Merge pull request #293 from biocore/st_dh_hotfix_vioscreen

Vioscreen Hotfix - Registry Table

microsetta_private_api/api/_survey.py

@@ -44,7 +44,8 @@ def read_survey_templates(account_id, source_id, language_tag, token_info):
 
 
 def read_survey_template(account_id, source_id, survey_template_id,
-                         language_tag, token_info, survey_redirect_url=None):
+                         language_tag, token_info, survey_redirect_url=None,
+                         vioscreen_ext_sample_id=None):
     _validate_account_access(token_info, account_id)
 
     # TODO: can we get rid of source_id?  I don't have anything useful to do
@@ -58,14 +59,23 @@ def read_survey_template(account_id, source_id, survey_template_id,
 
         # For external surveys, we generate links pointing out
         if survey_template_id == SurveyTemplateRepo.VIOSCREEN_ID:
-
+            if vioscreen_ext_sample_id:
+                # User is about to start a vioscreen survey for this sample
+                # record this in the database.
+                db_vioscreen_id = survey_template_repo.create_vioscreen_id(
+                    account_id, source_id, vioscreen_ext_sample_id
+                )
+            else:
+                raise ValueError("Vioscreen Template requires "
+                                 "vioscreen_ext_sample_id parameter.")
             url = vioscreen.gen_survey_url(
-                language_tag, survey_redirect_url
+                db_vioscreen_id, language_tag, survey_redirect_url
             )
             # TODO FIXME HACK: This field's contents are not specified!
             info.survey_template_text = {
                 "url": url
             }
+            t.commit()
             return jsonify(info), 200
 
         # For local surveys, we generate the json representing the survey

microsetta_private_api/api/microsetta_private_api.yaml

@@ -551,6 +551,7 @@ paths:
         - $ref: '#/components/parameters/survey_template_id'
         - $ref: '#/components/parameters/language_tag'
         - $ref: '#/components/parameters/survey_redirect_url'
+        - $ref: '#/components/parameters/vioscreen_ext_sample_id'
       responses:
         '200':
           description: Successfully returned a specific survey template
@@ -1540,6 +1541,14 @@ components:
       schema:
         type: string
         example: "https://www.microsetta.org/accounts/72d2cc55-8522-4528-a85b-78be2ec0933f/sources/bfed3a1b-0855-4dce-9398-7c54f5b4ac8f"
+    vioscreen_ext_sample_id:
+      name: vioscreen_ext_sample_id
+      in: query
+      description: Identifies sample for vioscreen templates, indicates the user is being redirected to the response url and so vioscreen id should be logged
+      schema:
+        $ref: '#/components/schemas/sample_id'
+      required: False
+
     source_type:
       name: source_type
       in: query

microsetta_private_api/db/migration_support.py

@@ -384,10 +384,32 @@ def migrate_70(TRN):
         if len(offending_ids) != 0:
             raise Exception("Couldn't resolve vioscreen/primary split :(")
 
+    @staticmethod
+    def migrate_74(TRN):
+        TRN.add("SELECT DISTINCT "
+                "ag_login_id, "
+                "ag_login_surveys.source_id, "
+                "ag_kit_barcode_id, "
+                "ag_login_surveys.survey_id "
+                "FROM "
+                "ag_login_surveys LEFT JOIN "
+                "source_barcodes_surveys USING (survey_id) LEFT JOIN "
+                "ag_kit_barcodes USING (barcode) "
+                "WHERE vioscreen_status is not null "
+                )
+        rows = TRN.execute()[-1]
+        for r in rows:
+            TRN.add("INSERT INTO vioscreen_registry("
+                    "account_id, source_id, sample_id, vio_id) "
+                    "VALUES(%s, %s, %s, %s)",
+                    (r[0], r[1], r[2], r[3]))
+        TRN.execute()
+
     MIGRATION_LOOKUP = {
         "0048.sql": migrate_48.__func__,
         "0050.sql": migrate_50.__func__,
-        "0070.sql": migrate_70.__func__
+        "0070.sql": migrate_70.__func__,
+        "0074.sql": migrate_74.__func__,
         # ...
     }
 

microsetta_private_api/db/patches/0074.sql

@@ -0,0 +1,14 @@
+-- create table to track vioscreen survey ids
+CREATE TABLE ag.vioscreen_registry
+(
+    account_id uuid NOT NULL,
+    source_id uuid NOT NULL,
+    sample_id uuid,
+    vio_id varchar NOT NULL,
+    CONSTRAINT fk_account FOREIGN KEY (account_id) REFERENCES ag.account( id ),
+    CONSTRAINT fk_source FOREIGN KEY (source_id) REFERENCES ag.source( id ),
+    CONSTRAINT fk_sample FOREIGN KEY (sample_id) REFERENCES ag.ag_kit_barcodes( ag_kit_barcode_id )
+);
+
+CREATE INDEX vio_reg_by_vio_id ON ag.vioscreen_registry (vio_id);
+CREATE INDEX vio_reg_by_sample ON ag.vioscreen_registry (account_id, source_id, sample_id);

microsetta_private_api/repo/survey_template_repo.py

@@ -11,6 +11,7 @@
 from microsetta_private_api.model.survey_template_trigger import \
         SurveyTemplateTrigger
 import copy
+import secrets
 
 
 class SurveyTemplateRepo(BaseRepo):
@@ -209,3 +210,23 @@ def _get_question_triggers(self, survey_question_id):
 
             rows = cur.fetchall()
             return [SurveyTemplateTrigger(x[0], x[1]) for x in rows]
+
+    def create_vioscreen_id(self, account_id, source_id,
+                            vioscreen_ext_sample_id):
+        with self._transaction.cursor() as cur:
+            cur.execute("SELECT vio_id FROM vioscreen_registry WHERE "
+                        "account_id=%s AND "
+                        "source_id=%s AND "
+                        "sample_id=%s",
+                        (account_id, source_id, vioscreen_ext_sample_id))
+            rows = cur.fetchall()
+            if rows is None or len(rows) == 0:
+                vioscreen_id = secrets.token_hex(8)
+                cur.execute("INSERT INTO vioscreen_registry("
+                            "account_id, source_id, sample_id, vio_id) "
+                            "VALUES(%s, %s, %s, %s)",
+                            (account_id, source_id, vioscreen_ext_sample_id,
+                             vioscreen_id))
+            else:
+                vioscreen_id = rows[0][0]
+        return vioscreen_id

microsetta_private_api/util/vioscreen.py

@@ -1,5 +1,4 @@
 import base64
-import secrets
 import uuid
 from urllib.parse import urljoin
 
@@ -16,7 +15,7 @@
 from microsetta_private_api.config_manager import SERVER_CONFIG
 
 
-def gen_survey_url(language_tag, survey_redirect_url):
+def gen_survey_url(user_id, language_tag, survey_redirect_url):
     if not survey_redirect_url:
         raise BadRequest("Food Frequency Questionnaire Requires "
                          "survey_redirect_url")
@@ -25,7 +24,7 @@ def gen_survey_url(language_tag, survey_redirect_url):
     url = SERVER_CONFIG["vioscreen_endpoint"] + "/remotelogin.aspx?%s" % \
         url_encode(
               {
-                  b"Key": encrypt_key(secrets.token_hex(8),
+                  b"Key": encrypt_key(user_id,
                                       language_tag,
                                       survey_redirect_url),
                   b"RegCode": regcode.encode()