remove redundant tests

kbaseapps · Aug 28, 2024 · 4b1b88b · 4b1b88b
1 parent 35030a0
commit 4b1b88b
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Showing 2 changed files with 14 additions and 45 deletions.
diff --git a/lib/GenomeFileUtil/core/GenomeInterface.py b/lib/GenomeFileUtil/core/GenomeInterface.py
@@ -12,10 +12,7 @@
 from installed_clients.AssemblySequenceAPIServiceClient import AssemblySequenceAPI
 from installed_clients.DataFileUtilClient import DataFileUtil
 from installed_clients.WSLargeDataIOClient import WsLargeDataIO
-from GenomeFileUtil.core.GenomeUtils import (
-    set_taxon_data, set_default_taxon_data, sort_dict,
-    set_up_single_params, validate_mass_params
-)
+from GenomeFileUtil.core import GenomeUtils
 
 MAX_GENOME_SIZE = 2**30
 
@@ -40,14 +37,14 @@ def __init__(self, config):
         self.ws_large_data = WsLargeDataIO(self.callback_url)
 
     def save_one_genome(self, params):
-        mass_params = set_up_single_params(
+        mass_params = GenomeUtils.set_up_single_params(
             params, _WS, self._validate_genome_input_params, self.dfu.ws_name_to_id
         )
         return self._save_genome_mass(mass_params)[0]
 
     # NOTE If there is more than 1GB of data or more than 10,000 genomes to upload, the workspace will fail.
     def save_genome_mass(self, params):
-        validate_mass_params(params, self._validate_genome_input_params)
+        GenomeUtils.validate_mass_params(params, self._validate_genome_input_params)
         return self._save_genome_mass(params)
 
     def _validate_genome_input_params(self, genome_input):
@@ -212,7 +209,7 @@ def _save_genome_mass(self, params):
                 data['warnings'] = self.validate_genome(data)
 
             # sort data
-            data = sort_dict(data)
+            data = GenomeUtils.sort_dict(data)
             # dump genome to scratch for upload
             data_path = os.path.join(self.scratch, name + ".json")
             json.dump(data, open(data_path, 'w'))
@@ -287,9 +284,9 @@ def _update_genome(self, genome):
         # NOTE: Metagenome object does not have a 'taxon_assignments' field
         if 'taxon_assignments' in genome and genome['taxon_assignments'].get('ncbi'):
             tax_id = int(genome['taxon_assignments']['ncbi'])
-            set_taxon_data(tax_id, self.re_api_url, genome)
+            GenomeUtils.set_taxon_data(tax_id, self.re_api_url, genome)
         else:
-            set_default_taxon_data(genome)
+            GenomeUtils.set_default_taxon_data(genome)
 
         if any([x not in genome for x in ('dna_size', 'md5', 'gc_content', 'num_contigs')]):
             if 'assembly_ref' in genome:

diff --git a/test/problematic_tests/save_genome_test.py b/test/problematic_tests/save_genome_test.py
@@ -234,42 +234,14 @@ def test_genomes_with_hidden(self):
         ret = self.genome_interface.save_genome_mass(params)[0]
         self.check_save_one_genome_output(ret, genome_name)
 
-    # def test_bad_genomes_params_missing_wsid(self):
-    #     self.start_test()
-    #     invalidate_params = {
-    #         'missing_workspace_id': 'workspace_id',
-    #         'name': 'name',
-    #         'data': 'data',
-    #     }
-    #     error_msg = "workspace_id is required"
-    #     self.fail_save_genome(invalidate_params, error_msg, mass=True)
-
-    # def test_bad_genomes_params_empty_inputs(self):
-    #     self.start_test()
-    #     invalidate_params = {
-    #         'workspace_id': self.wsID,
-    #         'inputs': []
-    #     }
-    #     error_msg = "inputs field is required and must be a non-empty list"
-    #     self.fail_save_genome(invalidate_params, error_msg, mass=True)
-
-    # def test_bad_genomes_params_invalidate_entry_type(self):
-    #     self.start_test()
-    #     invalidate_params = {
-    #         'workspace_id': self.wsID,
-    #         'inputs': [['name', 'data']],
-    #     }
-    #     error_msg = "Entry #1 in inputs field is not a mapping as required"
-    #     self.fail_save_genome(invalidate_params, error_msg, mass=True)
-
-    # def test_bad_genomes_params_missing_parameter(self):
-    #     self.start_test()
-    #     invalidate_params = {
-    #         'workspace_id': self.wsID,
-    #         'inputs': [{'data': 'data'}],
-    #     }
-    #     error_msg = "Entry #1 in inputs field has invalid params: name parameter is required, but missing"
-    #     self.fail_save_genome(invalidate_params, error_msg, mass=True)
+    def test_bad_genomes_params_missing_parameter(self):
+        self.start_test()
+        invalidate_params = {
+            'workspace_id': self.wsID,
+            'inputs': [{'data': 'data'}],
+        }
+        error_msg = "Entry #1 in inputs field has invalid params: name parameter is required, but missing"
+        self.fail_save_genome(invalidate_params, error_msg, mass=True)
 
     def test_GenomeInterface_check_dna_sequence_in_features(self):
         # no feature in genome