Testing and bug fixes

Author: cjgrady

apache/syftorium.wsgi

@@ -1,5 +1,5 @@
 import sys
 sys.path.append('/opt/lifemapper/')
 
-from flask_app.application import create_app
+from flask_app.application import create_app  # noqa: E402
 application = create_app()

flask_app/resolver/config.py

@@ -1,5 +1,5 @@
 """Solr configuration parameters."""
-import os
+
 
 SOLR_SERVER = 'http://localhost'
 SOLR_PORT = 8983

flask_app/resolver/models.py

@@ -1,5 +1,6 @@
 """Models for Resolver."""
 
+
 # .....................................................................................
 class Ark:
     """Class containing Ark information."""

flask_app/sp_cache/process_dwca.py

@@ -57,7 +57,7 @@ def post_results(post_recs, collection_id, mod_time):
             these records.
         mod_time (tuple): A tuple of year, month, day modification time.
     """
-    solr_response = controller.update_collection_occurrences(collection_id, post_recs)
+    _ = controller.update_collection_occurrences(collection_id, post_recs)
     resolver_recs = []
     for rec in post_recs:
         url = '{}api/v1/sp_cache/collection/{}/specimens/{}'.format(
@@ -218,7 +218,7 @@ def process_dwca_directory(in_directory, out_directory):
             process_dwca(dwca_filename, collection_id)
             shutil.move(
                 dwca_filename,
-                os.path.join(out_directory,os.path.basename(dwca_filename))
+                os.path.join(out_directory, os.path.basename(dwca_filename))
             )
         except Exception as err:
             print('Failed to process {}, {}'.format(dwca_filename, err))

flask_app/sp_cache/routes.py

@@ -87,6 +87,9 @@ def collection_occurrences_modify(collection_id):
 
     Args:
         collection_id (str): An identifier associated with these specimens.
+
+    Returns:
+        tuple: Tuple of empty string and 204 indicating successful delete.
     """
     if request.method.lower() in ['post', 'put']:
         # Write data to file system for another process to pick up and handle

flask_app/sp_cache/solr_controller.py

@@ -110,7 +110,10 @@ def delete_collection_occurrences(collection_id, identifiers):
     """
     sp_solr = get_specimen_solr()
     sp_solr.delete(
-        q=['collection_id:{}'.format(collection_id),'identiifer:{}'.format(identifier)]
+        q=[
+            'collection_id:{}'.format(collection_id),
+            'identiifer:{}'.format(identifiers)
+        ]
     )
 
 
@@ -127,7 +130,10 @@ def get_specimen(collection_id, identifier):
     """
     sp_solr = get_specimen_solr()
     rec = sp_solr.search(
-        q=['collection_id:{}'.format(collection_id),'identiifer:{}'.format(identifier)]
+        q=[
+            'collection_id:{}'.format(collection_id),
+            'identiifer:{}'.format(identifier)
+        ]
     )
     if rec.hits > 0:
         return SpecimenRecord(rec.docs[0])

lm_tests/sp_cache_tests.py

@@ -25,23 +25,29 @@ def __init__(self, collection_values_json, collection_endpoint):
 
     # .............................
     def __repr__(self):
-        """Return a string representation of this test."""
+        """Return a string representation of this test.
+
+        Returns:
+            str: A string representation of the instance.
+        """
         return self.test_name
 
     # .............................
     def run_test(self):
-        """Run the test."""
+        """Run the test.
+
+        Raises:
+            LmTestFailure: Raised if a collection exists when it shouldn't.
+        """
         collection_id = self.collection_config['collection_id']
         # Make sure that the collection doesn't exist
-        try:
-            requests.get('{}/{}'.format(self.collection_endpoint, collection_id))
-            raise ValueError(
-                'Found collection: {} when it should not exist (1)'.format(
+        req = requests.get('{}/{}'.format(self.collection_endpoint, collection_id))
+        if req.status_code != 404:
+            raise test_base.LmTestFailure(
+                'Found collection: {} when it should not exist (before_post)'.format(
                     collection_id
                 )
             )
-        except requests.NotFound:
-            pass
 
         # POST the collection
         requests.post(self.collection_endpoint, json=self.collection_config)
@@ -50,20 +56,22 @@ def run_test(self):
         collection_get_response = requests.get(
             '{}/{}'.format(self.collection_endpoint, collection_id)
         )
+        if collection_get_response.status_code != 200:
+            raise test_base.LmTestFailure(
+                'Collection {} not found when expected.'.format(collection_id)
+            )
 
         # DELETE the collection
         requests.delete('{}/{}'.format(self.collection_endpoint, collection_id))
 
         # Make sure that the collection is gone again
-        try:
-            requests.get('{}/{}'.format(self.collection_endpoint, collection_id))
-            raise ValueError(
-                'Found collection: {} when it should not exist (2)'.format(
+        req = requests.get('{}/{}'.format(self.collection_endpoint, collection_id))
+        if req.status_code != 404:
+            raise test_base.LmTestFailure(
+                'Found collection: {} when it should not exist (after delete)'.format(
                     collection_id
                 )
             )
-        except requests.NotFound:
-            pass
 
 
 # .....................................................................................
@@ -87,12 +95,20 @@ def __init__(self, dwca_filename, occurrence_endpoint):
 
     # .............................
     def __repr__(self):
-        """Return a string representation of this test."""
+        """Return a string representation of this test.
+
+        Returns:
+            str: A string representation of the instance.
+        """
         return self.test_name
 
     # .............................
     def run_test(self):
-        """Run the test."""
+        """Run the test.
+
+        Raises:
+            LmTestFailure: Raised if the data cannot be posted successfully.
+        """
         with open(self.dwca_filename, mode='rb') as dwca_file:
             data = dwca_file.read()
         resp = requests.post(self.occurrence_endpoint, data=data)

lm_tests/spcache_collection_lmtest.json

@@ -13,4 +13,4 @@
             "public_key": "blah blah blah"
         }
     }
-}
+}

lm_tests/spcache_collection_occurrences_lmtest.json

@@ -5,4 +5,4 @@
         "occurrence_endpoint": "https://notyeti-195.lifemapper.org/api/v1/sp_cache/collection/test_collection/occurrences/",
         "dwca_filename": "/DATA/envs/lmtest/test_data/dwc_update.zip"
     }
-}
+}

solr_cores/spcoco/conf/schema.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <schema name="spcoco" version="0.1">
-  
-   
+
+
    <!-- =========================================== -->
    <!-- Recommended fields for Solr -->
    <!-- =========================================== -->
@@ -11,20 +11,20 @@
    <!-- Specify resolver fields -->
    <!-- =========================================== -->
    <field name="dataset_guid" type="string" indexed="true" stored="true" />
-   
+
    <!-- ARK metadata -->
    <!-- similar to DC Creator, Contributor, Publisher -->
    <!-- DWC institutionCode -->
    <field name="who" type="string" indexed="true" stored="true" />
-   
+
    <!-- similar to DC Title -->
    <!-- DWC basisOfRecord -->
    <field name="what" type="string" indexed="true" stored="true" />
-   
+
    <!-- similar to DC Date -->
    <!-- DWC yyyy-mm-dd (concatenated fields) -->
    <field name="when" type="string" indexed="true" stored="true" />
-   
+
    <!-- similar to DC Identifier, optional as this is the ARK -->
    <!-- ARK pointing to Specify resolver -->
    <field name="where" type="string" indexed="true" stored="true" />
@@ -33,11 +33,11 @@
    <!-- redirection URL -->
    <!-- URL pointing to Specify API -->
    <field name="url" type="string" indexed="true" stored="true" />
-      
+
    <!-- =========================================== -->
    <!-- Recommended fields for Solr -->
    <!-- =========================================== -->
-   <uniqueKey>id</uniqueKey>   
+   <uniqueKey>id</uniqueKey>
 
    <!-- =========================================== -->
    <!-- Field types -->
@@ -49,7 +49,7 @@
    <fieldType name="multistring" class="solr.StrField" sortMissingLast="true" />
    <fieldType name="int" class="solr.TrieIntField" precisionStep="0" positionIncrementGap="0" />
    <fieldType name="long" class="solr.TrieLongField" precisionStep="0" positionIncrementGap="0" />
-   <fieldType name="tdouble" class="solr.TrieDoubleField" precisionStep="8" omitNorms="true" positionIncrementGap="0" />   
+   <fieldType name="tdouble" class="solr.TrieDoubleField" precisionStep="8" omitNorms="true" positionIncrementGap="0" />
    <fieldType name="boolean" class="solr.BoolField" omitNorms="true" />
 
 </schema>