Merge pull request #274 from wasade/pulldown

Migrate metadata pulldown from -admin to -private-api

microsetta_private_api/admin/admin_impl.py

@@ -9,6 +9,8 @@
 from microsetta_private_api.repo.event_log_repo import EventLogRepo
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.admin_repo import AdminRepo
+from microsetta_private_api.repo.metadata_repo import (retrieve_metadata,
+                                                       drop_private_columns)
 from microsetta_private_api.tasks import send_email as celery_send_email
 from microsetta_private_api.admin.email_templates import EmailMessage
 from microsetta_private_api.util.redirects import build_login_redirect
@@ -86,6 +88,27 @@ def sample_pulldown_multiple_survey(token_info,
     return jsonify(sample_pulldown), 200
 
 
+def qiita_compatible_metadata(token_info, include_private, body):
+    validate_admin_access(token_info)
+
+    samples = body.get('sample_barcodes')
+    if samples is None:
+        return jsonify(code=404, message='No samples provided'), 404
+
+    # TODO: this call constructs transactions implicitly. It would be
+    # better for the transaction to be established and passed in,
+    # similar to how other "repo" objects are managed
+    df, errors = retrieve_metadata(samples)
+
+    if errors:
+        return jsonify(code=404, message=str(errors)), 404
+
+    if not include_private:
+        df = drop_private_columns(df)
+
+    return jsonify(df.to_dict(orient='index')), 200
+
+
 def token_grants_admin_access(token_info):
     with Transaction() as t:
         account_repo = AccountRepo(t)

microsetta_private_api/admin/tests/test_admin_api.py

@@ -715,3 +715,65 @@ def test_get_daklapack_articles(self):
 
         self.assertEqual(len(article_dicts_list), len(response_obj))
         self.assertEqual(FIRST_DAKLAPACK_ARTICLE, response_obj[0])
+
+    def test_metadata_qiita_compatible_invalid(self):
+        data = json.dumps({'sample_barcodes': ['bad']})
+        response = self.client.post('/api/admin/metadata/qiita-compatible',
+                                    content_type='application/json',
+                                    data=data,
+                                    headers=MOCK_HEADERS)
+        self.assertEqual(404, response.status_code)
+        data = json.dumps({'sample_barcodes': ['bad', '000004216']})
+        response = self.client.post('/api/admin/metadata/qiita-compatible',
+                                    content_type='application/json',
+                                    data=data,
+                                    headers=MOCK_HEADERS)
+        self.assertEqual(404, response.status_code)
+
+    def test_metadata_qiita_compatible_valid(self):
+        data = json.dumps({'sample_barcodes': ['000004216', '000004213']})
+        response = self.client.post('/api/admin/metadata/qiita-compatible',
+                                    content_type='application/json',
+                                    data=data,
+                                    headers=MOCK_HEADERS)
+        self.assertEqual(200, response.status_code)
+        result = json.loads(response.data)
+        self.assertEqual(set(result.keys()), {'000004216', '000004213'})
+
+    def test_metadata_qiita_compatible_valid_private(self):
+        data = json.dumps({'sample_barcodes': ['000004216', '000004213']})
+        response = self.client.post('/api/admin/metadata/qiita-compatible'
+                                    '?include_private=True',
+                                    content_type='application/json',
+                                    data=data,
+                                    headers=MOCK_HEADERS)
+        self.assertEqual(200, response.status_code)
+        result = json.loads(response.data)
+        self.assertEqual(set(result.keys()), {'000004216', '000004213'})
+        obs = {c.lower() for c in result['000004216']}
+        self.assertIn('about_yourself_text', obs)
+
+    def test_metadata_qiita_compatible_valid_no_private(self):
+        data = json.dumps({'sample_barcodes': ['000004216', '000004213']})
+        response = self.client.post('/api/admin/metadata/qiita-compatible'
+                                    '?include_private=False',
+                                    content_type='application/json',
+                                    data=data,
+                                    headers=MOCK_HEADERS)
+        self.assertEqual(200, response.status_code)
+        result = json.loads(response.data)
+        self.assertEqual(set(result.keys()), {'000004216', '000004213'})
+        obs = {c.lower() for c in result['000004216']}
+        self.assertNotIn('about_yourself_text', obs)
+
+        # sanity check the the default is false
+        data = json.dumps({'sample_barcodes': ['000004216', '000004213']})
+        response = self.client.post('/api/admin/metadata/qiita-compatible',
+                                    content_type='application/json',
+                                    data=data,
+                                    headers=MOCK_HEADERS)
+        self.assertEqual(200, response.status_code)
+        result = json.loads(response.data)
+        self.assertEqual(set(result.keys()), {'000004216', '000004213'})
+        obs = {c.lower() for c in result['000004216']}
+        self.assertNotIn('about_yourself_text', obs)

microsetta_private_api/api/microsetta_private_api.yaml

@@ -1143,7 +1143,42 @@ paths:
         - $ref: '#/components/parameters/sample_barcode'
       responses:
         '200':
-          description: QIIME-compatible sample metadata
+          description: Summarized sample metadata
+          content:
+            application/json:
+              schema:
+                type: object
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
+        '404':
+          $ref: '#/components/responses/404NotFound'
+
+  '/admin/metadata/qiita-compatible':
+    post:
+      operationId: microsetta_private_api.admin.admin_impl.qiita_compatible_metadata
+      tags:
+        - Admin
+      summary: Retrieve Qiita compatible metadata in JSON for a set of samples
+      description: Retrieve Qiita compatible metadata in JSON for a set of samples
+      parameters:
+        - $ref: '#/components/parameters/include_private'
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                'sample_barcodes':
+                  type: array
+                  items:
+                    # not using the defined schema for sample_barcode as it is 
+                    # readOnly
+                    type: string
+      responses:
+        '200':
+          description: Summarized sample metadata
           content:
             application/json:
               schema:
@@ -1431,6 +1466,12 @@ components:
       description: true if computed statistics about projects should be included in projects list (takes longer)
       schema:
         type: boolean
+    include_private:
+      name: include_private
+      in: query
+      description: include private information in a metadata pulldown; may be true or false. Optional.
+      schema:
+        $ref: '#/components/schemas/include_private'
 
   responses:
     401Unauthorized:   # Can be referenced as '#/components/responses/401Unauthorized'
@@ -1976,6 +2017,11 @@ components:
         - code
         - message
 
+    # metadata section
+    include_private:
+      type: boolean
+      default: false
+
   examples:
     human_adult_source:
       value:

microsetta_private_api/repo/metadata_repo/__init__.py

@@ -0,0 +1,3 @@
+from ._repo import retrieve_metadata, drop_private_columns
+
+__all__ = ['retrieve_metadata', 'drop_private_columns']