always use alias for index names

app/properties_configuration/config/groups.yml

-chembl_26_molecule:
+chembl_molecule:
   download:
     default: ['molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type', 'max_phase',
     'molecule_properties.full_mwt', '_metadata.related_targets.count', '_metadata.related_activities.count',
@@ -83,7 +83,7 @@ chembl_26_molecule:
     default: ['helm_notation']
   biocomponents:
     default: ['molecule_chembl_id', 'biotherapeutic.biocomponents']
-chembl_26_assay:
+chembl_assay:
   download:
     default: ['assay_chembl_id', 'assay_type', 'description', 'assay_organism', '_metadata.related_compounds.count',
     '_metadata.related_activities.count', 'bao_format', 'bao_label', 'confidence_score',
@@ -104,7 +104,7 @@ chembl_26_assay:
     'assay_parameters', 'assay_classifications_level1', 'assay_classifications_level2', 'assay_classifications_level3']
   assay_parameters:
     default: ['assay_parameters_report_card_rows']
-chembl_26_target:
+chembl_target:
   download:
     default: ['target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
     '_metadata.related_compounds.count', '_metadata.related_activities.count', 'tax_id', 'species_group_flag']
@@ -121,7 +121,7 @@ chembl_26_target:
     'target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
     '_metadata.related_compounds.count', '_metadata.related_activities.count']
     optional: ['tax_id', 'species_group_flag']
-chembl_26_document:
+chembl_document:
   download:
     default: ['document_chembl_id', 'journal_full_title', 'src_id', '_metadata.source', 'title', 'pubmed_id', 'doi',
     'patent_id', 'authors', 'year', 'volume', 'issue', 'first_page', 'last_page', 'doc_type', 'abstract',
@@ -130,7 +130,7 @@ chembl_26_document:
     default: ['document_chembl_id', 'journal_full_title', '_metadata.source', 'title', 'pubmed_id', 'doi', 'patent_id',
     'authors', 'year', 'volume', 'issue', 'first_page', 'last_page', '_metadata.related_activities.count']
     optional: ['src_id', 'abstract', '_metadata.related_compounds.count', '_metadata.related_targets.count']
-chembl_26_cell_line:
+chembl_cell_line:
   download:
     default: ['cell_chembl_id', 'cell_name', 'cell_description', 'cell_source_organism', 'cell_source_tissue',
     'cell_source_tax_id', 'clo_id', 'efo_id', 'cellosaurus_id', 'cl_lincs_id', '_metadata.related_compounds.count',
@@ -140,14 +140,14 @@ chembl_26_cell_line:
     '_metadata.related_activities.count']
     optional: ['cell_source_tax_id', 'clo_id', 'efo_id', 'cellosaurus_id', 'cl_lincs_id',
     '_metadata.related_compounds.count']
-chembl_26_tissue:
+chembl_tissue:
   download:
     default: ['tissue_chembl_id', 'pref_name', 'uberon_id', 'efo_id', 'bto_id', 'caloha_id',
     '_metadata.related_compounds.count', '_metadata.related_activities.count']
   browser_table:
     default: ['tissue_chembl_id', 'pref_name', 'uberon_id', 'efo_id', '_metadata.related_activities.count']
     optional: ['bto_id', 'caloha_id', '_metadata.related_compounds.count']
-chembl_26_drug_indication_by_parent:
+chembl_drug_indication_by_parent:
   download:
     default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
     'drug_indication.max_phase_for_ind', 'parent_molecule.first_approval', 'drug_indication.mesh_id',
@@ -163,7 +163,7 @@ chembl_26_drug_indication_by_parent:
   report_card_table:
     default: ['drug_indication.mesh_id', 'drug_indication.mesh_heading', 'efo_ids', 'efo_terms',
     'drug_indication.max_phase_for_ind', 'parent_molecule.first_approval', 'drug_indication.indication_refs']
-chembl_26_mechanism_by_parent_target:
+chembl_mechanism_by_parent_target:
   download:
     default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
     'mechanism_of_action.max_phase', 'parent_molecule.first_approval', 'parent_molecule.usan_stem',
@@ -189,7 +189,7 @@ chembl_26_mechanism_by_parent_target:
     default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
     'mechanism_of_action.max_phase', 'parent_molecule.first_approval', 'parent_molecule.usan_stem',
     'mechanism_of_action.mechanism_refs']
-chembl_26_activity:
+chembl_activity:
   download:
     default: ['molecule_chembl_id', 'molecule_pref_name', '_metadata.parent_molecule_data.max_phase',
     '_metadata.parent_molecule_data.full_mwt', '_metadata.parent_molecule_data.num_ro5_violations',

app/properties_configuration/config/override.yml

-chembl_26_molecule:
+chembl_molecule:
   'molecule_properties.full_mwt':
     label: 'Molecular Weight'
     label_mini: 'Mol. Wt.'
@@ -109,7 +109,7 @@ chembl_26_molecule:
     type: 'string'
     aggregatable: false
     sortable: true
-chembl_26_assay:
+chembl_assay:
   '_metadata.related_compounds.count':
     label: 'Compounds'
     label_mini: 'Compounds'
@@ -155,7 +155,7 @@ chembl_26_assay:
   'assay_classifications_level3':
     based_on: 'assay_classifications'
     label: 'Assay Classification L3'
-chembl_26_target:
+chembl_target:
   'pref_name':
     label: 'Name'
   'uniprot_accessions':
@@ -203,7 +203,7 @@ chembl_26_target:
     type: 'double'
     aggregatable: false
     sortable: true
-chembl_26_document:
+chembl_document:
   'journal_full_title':
     label: 'Journal'
   'src_id':
@@ -230,7 +230,7 @@ chembl_26_document:
     label: 'Targets'
   '_metadata.related_activities.count':
     label: 'Activities'
-chembl_26_cell_line:
+chembl_cell_line:
   'clo_id':
     label: 'CLO ID'
   'cl_lincs_id':
@@ -239,14 +239,14 @@ chembl_26_cell_line:
     label: 'Compounds'
   '_metadata.related_activities.count':
     label: 'Activities'
-chembl_26_tissue:
+chembl_tissue:
   'bto_id':
     label: 'BTO ID'
   '_metadata.related_compounds.count':
     label: 'Compounds'
   '_metadata.related_activities.count':
     label: 'Activities'
-chembl_26_drug_indication_by_parent:
+chembl_drug_indication_by_parent:
   'drug_indication.max_phase_for_ind':
     label: 'Max Phase for Indication'
   'parent_molecule.first_approval':
@@ -265,7 +265,7 @@ chembl_26_drug_indication_by_parent:
     label: 'References'
   'parent_molecule._metadata.drug.drug_data.synonyms':
     label: 'Synonyms'
-chembl_26_mechanism_by_parent_target:
+chembl_mechanism_by_parent_target:
   'mechanism_of_action.max_phase':
     label: 'Max Phase'
   'parent_molecule.first_approval':
@@ -305,7 +305,7 @@ chembl_26_mechanism_by_parent_target:
   'drug_atc_codes_level_1':
     based_on: 'parent_molecule._metadata.atc_classifications'
     label: 'Level 1 ATC Codes'
-chembl_26_activity:
+chembl_activity:
   '_metadata.parent_molecule_data.max_phase':
     label: 'Molecule Max Phase'
   '_metadata.parent_molecule_data.full_mwt':

app/properties_configuration/tests/data/test_default_sorting.yml

-chembl_26_molecule:
+chembl_molecule:
   # this is as elasticsearch would receve the object to sort the dataset
   # see https://www.elastic.co/guide/en/elasticsearch/reference/current/search-request-sort.html
   sorted_table: [

app/swagger/swagger.yaml

@@ -36,7 +36,7 @@ paths:
           description: 'name of the index to query'
           required: true
           type: 'string'
-          default: 'chembl_26_molecule'
+          default: 'chembl_molecule'
         - name: 'es_query'
           in: 'formData'
           description: 'stringifyied version of the query to send to elasticsearch'

app/usage_statistics/test/test_statistics_saver.py

@@ -41,7 +41,7 @@ class TestStatisticsSaver(unittest.TestCase):
             }
         }
 
-        es_index = 'chembl_26_molecule'
+        es_index = 'chembl_molecule'
         es_request_digest = 'somedigest'
         is_cached = True
         request_date = datetime.now().timestamp() * 1000

functional_tests/specific_tests/fun_test_query_with_context.py

@@ -47,7 +47,7 @@ def run_test(server_base_url, delayed_jobs_server_base_path):
     }
 
     payload = {
-        'index_name': 'chembl_26_molecule',
+        'index_name': 'chembl_molecule',
         'es_query': json.dumps(es_query),
         'context_obj': json.dumps(context_obj),
         'id_property': 'molecule_chembl_id',

functional_tests/specific_tests/fun_test_simple_query.py

@@ -23,7 +23,7 @@ def run_test(server_base_url, delayed_jobs_server_base_path):
 
     url = utils.get_url_for_get_es_data(server_base_url)
     print('url: ', url)
-    index_name = 'chembl_26_molecule'
+    index_name = 'chembl_molecule'
     print('index_name: ', index_name)
     es_query = {
         "size": 24,

utils/try_many_ids_queries.py

@@ -61,7 +61,7 @@ def run():
         print('With {} compounds'.format(num_compounds))
 
         start_time = time.time()
-        res = es_conn.search(index="chembl_26_activity", body={"query": terms_query})
+        res = es_conn.search(index="chembl_activity", body={"query": terms_query})
         end_time = time.time()
         time_taken_terms = end_time - start_time
 
@@ -71,7 +71,7 @@ def run():
         script_query = get_script_query(ids)
 
         start_time = time.time()
-        res = es_conn.search(index="chembl_26_activity", body={"query": script_query})
+        res = es_conn.search(index="chembl_activity", body={"query": script_query})
         end_time = time.time()
         time_taken_script = end_time - start_time