Fix pre-commit format

omero_search_engine/api/v1/resources/query_handler.py

@@ -44,7 +44,7 @@ def check_get_names(idr_, resource, attribute, return_exact=False):
     if idr_:
         idr_ = idr_.strip()
     pr_names = get_resource_names(resource)
-    all_act_names=[]
+    all_act_names = []
     if pr_names:
         if not return_exact:
             for data_source, pr_names_ in pr_names.items():
@@ -53,8 +53,8 @@ def check_get_names(idr_, resource, attribute, return_exact=False):
                     for name in pr_names_
                     if name[attribute] and idr_.lower() in name[attribute].lower()
                 ]
-                print (act_name, data_source)
-                all_act_names=all_act_names+act_name
+                print(act_name, data_source)
+                all_act_names = all_act_names + act_name
         else:
             # This should be modified to query specific data source specific
             for data_source, pr_names_ in pr_names.items():
@@ -465,7 +465,7 @@ def search_query(
         "-------------------------------------------------"
     )  # noqa
     # search_omero_app.logger.info("1. query: %s" % query)
-    search_omero_app.logger.info("2. main_attributes: %s "%main_attributes)
+    search_omero_app.logger.info("2. main_attributes: %s " % main_attributes)
     search_omero_app.logger.info(resource)
     search_omero_app.logger.info(
         "-------------------------------------------------"

omero_search_engine/api/v1/resources/resource_analyser.py

@@ -631,7 +631,7 @@ def search_value_for_resource(
 Search using key, part of the value and resource
 """
 key_part_values_buckets_template = Template(
-"""{"query":{"bool":{"must":[{"bool":{"must":[{
+    """{"query":{"bool":{"must":[{"bool":{"must":[{
 "match":{"Attribute.keyrnamenormalize":"$name"}},
 {"wildcard":{"Value.keyvaluenormalize":"*$value*"}
 }]}},{"bool":{"must":[{"match":{"resource.keyresource":"$resource"}
@@ -680,29 +680,34 @@ def search_value_for_resource(
 "bool": {"must": {"match":{"resource.keyresource": "$resource"}}}}]}}}"""
 )
 
-resource_key_values_buckets_template = Template(
+resource_key_values_buckets_template = Template(  # noqa
     """
 {"query":{"bool":{"must":[{"bool":{
 "must":{"wildcard":{"Value.keyvaluenormalize":"*$value*"}}}},{
 "bool": {"must": {"match":{"resource.keyresource": "$resource"}}}},{"bool":{
 "must":{"terms":{ "data_source.keyvalue":$data_source}}}}]}},
-"size": 9999, "sort":[{ "_script": {"script": "doc['Value.keyvaluenormalize'].value.length()","type": "number","order": "asc"}},{"items_in_the_bucket": "desc"}, {"id": "asc"}]}"""
+"size": 9999, "sort":[{ "_script":
+{"script": "doc['Value.keyvaluenormalize'].value.length()",
+"type": "number","order": "asc"}},
+{"items_in_the_bucket": "desc"}, {"id": "asc"}]}"""
 )
 
 key_values_buckets_template_2 = Template(
     """
-{"query":{"bool":{"must":[{"bool":{"must":{"match":{"resource.keyresource":"$resource"}}}}]}}} """
+{"query":{"bool":{"must":[{"bool":
+{"must":{"match":{"resource.keyresource":"$resource"}}}}]}}} """
 )
 
 key_values_buckets_template_with_data_source = Template(
     """
-{"query":{"bool":{"must":[{"bool":{"must":{"match":{"resource.keyresource":"$resource"}}}},{"bool": {"must":{"match": {"data_source.keyvalue":$data_source}}}}]}}} """
+{"query":{"bool":{"must":[{"bool":{"must":{"match":{"resource.keyresource":"$resource"}}}},
+{"bool":{"must":{"match": {"data_source.keyvalue":$data_source}}}}]}}} """
 )
-
 key_values_buckets_template_search_name = Template(
     """
-{"query":{"bool":{"must":[{"bool":{"must":{"match":{"resource.keyresource":"$resource"}}}},{"bool": {"must":{"wildcard": {"resourcename.keyresourcename":"*$name*"}}}}]}}} """
-)
+{"query":{"bool":{"must":[{"bool":{"must":{"match":{"resource.keyresource":"$resource"}}}},
+{"bool": {"must":{"wildcard": {"resourcename.keyresourcename":"*$name*"}}}}]}}} """
+)  # noqa
 
 
 def connect_elasticsearch(es_index, query, count=False):

omero_search_engine/api/v1/resources/urls.py

@@ -51,8 +51,8 @@ def index():
 @resources.route("/data_resources/", methods=["GET"])
 def return_data_resources():
     """
-     file: swagger_docs/datasources.yml
-     """
+    file: swagger_docs/datasources.yml
+    """
     """
     used to return the available data resources
     """

omero_search_engine/api/v1/resources/utils.py

@@ -1170,13 +1170,12 @@ def search_resource_annotation(
                 main_attributes = {}
                 main_attributes["and_main_attributes"] = [clause]
 
-
         and_filters = query_details.get("and_filters")
         or_filters = query_details.get("or_filters")
         case_sensitive = query_details.get("case_sensitive")
         # check and fid if possible names and values inside
         # filters conditions
-        #check_filters is cpmmented as it has no actual use and take time to excute
+        # check_filters is cpmmented as it has no actual use and take time to excute
         # check_filters(table_, [and_filters, or_filters], case_sensitive)
         query_string = elasticsearch_query_builder(
             and_filters, or_filters, case_sensitive, main_attributes

unit_tests/test_app.py

@@ -36,7 +36,7 @@
 
 from omero_search_engine.validation.results_validator import (
     Validator,
-    check_number_images_sql_containers_using_ids,
+    # check_number_images_sql_containers_using_ids,
 )
 from omero_search_engine.cache_functions.elasticsearch.transform_data import (
     delete_es_index,
@@ -160,7 +160,7 @@ def test_add_submit_query_delete_es_index(self):
         """'
         test submit query and get results
         """
-        table = "image1"
+        # table = "image1"
         table_2 = "image"
         es_index = "image_keyvalue_pair_metadata_1"
         es_index_2 = "key_values_resource_cach"
@@ -233,11 +233,10 @@ def test_or_query(self):
                 )
                 self.assertTrue(validator.identical)
 
-    #def test_no_images_containers(self):
+    # def test_no_images_containers(self):
     #    for data_source in search_omero_app.config.database_connectors.keys():
     #        self.assertTrue(check_number_images_sql_containers_using_ids(data_source))
 
-
     def test_multi_or_quries(self):
         pass