Merge pull request #600 from biocore/csymons_skin_scoring_app_working

Skin Scoring App

Author: cassidysymons

microsetta_private_api/api/__init__.py

@@ -25,7 +25,8 @@
     read_survey_template, read_survey_templates, read_answered_survey,
     read_answered_surveys, submit_answered_survey,
     read_answered_survey_associations, top_food_report,
-    read_myfoodrepo_available_slots
+    read_myfoodrepo_available_slots, get_skin_scoring_app_credentials,
+    post_skin_scoring_app_credentials
 )
 from ._sample import (
     read_sample_association, associate_sample, read_sample_associations,
@@ -103,6 +104,8 @@
     'read_answered_survey_associations',
     'top_food_report',
     'read_myfoodrepo_available_slots',
+    'get_skin_scoring_app_credentials',
+    'post_skin_scoring_app_credentials',
     'read_sample_association',
     'associate_sample',
     'read_sample_associations',

microsetta_private_api/api/_survey.py

@@ -34,31 +34,40 @@ def read_survey_templates(account_id, source_id, language_tag, token_info):
     with Transaction() as t:
         source_repo = SourceRepo(t)
         source = source_repo.get_source(account_id, source_id)
+
         if source is None:
             return jsonify(code=404, message="No source found"), 404
+
         template_repo = SurveyTemplateRepo(t)
+
         if source.source_type == Source.SOURCE_TYPE_HUMAN:
-            return jsonify([template_repo.get_survey_template_link_info(x)
-                           for x in [
-                                SurveyTemplateRepo.VIOSCREEN_ID,
-                                SurveyTemplateRepo.POLYPHENOL_FFQ_ID,
-                                SurveyTemplateRepo.SPAIN_FFQ_ID,
-                                SurveyTemplateRepo.BASIC_INFO_ID,
-                                SurveyTemplateRepo.AT_HOME_ID,
-                                SurveyTemplateRepo.LIFESTYLE_ID,
-                                SurveyTemplateRepo.GUT_ID,
-                                SurveyTemplateRepo.GENERAL_HEALTH_ID,
-                                SurveyTemplateRepo.HEALTH_DIAG_ID,
-                                SurveyTemplateRepo.ALLERGIES_ID,
-                                SurveyTemplateRepo.DIET_ID,
-                                SurveyTemplateRepo.DETAILED_DIET_ID,
-                                SurveyTemplateRepo.OTHER_ID
-                            ]]), 200
+            template_ids = [
+                SurveyTemplateRepo.VIOSCREEN_ID,
+                SurveyTemplateRepo.POLYPHENOL_FFQ_ID,
+                SurveyTemplateRepo.SPAIN_FFQ_ID,
+                SurveyTemplateRepo.BASIC_INFO_ID,
+                SurveyTemplateRepo.AT_HOME_ID,
+                SurveyTemplateRepo.LIFESTYLE_ID,
+                SurveyTemplateRepo.GUT_ID,
+                SurveyTemplateRepo.GENERAL_HEALTH_ID,
+                SurveyTemplateRepo.HEALTH_DIAG_ID,
+                SurveyTemplateRepo.ALLERGIES_ID,
+                SurveyTemplateRepo.DIET_ID,
+                SurveyTemplateRepo.DETAILED_DIET_ID,
+                SurveyTemplateRepo.OTHER_ID
+            ]
+            if template_repo.check_display_skin_scoring_app(
+                account_id, source_id
+            ):
+                template_ids.append(SurveyTemplateRepo.SKIN_SCORING_APP_ID)
+
         elif source.source_type == Source.SOURCE_TYPE_ANIMAL:
-            return jsonify([template_repo.get_survey_template_link_info(x)
-                           for x in [2]]), 200
+            template_ids = [2]
         else:
-            return jsonify([]), 200
+            template_ids = []
+
+        return jsonify([template_repo.get_survey_template_link_info(x)
+                        for x in template_ids]), 200
 
 
 def _remote_survey_url_vioscreen(transaction, account_id, source_id,
@@ -181,6 +190,23 @@ def _remote_survey_url_spain_ffq(transaction, account_id, source_id):
     return SERVER_CONFIG['spain_ffq_url']
 
 
+def _remote_survey_url_skin_scoring_app(transaction,
+                                        account_id,
+                                        source_id):
+    st_repo = SurveyTemplateRepo(transaction)
+
+    # Confirm that the user has credentials allocated
+    ssa_u, _ = st_repo.get_skin_scoring_app_credentials_if_exists(
+            account_id,
+            source_id
+        )
+
+    if ssa_u is None:
+        raise NotFound("Sorry, you were not allocated credentials")
+
+    return SERVER_CONFIG['skin_app_url']
+
+
 def read_survey_template(account_id, source_id, survey_template_id,
                          language_tag, token_info, survey_redirect_url=None,
                          vioscreen_ext_sample_id=None,
@@ -220,6 +246,11 @@ def read_survey_template(account_id, source_id, survey_template_id,
                 url = _remote_survey_url_spain_ffq(t,
                                                    account_id,
                                                    source_id)
+            elif survey_template_id == \
+                    SurveyTemplateRepo.SKIN_SCORING_APP_ID:
+                url = _remote_survey_url_skin_scoring_app(t,
+                                                          account_id,
+                                                          source_id)
             else:
                 raise ValueError(f"Cannot generate URL for survey "
                                  f"{survey_template_id}")
@@ -499,3 +530,59 @@ def read_myfoodrepo_available_slots():
     resp = jsonify(code=200, number_of_available_slots=available,
                    total_number_of_slots=total)
     return resp, 200
+
+
+def get_skin_scoring_app_credentials(account_id, source_id, token_info):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        st_repo = SurveyTemplateRepo(t)
+        ssa_u, ssa_s = st_repo.get_skin_scoring_app_credentials_if_exists(
+            account_id, source_id
+        )
+        response_obj = {
+            "app_username": ssa_u,
+            "app_studycode": ssa_s
+        }
+        return jsonify(response_obj), 200
+
+
+def post_skin_scoring_app_credentials(account_id, source_id, token_info):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        st_repo = SurveyTemplateRepo(t)
+
+        # First, confirm that the source doesn't already have credentials
+        ssa_u, _ = st_repo.get_skin_scoring_app_credentials_if_exists(
+            account_id, source_id
+        )
+
+        # This shouldn't happen, but if it does, return an error
+        if ssa_u is not None:
+            return jsonify(
+                code=400,
+                message="Credentials already exist"
+            ), 400
+
+        # Now, try to allocate credentials and create an entry in the skin
+        # scoring app registry table
+        ssa_u, ssa_s = st_repo.create_skin_scoring_app_entry(
+            account_id, source_id
+        )
+        t.commit()
+
+        if ssa_u is None:
+            # No credentials were available
+            return jsonify(
+                code=404,
+                message="No credentials available"
+            ), 404
+        else:
+            # Credentials were successfully allocated
+            return jsonify(
+                {
+                    "app_username": ssa_u,
+                    "app_studycode": ssa_s
+                }
+            ), 201

microsetta_private_api/api/microsetta_private_api.yaml

@@ -1024,6 +1024,64 @@ paths:
         '404':
           $ref: '#/components/responses/404NotFound'
 
+  '/accounts/{account_id}/sources/{source_id}/surveys/skin_scoring_app_credentials':
+    get:
+      operationId: microsetta_private_api.api.get_skin_scoring_app_credentials
+      tags:
+        - Surveys (By Source)
+      summary: Get skin scoring app credentials associated with source, if they exist
+      description: Get skin scoring app credentials associated with source, if they exist
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+        - $ref: '#/components/parameters/source_id'
+      responses:
+        '200':
+          description: Credentials for skin scoring app
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  app_username:
+                    type: string
+                    nullable: true
+                  app_studycode:
+                    type: string
+                    nullable: true
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
+    post:
+      operationId: microsetta_private_api.api.post_skin_scoring_app_credentials
+      tags:
+        - Surveys (By Source)
+      summary: Create association between a set of skin scoring app credentials and a source
+      description: Create association between a set of skin scoring app credentials and a source
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+        - $ref: '#/components/parameters/source_id'
+      responses:
+        '201':
+          description: Credentials for skin scoring app
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  app_username:
+                    type: string
+                  app_studycode:
+                    type: string
+        '400':
+          description: 'Credentials already exist for source'
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
+        '404':
+          $ref: '#/components/responses/404NotFound'
+
   '/accounts/{account_id}/sources/{source_id}/samples':
     get:
       operationId: microsetta_private_api.api.read_sample_associations

microsetta_private_api/api/tests/test_api.py

@@ -181,7 +181,8 @@
     'sample_projects': ['American Gut Project'],
     'account_id': None,
     'source_id': None,
-    'sample_site': None}
+    'sample_site': None,
+    'sample_project_ids': [1]}
 
 DUMMY_FILLED_SAMPLE_INFO = {
     'sample_barcode': BARCODE,
@@ -195,7 +196,8 @@
     'sample_projects': ['American Gut Project'],
     'account_id': 'foobar',
     'source_id': 'foobarbaz',
-    'sample_site': 'Saliva'}
+    'sample_site': 'Saliva',
+    'sample_project_ids': [1]}
 
 ACCT_ID_KEY = "account_id"
 ACCT_TYPE_KEY = "account_type"
@@ -594,7 +596,8 @@ def create_dummy_sample_objects(filled=False):
                     info_dict['account_id'],
                     None,
                     info_dict["sample_projects"],
-                    None)
+                    None,
+                    sample_project_ids=info_dict["sample_project_ids"])
 
     return sample_info, sample
 # endregion help methods
@@ -2244,6 +2247,10 @@ def test_associate_sample_to_source_success(self):
         exp['account_id'] = ACCT_ID_1
         exp['kit_id'] = None
 
+        # Remove the sample_project_ids element since we don't expect that
+        # to come out of the API
+        exp.pop("sample_project_ids")
+
         self.assertEqual(get_resp_obj, [exp])
 
         # TODO: We should also have tests of associating a sample to a source

microsetta_private_api/db/migration_support.py

@@ -795,6 +795,35 @@ def migrate_133(TRN):
                     print("No mapping: " + ffq_id + " - " + barcode)
         TRN.execute()
 
+    @staticmethod
+    def migrate_144(TRN):
+        # We need to load the credentials that the vendor provided in CSV form
+        # Format is username, studycode and includes a header row
+        skin_app_credentials_path = SERVER_CONFIG["skin_app_credentials_path"]
+        if not os.path.exists(skin_app_credentials_path):
+            print(
+                "Credentials for app not found:" + skin_app_credentials_path
+            )
+            return
+
+        with open(skin_app_credentials_path) as csv_file:
+            csv_contents = csv.reader(csv_file)
+            header = True
+
+            for csv_row in csv_contents:
+                if header:
+                    header = False
+                    continue
+                app_username, app_studycode = csv_row
+
+                TRN.add(
+                    "INSERT INTO ag.skin_scoring_app_credentials "
+                    "(app_username, app_studycode) "
+                    "VALUES (%s, %s)",
+                    (app_username, app_studycode)
+                )
+        TRN.execute()
+
     MIGRATION_LOOKUP = {
         "0048.sql": migrate_48.__func__,
         "0050.sql": migrate_50.__func__,
@@ -806,7 +835,8 @@ def migrate_133(TRN):
         # "0082.sql": migrate_82.__func__
         # ...
         "0096.sql": migrate_96.__func__,
-        "0133.sql": migrate_133.__func__
+        "0133.sql": migrate_133.__func__,
+        "0144.sql": migrate_144.__func__
     }
 
     @classmethod

microsetta_private_api/db/patches/0144.sql

@@ -0,0 +1,27 @@
+-- The organization that hosts the skin-scoring app provides us with username
+-- and studycode pairings for participants to access the app. We need to store
+-- these pairings, as well as a flag for whether the pairing has been
+-- allocated to a participant. We explicitly store this flag to avoid reuse
+-- if sources (and their related survey databsase records) were to be deleted.
+CREATE TABLE ag.skin_scoring_app_credentials (
+    app_username VARCHAR PRIMARY KEY,
+    app_studycode VARCHAR NOT NULL,
+    credentials_allocated BOOLEAN NOT NULL DEFAULT FALSE
+);
+
+-- And we create a registry table, similar to all of the other external
+-- surveys we've hosted in the past, to link the username to the account and
+-- source that used it.
+CREATE TABLE ag.skin_scoring_app_registry (
+    app_username VARCHAR PRIMARY KEY,
+    account_id UUID NOT NULL,
+    source_id UUID,
+    deleted BOOLEAN NOT NULL DEFAULT false,
+    creation_timestamp TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+
+    CONSTRAINT fk_skin_scoring_app_username FOREIGN KEY (app_username) REFERENCES ag.skin_scoring_app_credentials(app_username),
+    CONSTRAINT fk_skin_scoring_app_registry_account FOREIGN KEY (account_id) REFERENCES ag.account(id),
+    CONSTRAINT fk_skin_scoring_app_registry_source FOREIGN KEY (source_id) REFERENCES ag.source(id)
+);
+
+CREATE INDEX skin_scoring_app_registry_source ON ag.skin_scoring_app_registry (account_id, source_id);

microsetta_private_api/model/sample.py

@@ -6,7 +6,7 @@ class Sample(ModelBase):
     def __init__(self, sample_id, datetime_collected, site, notes, barcode,
                  latest_scan_timestamp, source_id, account_id,
                  latest_sample_information_update, sample_projects,
-                 latest_scan_status, kit_id=None):
+                 latest_scan_status, kit_id=None, sample_project_ids=None):
         self.id = sample_id
         # NB: datetime_collected may be None if sample not yet used
         self.datetime_collected = datetime_collected
@@ -28,9 +28,14 @@ def __init__(self, sample_id, datetime_collected, site, notes, barcode,
         self.accession_urls = []
         self.kit_id = kit_id
 
+        self._sample_project_ids = sample_project_ids
+
     def set_accession_urls(self, accession_urls):
         self.accession_urls = accession_urls
 
+    def get_project_ids(self):
+        return self._sample_project_ids
+
     @property
     def edit_locked(self):
         # If a sample has been scanned and is valid, it is locked.
@@ -47,7 +52,8 @@ def remove_locked(self):
     def from_db(cls, sample_id, date_collected, time_collected,
                 site, notes, barcode, latest_scan_timestamp,
                 latest_sample_information_update, source_id,
-                account_id, sample_projects, latest_scan_status):
+                account_id, sample_projects, latest_scan_status,
+                sample_project_ids):
         datetime_collected = None
         # NB a sample may NOT have date and time collected if it has been sent
         # out but not yet used
@@ -56,7 +62,8 @@ def from_db(cls, sample_id, date_collected, time_collected,
                                                   time_collected)
         return cls(sample_id, datetime_collected, site, notes, barcode,
                    latest_scan_timestamp, latest_sample_information_update,
-                   source_id, account_id, sample_projects, latest_scan_status)
+                   source_id, account_id, sample_projects, latest_scan_status,
+                   sample_project_ids=sample_project_ids)
 
     def to_api(self):
         return {