Merge pull request #31 from kbase/dev-fix-tests

Make tests pass

.travis.yml

@@ -1,25 +1,28 @@
 sudo: required
 language: python
-python: "3.7"
+python: "3.7.5"
 
 env:
     # TODO add more arango versions when they exist
     # TODO could split tests so non-arango tests aren't run for every version
     - ARANGODB_VER=3.5.0 ARANGODB_V=35
 
 install:
+  - python --version
+  - which python
   - export ARANGO_FILE=arangodb3-linux-$ARANGODB_VER.tar.gz
   - wget https://download.arangodb.com/arangodb$ARANGODB_V/Community/Linux/$ARANGO_FILE
   - tar xfz $ARANGO_FILE
   - export ARANGO=`pwd`/arangodb3-$ARANGODB_VER/bin/arangodb
   - export ARANGOD=`pwd`/arangodb3-$ARANGODB_VER/usr/sbin/arangod
 
-  - pip install pipenv coverage pytest-cov python-coveralls flake8
+  # TODO move everything except pipenv to Pipfile dev section and change to make test
+  - pip install pipenv coverage pytest-cov coveralls flake8
   - pipenv install
 
 script:
-# TODO FLAKE8 lots of errors. Need to be fixed, but later
-#  - flake8 src
+# TODO change to make test
+  - flake8 .
   - mkdir arangodata
   - $ARANGO start --server.arangod=$ARANGOD --starter.mode single --starter.data-dir ./arangodata
   - export PYTHONPATH=$(pwd):$(pwd)/src; pytest --verbose --cov=. .

Pipfile

@@ -4,6 +4,7 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
+flake8 = "*"
 
 [packages]
 requests = "==2.22.0"

relation_engine/batchload/time_travelling_database.py

@@ -250,7 +250,7 @@ def register_load_start(
 
         try:
             self._database.aql.execute(
-                f'INSERT @d in @@col',
+                'INSERT @d in @@col',
                 bind_vars={'d': doc, '@col': self._registry_collection.name}
             )
         except _AQLQueryExecuteError as e:
@@ -273,7 +273,7 @@ def register_load_complete(self, load_namespace, load_version, current_time):
 
         try:
             self._database.aql.execute(
-                f'UPDATE @d in @@col',
+                'UPDATE @d in @@col',
                 bind_vars={'d': doc, '@col': self._registry_collection.name}
             )
         except _AQLQueryExecuteError as e:
@@ -294,7 +294,7 @@ def register_load_rollback(self, load_namespace, load_version):
 
         try:
             self._database.aql.execute(
-                f'UPDATE @d in @@col',
+                'UPDATE @d in @@col',
                 bind_vars={'d': doc, '@col': self._registry_collection.name}
             )
         # could combine some of this code with the above method... meh

relation_engine/ontologies/obograph/helper_scripts/go_obograph_download_archive.py

@@ -34,9 +34,9 @@ def main():
 
     root = requests.get(GO_RELEASES_URL).text
     # hacky hacky hacky, could be much less fragile, but who cares
-    for l in root.split('\n'):
-        if GO_RELEASES_URL in l and INDEX_HTML in l:
-            date = l.split(GO_RELEASES_URL)[-1].split('/' + INDEX_HTML)[0]
+    for line in root.split('\n'):
+        if GO_RELEASES_URL in line and INDEX_HTML in line:
+            date = line.split(GO_RELEASES_URL)[-1].split('/' + INDEX_HTML)[0]
             download_obograph(a.dir, date)
 
 

relation_engine/taxa/gtdb/parsers.py

@@ -37,13 +37,13 @@ def __iter__(self):
         for line in self._fh:
             accession, lineage = line.strip().split('\t')
             lineage = _get_lineage(lineage)
-            for l in lineage:
-                l_id = _taxon_to_id(l)
+            for lin in lineage:
+                l_id = _taxon_to_id(lin)
                 if l_id not in seen_taxa:
                     yield {
                         'id': l_id,
-                        'rank': _TAXA_TYPES[l['abbrev']],
-                        'name': l['name']
+                        'rank': _TAXA_TYPES[lin['abbrev']],
+                        'name': lin['name']
                     }
                 seen_taxa.add(l_id)
             yield {