelset.automated_annotation = automated_annotation
                     # cast rank to int
-                    if labelset.rank:
+                    if labelset.rank and str(labelset.rank).isdigit():
                         labelset.rank = int(labelset.rank)
                     labelsets.append(labelset)
                 cta.labelsets = labelsets