Closes #6

WIP
saphetor · Apr 13, 2018 · f9911da · f9911da
1 parent 82263b8
commit f9911da
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/scripts/varsome_api_annotate_vcf.py b/scripts/varsome_api_annotate_vcf.py
@@ -22,7 +22,7 @@
 __author__ = 'ckopanos'
 
 
-def annotate_vcf(argv):
+def annotate_vcf():
     parser = argparse.ArgumentParser(description='VCF Annotator command line')
     parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True)
     parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
@@ -53,4 +53,4 @@ def annotate_vcf(argv):
 
 
 if __name__ == "__main__":
-    annotate_vcf(sys.argv[1:])
+    annotate_vcf()
diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py
@@ -24,7 +24,7 @@
 __author__ = 'ckopanos'
 
 
-def annotate_variant(argv):
+def annotate_variant():
     parser = argparse.ArgumentParser(description='Sample VarSome API calls')
     parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
     parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
@@ -124,4 +124,4 @@ def annotate_variant(argv):
 
 
 if __name__ == "__main__":
-    annotate_variant(sys.argv[1:])
+    annotate_variant()
diff --git a/varsome_api/client.py b/varsome_api/client.py
@@ -50,7 +50,7 @@ def __repr__(self):
 
 
 class VarSomeAPIClientBase(object):
-    _api_url = 'https://api.varsome.com'
+    _api_url = 'https://test-api.varsome.com'
     _accepted_methods = ('GET', 'POST')
 
     def __init__(self, api_key=None, logger=None):

diff --git a/varsome_api/tests/test_client.py b/varsome_api/tests/test_client.py
@@ -141,7 +141,7 @@ def __init__(self, methodName='runTest'):
         self.annotator = TestVCFAnnotator(API_KEY)
 
     def test_annotate_vcf(self):
-        """Check that we can annotate a vcf file"""
+        """Check that wepara can annotate a vcf file"""
         output_vcf_file = NamedTemporaryFile(delete=False)
         output_vcf_file.close()
         self.annotator.annotate(VARIANTS_VCF_FILE, output_vcf_file.name)