Use ingest api https endpoints (#112)

Author: samanehsan

adapter_pipelines/submit_example.json

@@ -16,7 +16,7 @@
   "submit.input_bundle_uuid": "274e8e51-76b7-4fe6-b766-65df0a4e85bb",
   "submit.reference_bundle": "bf51d668-3e14-4843-9bc7-5d676fdf0e01",
   "submit.format_map": "gs://foo/format_map.json",
-  "submit.submit_url": "http://api.ingest.staging.data.humancellatlas.org/",
+  "submit.submit_url": "https://api.ingest.staging.data.humancellatlas.org/",
   "submit.method": "SmartSeq2SingleCell",
   "submit.analysis_file_version": "5.3.4",
   "submit.analysis_protocol_schema_version": "8.0.3",

pipeline_tools/create_envelope.py

@@ -47,7 +47,7 @@ def build_envelope(submit_url, analysis_protocol_path, analysis_process_path, ra
         analysis_protocol_dict = json.load(f)
 
     # URL for getting and creating the analysis protocol, e.g.
-    # http://api.ingest.{deployment}.data.humancellatlas.org/submissionEnvelopes/{envelope_id}/protocols
+    # https://api.ingest.{deployment}.data.humancellatlas.org/submissionEnvelopes/{envelope_id}/protocols
     analysis_protocol_url = get_subject_url(endpoint_dict=envelope_dict, subject='protocols')
 
     # Check if an analysis_protocol already exists in the submission envelope from a previous attempt
@@ -88,7 +88,7 @@ def build_envelope(submit_url, analysis_protocol_path, analysis_process_path, ra
     link_url = get_subject_url(endpoint_dict=analysis_process_response, subject='protocols')
 
     # URL for linking the analysis protocol to analysis process, e.g.
-    # http://api.ingest.integration.data.humancellatlas.org/protocols/{protocol_document_id}
+    # https://api.ingest.integration.data.humancellatlas.org/protocols/{protocol_document_id}
     analysis_protocol_entity_url = get_subject_url(analysis_protocol_response, 'self')
 
     print('Linking analysis_protocol {0} to analysis_process at {1}'.format(analysis_protocol_entity_url, link_url))

pipeline_tools/tests/data/add_protocol_response.json

@@ -21,17 +21,17 @@
   "validationErrors" : null,
   "_links" : {
     "self" : {
-      "href" : "http://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54"
+      "href" : "https://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54"
     },
     "protocol" : {
-      "href" : "http://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54",
+      "href" : "https://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54",
       "title" : "A single protocol"
     },
     "validating" : {
-      "href" : "http://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54/validatingEvent"
+      "href" : "https://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54/validatingEvent"
     },
     "submissionEnvelopes" : {
-      "href" : "http://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54/submissionEnvelopes",
+      "href" : "https://api.ingest.integration.data.humancellatlas.org/protocols/5bcb9777593d3c0007227a54/submissionEnvelopes",
       "title" : "Access or create new submission envelopes"
     }
   }

pipeline_tools/tests/data/response.json

@@ -1,47 +1,47 @@
 {
   "_links": {
     "projects": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/projects{?page,size,sort}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/projects{?page,size,sort}",
       "templated": true,
       "title": "Access or create projects. Creation can only be done inside a submission envelope"
     },
     "schemas": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/schemas{?page,size,sort}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/schemas{?page,size,sort}",
       "templated": true
     },
     "bundleManifests": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/bundleManifests{?page,size,sort}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/bundleManifests{?page,size,sort}",
       "templated": true,
       "title": "Access or create bundle manifests (describing which submitted contents went into which bundle in the datastore)"
     },
     "protocols": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/protocols{?page,size,sort}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/protocols{?page,size,sort}",
       "templated": true,
       "title": "Access or create protocols"
     },
     "biomaterials": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/biomaterials{?page,size,sort,projection}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/biomaterials{?page,size,sort,projection}",
       "templated": true
     },
     "processes": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/processes{?page,size,sort,projection}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/processes{?page,size,sort,projection}",
       "templated": true
     },
     "files": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/files{?page,size,sort}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/files{?page,size,sort}",
       "templated": true,
       "title": "Access or create, within a submission envelope, a new assay"
     },
     "submissionEnvelopes": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes{?page,size,sort}",
+      "href": "https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes{?page,size,sort}",
       "templated": true,
       "title": "Access or create new submission envelopes"
     },
     "user": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/user"
+      "href": "https://api.ingest.dev.data.humancellatlas.org/user"
     },
     "profile": {
-      "href": "http://api.ingest.dev.data.humancellatlas.org/profile"
+      "href": "https://api.ingest.dev.data.humancellatlas.org/profile"
     }
   }
 }

pipeline_tools/tests/test_confirm_submission.py

@@ -10,7 +10,7 @@
 class TestConfirmSubmission(object):
 
     def test_wait_for_valid_status_success(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 200
@@ -24,7 +24,7 @@ def _request_callback(request, context):
         assert requests_mock.call_count == 1
 
     def test_wait_for_valid_status_retries_if_not_valid(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 200
@@ -36,7 +36,7 @@ def _request_callback(request, context):
         assert requests_mock.call_count == 3
 
     def test_wait_for_valid_status_retries_on_error(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 500
@@ -48,7 +48,7 @@ def _request_callback(request, context):
         assert requests_mock.call_count == 3
 
     def test_wait_for_valid_status_retries_on_read_timeout_error(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 500
@@ -60,7 +60,7 @@ def _request_callback(request, context):
         assert requests_mock.call_count == 3
 
     def test_confirm_success(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 200
@@ -72,7 +72,7 @@ def _request_callback(request, context):
         assert requests_mock.call_count == 1
 
     def test_confirm_retries_on_error(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 500
@@ -84,7 +84,7 @@ def _request_callback(request, context):
         assert requests_mock.call_count == 3
 
     def test_confirm_retries_on_read_timeout_error(self, requests_mock):
-        envelope_url = 'http://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
+        envelope_url = 'https://api.ingest.dev.data.humancellatlas.org/submissionEnvelopes/abcde'
 
         def _request_callback(request, context):
             context.status_code = 500