Prepare app for production

lib/kb_djornl/__init__.py

@@ -21,7 +21,7 @@
 
 
 def run_rwr_cv(config, clients):  # pylint: disable=too-many-locals
-    """ run RWR_CV and generate a report """
+    """run RWR_CV and generate a report"""
     params = config.get("params")
     shared = config.get("shared")
     dfu = clients["dfu"]
@@ -110,7 +110,7 @@ def run_rwr_cv(config, clients):  # pylint: disable=too-many-locals
 def run_rwr_loe(
     config, clients
 ):  # pylint: disable=too-many-locals, too-many-statements
-    """ run RWR_LOE and generate a report """
+    """run RWR_LOE and generate a report"""
     params = config.get("params")
     shared = config.get("shared")
     dfu = clients["dfu"]

lib/kb_djornl/utils.py

@@ -14,7 +14,7 @@
 def create_tair10_featureset(
     genes, config, dfu, gsu
 ):  # pylint: disable=too-many-locals
-    """ Create an Arabidopsis thaliana featureset from a list of genes. """
+    """Create an Arabidopsis thaliana featureset from a list of genes."""
     params = config.get("params")
     workspace_id = params["workspace_id"]
     genome_ref = "Phytozome_Genomes/Athaliana_TAIR10"
@@ -56,7 +56,7 @@ def create_tair10_featureset(
 
 
 def cytoscape_node(node, rank, seed=False):
-    """ convert nodedata into cytoscape format """
+    """convert nodedata into cytoscape format"""
     return dict(
         defline=node["defline"],
         geneSymbols=node["gene_symbols"],
@@ -71,7 +71,7 @@ def cytoscape_node(node, rank, seed=False):
 
 
 def cytoscape_edge(edge):
-    """ convert edge data into cytoscape format """
+    """convert edge data into cytoscape format"""
     return dict(
         id=edge["_id"],
         edgeType=edge["edge_type"],
@@ -170,42 +170,42 @@ def fork_rwr_loe(reports_path, params, dfu):  # pylint: disable=too-many-locals
 
 
 def genes_to_rwr_tsv(genes):
-    """ convert a list of genes to a tsv string for use with RWR tools"""
+    """convert a list of genes to a tsv string for use with RWR tools"""
     return "".join([f"report\t{gene}\n" for gene in genes])
 
 
 def get_wsurl():
-    """ Get the workspace url for this environment. """
+    """Get the workspace url for this environment."""
     config_file = os.environ.get("KB_DEPLOYMENT_CONFIG")
     config_p = configparser.ConfigParser()
     config_p.read(config_file)
     return config_p["kb_djornl"]["workspace-url"]
 
 
 def get_genes_from_tair10_featureset(featureset_ref, dfu):
-    """ Read genes from a A. thaliana featureset. """
+    """Read genes from a A. thaliana featureset."""
     featureset_response = dfu.get_objects({"object_refs": [featureset_ref]})
     featureset = featureset_response["data"][0]["data"]
     return featureset["element_ordering"]
 
 
 def load_manifest():
-    """ Load the manifest yaml file """
+    """Load the manifest yaml file"""
     manifest_path = os.path.join(DATA_ROOT, "prerelease/manifest.yaml")
     with open(manifest_path) as manifest_file:
         manifest = yaml.safe_load(manifest_file)
     return manifest
 
 
 def normalized_node_id(node_id):
-    """ normalize node id """
+    """normalize node id"""
     if "/" in node_id:
         return node_id.split("/")[1]
     return node_id
 
 
 def object_info_as_dict(object_info):
-    """ Convert a KBase object_info list into a dictionary. """
+    """Convert a KBase object_info list into a dictionary."""
     [
         _id,
         _name,
@@ -288,7 +288,7 @@ def put_graph_metadata(metadata, config):  # pylint: disable=too-many-locals
 
 
 def query_sqlite(genes):  # pylint: disable=too-many-locals
-    """ Query the data loaded into sqlite3 based on seed genes """
+    """Query the data loaded into sqlite3 based on seed genes"""
     networks_path = os.path.join(DATA_ROOT, "networks.db")
     con = sqlite3.connect(networks_path)
     manifest = load_manifest()

scripts/postinstall.py

@@ -13,7 +13,7 @@
 
 
 def download_assets(assets, endpoint, cookies):
-    """Download assets from endpoint using cookies. """
+    """Download assets from endpoint using cookies."""
     destination_path = "test_local/workdir/tmp/reports"
     for asset in assets:
         asset_url = endpoint._replace(path=asset).geturl()

scripts/refdata-load.sh

@@ -6,7 +6,10 @@ set -e
 KB_ENV=$(grep -e kbase_endpoint /kb/module/work/config.properties \
     | cut -f3 -d'/' | cut -f1 -d. \
 )
-if [[ "$KB_ENV" == 'ci' ]]; then
+echo Detected environment $KB_ENV
+if [[ "$KB_ENV" == 'kbase' ]]; then
+    RWRTOOLS_BLOB_URL='https://kbase.us/services/shock-api/node/e27516d4-e54d-4931-91f7-7d36c25fe3cc?download_raw'
+elif [[ "$KB_ENV" == 'ci' ]]; then
     RWRTOOLS_BLOB_URL='https://ci.kbase.us/services/shock-api/node/0481bd3b-14b4-40f9-a585-aee531235edc?download_raw';
 elif [[ "$KB_ENV" == 'appdev' ]]; then
     RWRTOOLS_BLOB_URL='https://appdev.kbase.us/services/shock-api/node/29d12bac-53b9-451f-8fc6-48124f1c2f8f?download_raw';

scripts/rwrtools-env-create.sh

@@ -4,7 +4,7 @@ set -x
 set -e
 
 source /miniconda/etc/profile.d/conda.sh
-conda env create -vv -f ./data/rwrtools.yml
+conda env create -v -f ./data/rwrtools.yml
 conda activate rwrtools
 R --no-restore --no-save << HEREDOC
 if (!requireNamespace("BiocManager", quietly = TRUE))

test/kb_djornl_server_test.py

@@ -24,35 +24,35 @@
 
 
 def echo(*args, **kwargs):
-    """ echo arguments """
+    """echo arguments"""
     print(args)
     print(kwargs)
     return defaultdict(dict)
 
 
 class EchoMock:  # pylint: disable=too-few-public-methods
-    """ echo mocker """
+    """echo mocker"""
 
     def __getattribute__(self, name):
         assert name
         return echo
 
 
 class MockDFU:
-    """ mock dfu """
+    """mock dfu"""
 
     def save_objects(self, params):
-        """ mock dfu save_objects """
+        """mock dfu save_objects"""
         assert self, params
         return [[None] * 11]
 
     def ws_name_to_id(self, name):
-        """ mock workspace name to id """
+        """mock workspace name to id"""
         assert self
         return len(name)
 
     def get_objects(self, params):
-        """ mock get_objects """
+        """mock get_objects"""
         assert self
         ref = params["object_refs"][0]
         mock_filenames = dict(
@@ -67,7 +67,7 @@ def get_objects(self, params):
 
 
 class kb_djornlTest(unittest.TestCase):  # pylint: disable=invalid-name
-    """ kb_djornl unit test class """
+    """kb_djornl unit test class"""
 
     @classmethod
     def setUpClass(cls):
@@ -129,12 +129,12 @@ def tearDownClass(cls):
             print("Test workspace was deleted")
 
     def setUp(self):
-        """ remove report dir before each test"""
+        """remove report dir before each test"""
         # the scratch dir is named shared in kb_djornlImpl
         shutil.rmtree(self.reports_path, ignore_errors=True)
 
     def _get_multiplex_params(self, multiplex):
-        """ Make parameters for RWR_CV and RWR_LOE mutliplex tests """
+        """Make parameters for RWR_CV and RWR_LOE mutliplex tests"""
         return {
             "workspace_id": self.workspace_id,
             "workspace_name": self.wsName,