remove old tests

gemmapy/gemmapy_api.py

@@ -1765,109 +1765,4 @@ def get_child_terms(self,terms:List[str])->List[str]:
     # update_results currenty unimplemented and not really essential
 
 
-# Tests
-if __name__ == '__main__':
-    # dv temp
-    import http.client
-    http.client.HTTPConnection.debuglevel = 0 # put 5 to debug
-
-    import sys
-    from pprint import pprint
-
-    api_instance = GemmaPy()
-
-    def get_dataset_annotations_test():
-        print('Testing get_dataset_annotations function:')
-        api_response = api_instance.get_dataset_annotations("GSE46416")
-        pprint(api_response.data)
-        print('')
-
-    def search_datasets_test():
-        print('Testing search_datasets function:')
-        api_response = api_instance.search_datasets(["bipolar"], taxon="human", limit=100)
-        for d in api_response.data:
-            if d.geeq is not None and  d.geeq.batch_corrected:
-                print(d.short_name, d.name, d.bio_assay_count)
-        print('')
-
-    def get_datasets_by_ids_test():
-        print('Testing get_datasets_by_ids function:')
-        api_response = api_instance.get_datasets_by_ids(["GSE46416"])
-        for d in api_response.data:
-            print(d.short_name, d.name, d.id, d.description)
-        print('')
-
-    def search_annotations_test():
-        print('Testing search_annotations function:')
-        api_response = api_instance.search_annotations(["GSE46416"])
-        print(api_response.data)
-
-    def get_dataset_object_test():
-        print('Testing get_dataset_object function:')
-        adata = api_instance.get_dataset_object("GSE46416")
-        print(adata)
-        print('\nUnstructured Info:')
-        for l in adata.uns: print('%s: %s' % (l, adata.uns[l]))
-        print('')
-        print('Observation metadata:')
-        print(adata.obs.iloc[1:10])
-        print('')
-        print('Vars metadata:')
-        print(adata.var.iloc[1:10])
-        print('')
-        print('Data:')
-        print(adata.X)
-        print('')
-
-        print('Subsetting the Experiment\nDisease levels')
-        print(adata.var['disease'].unique())
-        print('\nSubset: patients during manic phase and controls')
-        manic=adata[:,(adata.var['disease'] == 'reference_subject_role') |
-                      (adata.var['disease'] == 'bipolar_disorder_|_manic_phase_|')].copy()
-        print(manic)
-        print(manic.var)
-
-    def get_result_sets_test():
-        print('Testing get_result_sets function:')
-        df = api_instance.get_result_sets('GSE6711')
-        print(df)
-        df2 = api_instance.get_result_set(485406)
-        print(df2)
-
-    def get_differential_expression_values_test():
-        de = api_instance.get_differential_expression_values('GSE46416')
-        de['diffexpr'] = 'No'   # add extra column
-        #de['diffexpr'][(de['contrast_bipolar disorder, manic phase_logFoldChange']>1.0) &
-        #               (de['contrast_bipolar disorder, manic phase_pvalue']<0.05)] = 'Up'
-        de.loc[(de['contrast_bipolar disorder, manic phase_logFoldChange'] > 1.0) &
-                       (de['contrast_bipolar disorder, manic phase_pvalue'] < 0.05),'diffexpr'] = 'Up'
-        de.loc[(de['contrast_bipolar disorder, manic phase_logFoldChange'] < -1.0) &
-                       (de['contrast_bipolar disorder, manic phase_pvalue'] < 0.05),'diffexpr'] = 'Down'
-        de_up = de[de['diffexpr']=='Up']
-        de_up = de_up[['Probe','GeneSymbol', 'contrast_bipolar disorder, manic phase_pvalue',
-                       'contrast_bipolar disorder, manic phase_logFoldChange']].sort_values(
-                'contrast_bipolar disorder, manic phase_pvalue')
-        print('Upregulated probes')
-        with pd.option_context('display.max_rows', None, 'display.max_columns', None):
-            print(de_up[:10])
-
-        de_dn = de[de['diffexpr']=='Down']
-        de_dn = de_dn[['Probe','GeneSymbol', 'contrast_bipolar disorder, manic phase_pvalue',
-                       'contrast_bipolar disorder, manic phase_logFoldChange']].sort_values(
-                'contrast_bipolar disorder, manic phase_pvalue')
-        print('\nDownregulated probes')
-        with pd.option_context('display.max_rows', None, 'display.max_columns', None):
-            print(de_dn[:10])
-
-    def get_platform_annotations_test():
-        print('Testing get_platform_annotations function')
-        df = api_instance.get_platform_annotations('GPL96')
-        print(df)
-
-    if len(sys.argv) > 1:
-        fname = sys.argv[1]
-        dict = vars()
-        if fname in dict:
-            #print("Calling",fname)
-            func = dict[fname]
-            func()
+