From 44b3e4df6236f40eb4c41663b91e6bde1a3c3d17 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Mon, 23 Dec 2013 08:21:00 -0800 Subject: [PATCH] Use arvados.api('v1') accessor instead of arvados.service. refs #1773 --- crunch_scripts/pgp-survey-import | 18 +++++++++--------- .../tutorials/tutorial-trait-search.textile | 12 ++++++------ sdk/python/test_pipeline_template.py | 10 +++++----- 3 files changed, 20 insertions(+), 20 deletions(-) diff --git a/crunch_scripts/pgp-survey-import b/crunch_scripts/pgp-survey-import index 811dd11872..df5758bc57 100755 --- a/crunch_scripts/pgp-survey-import +++ b/crunch_scripts/pgp-survey-import @@ -30,7 +30,7 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): words = string.split(string.strip(line), "\t") if line_number == 0: headings = words - for t in arvados.service.traits().list( + for t in arvados.api('v1').traits().list( where=json.dumps({'name':words}), limit=1000 ).execute()['items']: @@ -38,28 +38,28 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): for i, trait_name in enumerate(words[3:], start=3): # find or create trait if trait_name not in traits: - traits_match = arvados.service.traits().list( + traits_match = arvados.api('v1').traits().list( where=json.dumps({'name':trait_name}) ).execute()['items'] if len(traits_match) > 0: traits[trait_name] = traits_match[0] else: - traits[trait_name] = arvados.service.traits().create( + traits[trait_name] = arvados.api('v1').traits().create( trait=json.dumps({'name':trait_name})).execute() out.write(separator) out.write(json.dumps(traits[trait_name])) separator = ",\n" else: - huID_links_match = arvados.service.links().list( + huID_links_match = arvados.api('v1').links().list( where=json.dumps({'link_class':'identifier','name':words[0]}) ).execute()['items'] if len(huID_links_match) > 0: human_uuid = huID_links_match[0]['head_uuid'] else: - human = arvados.service.humans().create( + human = arvados.api('v1').humans().create( body={} ).execute() - huID_link = arvados.service.links().create( + huID_link = arvados.api('v1').links().create( body={ 'link_class':'identifier', 'name':words[0], @@ -69,7 +69,7 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): ).execute() human_uuid = human['uuid'] human_trait = {} - for t in arvados.service.links().list( + for t in arvados.api('v1').links().list( limit=10000, where=json.dumps({ 'tail_uuid':human_uuid, @@ -87,7 +87,7 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): if trait_link['properties']['value'] != trait_value: # update database value to match survey response trait_link['properties']['value'] = trait_value - arvados.service.links().update( + arvados.api('v1').links().update( uuid=trait_link['uuid'], body={'properties':trait_link['properties']} ).execute() @@ -106,7 +106,7 @@ for input_file in arvados.CollectionReader(this_job_input).all_files(): 'name':'pgp-survey-response', 'properties': { 'value': trait_value } } - arvados.service.links().create( + arvados.api('v1').links().create( body=trait_link ).execute() out.write(",\n") diff --git a/doc/user/tutorials/tutorial-trait-search.textile b/doc/user/tutorials/tutorial-trait-search.textile index a7d78a7c9d..0908c1f62d 100644 --- a/doc/user/tutorials/tutorial-trait-search.textile +++ b/doc/user/tutorials/tutorial-trait-search.textile @@ -128,7 +128,7 @@ h2. Find Personal Genome Project identifiers from Arvados UUIDs "link_class": "identifier", "head_uuid": human_uuids }) ->>> pgpid_links = arvados.service.links().list(limit=1000, where=human_query).execute() +>>> pgpid_links = arvados.api('v1').links().list(limit=1000, where=human_query).execute() >>> map(lambda l: l['name'], pgpid_links['items']) [u'hu01024B', u'hu11603C', u'hu15402B', u'hu174334', u'hu1BD549', u'hu237A50', u'hu34A921', u'hu397733', u'hu414115', u'hu43860C', u'hu474789', u'hu553620', @@ -167,7 +167,7 @@ for p_link in provenance_links['items']: pgpid[p_link['head_uuid']] = pgpid[p_link['tail_uuid']] # get details (e.g., list of files) of each collection -collections = arvados.service.collections().list(where=json.dumps({ +collections = arvados.api('v1').collections().list(where=json.dumps({ "uuid": collection_uuids })).execute() @@ -205,7 +205,7 @@ Now we will use crunch to issue a 'grep' job to look for variant rs1126809 in ea 
>>> job = {}
 for c in collections['items']:
   if [] != filter(lambda f: re.search('^var-.*\.tsv\.bz2', f[1]), c['files']):
-    job[c['uuid']] = arvados.service.jobs().create(body={
+    job[c['uuid']] = arvados.api('v1').jobs().create(body={
       'script': 'grep',
       'script_parameters': {'input': c['uuid'], 'pattern': "rs1126809\\b"},
       'script_version': 'e7aeb42'
@@ -233,7 +233,7 @@ hu599905 qr1hi-8i9sb-i9ec9g8d7rt70xg
 Monitor job progress by refreshing the Jobs page in Workbench, or by using the API:
 
 
-
>>> map(lambda j: arvados.service.jobs().get(uuid=j['uuid']).execute()['success'], job.values())
+
>>> map(lambda j: arvados.api('v1').jobs().get(uuid=j['uuid']).execute()['success'], job.values())
 [None, True, None, None, None, None, None, None, None, None, None, None, None, None]
 

 
@@ -245,8 +245,8 @@ After the jobs have completed, check output file sizes.
 
 
>>> for collection_uuid in job:
   job_uuid = job[collection_uuid]['uuid']
-  job_output = arvados.service.jobs().get(uuid=job_uuid).execute()['output']
-  output_files = arvados.service.collections().get(uuid=job_output).execute()['files']
+  job_output = arvados.api('v1').jobs().get(uuid=job_uuid).execute()['output']
+  output_files = arvados.api('v1').collections().get(uuid=job_output).execute()['files']
   # Test the output size.  If greater than zero, that means 'grep' found the variant 
   if output_files[0][2] > 0:
     print("%s has variant rs1126809" % (pgpid[collection_uuid]))
diff --git a/sdk/python/test_pipeline_template.py b/sdk/python/test_pipeline_template.py
index bd780a30cf..d7cb105996 100644
--- a/sdk/python/test_pipeline_template.py
+++ b/sdk/python/test_pipeline_template.py
@@ -8,7 +8,7 @@ import apiclient
 
 class PipelineTemplateTest(unittest.TestCase):
     def runTest(self):
-        pt_uuid = arvados.service.pipeline_templates().create(
+        pt_uuid = arvados.api('v1').pipeline_templates().create(
             body={'name':__file__}
             ).execute()['uuid']
         self.assertEqual(len(pt_uuid), 27,
@@ -22,7 +22,7 @@ class PipelineTemplateTest(unittest.TestCase):
             'spass_box': False,
             'spass-box': [True, 'Maybe', False]
             }
-        update_response = arvados.service.pipeline_templates().update(
+        update_response = arvados.api('v1').pipeline_templates().update(
             uuid=pt_uuid,
             body={'components':components}
             ).execute()
@@ -34,19 +34,19 @@ class PipelineTemplateTest(unittest.TestCase):
         self.assertEqual(update_response['name'], __file__,
                          'update() response has a different name (%s, not %s)'
                          % (update_response['name'], __file__))
-        get_response = arvados.service.pipeline_templates().get(
+        get_response = arvados.api('v1').pipeline_templates().get(
             uuid=pt_uuid
             ).execute()
         self.assertEqual(get_response['components'], components,
                          'components got munged by server (%s -> %s)'
                          % (components, update_response['components']))
-        delete_response = arvados.service.pipeline_templates().delete(
+        delete_response = arvados.api('v1').pipeline_templates().delete(
             uuid=pt_uuid
             ).execute()
         self.assertEqual(delete_response['uuid'], pt_uuid,
                          'delete() response has wrong uuid (%s, not %s)'
                          % (delete_response['uuid'], pt_uuid))
         with self.assertRaises(apiclient.errors.HttpError):
-            geterror_response = arvados.service.pipeline_templates().get(
+            geterror_response = arvados.api('v1').pipeline_templates().get(
                 uuid=pt_uuid
                 ).execute()
-- 
2.39.5