Merge c7aefa2 into f717415

microsetta_private_api/api/implementation.py

@@ -15,6 +15,8 @@
 from flask import jsonify, render_template
 import jwt
 from base64 import b64decode
+
+from microsetta_private_api.model.address import Address
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.account_repo import AccountRepo
 from microsetta_private_api.repo.source_repo import SourceRepo
@@ -23,13 +25,16 @@
 from microsetta_private_api.repo.survey_answers_repo import SurveyAnswersRepo
 from microsetta_private_api.repo.sample_repo import SampleRepo
 
+from microsetta_private_api.model.account import Account
 from microsetta_private_api.model.source import Source
+from microsetta_private_api.model.source import human_info_from_api
 from microsetta_private_api.LEGACY.locale_data import american_gut
 
 from microsetta_private_api.util import vue_adapter
 
 import uuid
 import json
+from datetime import date
 
 TOKEN_KEY = "QvMWMnlOqBbNsM88AMxpzcJMbBUu/w8U9joIaNYjuEbwEYhLIB5FqEoFWnfLN3JZN4SD0LAtZOwFNqyMLmNruBLqEvbpjQzM6AY+BfXGxDVFL65c9Xw8ocd6t1nF6YvTpHGB4NJhUwngjIQmFx+6TCa5wArtEqUeoIc1ukVTYbioRkxzi5ju8cc9/PoInB0c7wugMz5ihAPWohpDc4kCotYv7C2K/e9J9CPdwbiLJKYKxO4zSQAqk+Sj4wRcn7bJqIOIT6BlvvnzRGXYG33qXAxGylM4UySj7ltwSGOIY0/JUvKEej3fX17C8wWtJvrjbFQacNhoglqfWq2GeOdRSA== "  # noqa: E501
 TEMP_ACCESS_TOKEN = "eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJodHRwOi8vbXlhcHAuY29tLyIsInN1YiI6InVzZXJzL3VzZXIxMjM0Iiwic2NvcGUiOiJzZWxmLCBhZG1pbnMiLCJqdGkiOiJkMzBkMzA5ZS1iZTQ5LTRjOWEtYjdhYi1hMGU3MTIwYmFlZDMiLCJpYXQiOjE1NzIzNzY4OTUsImV4cCI6MTU3MjM4MDQ5NX0.EMooERuy2Z4tC_TsXJe6Vx8yCgzTzI_qh84a5DsKPRw"  # noqa: E501
@@ -68,7 +73,38 @@ def verify_and_decode_token(access_token) -> dict:
 
 
 def register_account(body):
-    return not_yet_implemented()
+    # TODO: Do they register with GLOBUS first, then make the account here?
+    #  What should be done with the kit_name?
+    new_acct_id = str(uuid.uuid4())
+    with Transaction() as t:
+        kit_repo = KitRepo(t)
+        kit = kit_repo.get_kit(body['kit_name'])
+        if kit is None:
+            return jsonify(error=403, text="Incorrect kit_name"), 403
+
+        acct_repo = AccountRepo(t)
+        acct_repo.create_account(Account(
+            new_acct_id,
+            body['email'],
+            "standard",
+            "GLOBUS",  # TODO: This is dependent on their login token!
+            body['first_name'],
+            body['last_name'],
+            Address(
+                body['address']['street'],
+                body['address']['city'],
+                body['address']['state'],
+                body['address']['post_code'],
+                body['address']['country_code'],
+            )
+        ))
+        new_acct = acct_repo.get_account(new_acct_id)
+        t.commit()
+
+    response = jsonify(new_acct.to_api())
+    response.status_code = 201
+    response.headers['Location'] = '/api/accounts/%s' % new_acct_id
+    return response
 
 
 def read_account(token_info, account_id):
@@ -92,10 +128,16 @@ def update_account(account_id, body):
 
         # TODO: add 422 handling
 
-        acc.first_name = body["first_name"]
-        acc.last_name = body["last_name"]
-        acc.email = body["email"]
-        acc.address = body["address"]
+        acc.first_name = body['first_name']
+        acc.last_name = body['last_name']
+        acc.email = body['email']
+        acc.address = Address(
+            body['address']['street'],
+            body['address']['city'],
+            body['address']['state'],
+            body['address']['post_code'],
+            body['address']['country_code']
+        )
 
         acct_repo.update_account(acc)
         t.commit()
@@ -115,14 +157,32 @@ def create_source(account_id, body):
     with Transaction() as t:
         source_repo = SourceRepo(t)
         source_id = str(uuid.uuid4())
-        source_info = None
-        new_source = Source.from_json(source_id, account_id, source_info)
+
+        if body['source_type'] == 'human':
+            # TODO: Unfortunately, humans require a lot of special handling,
+            #  and we started mixing Source calls used for transforming to/
+            #  from the database with source calls to/from the api.
+            #  Would be nice to split this out better.
+            new_source = Source(source_id,
+                                account_id,
+                                'human',
+                                human_info_from_api(body,
+                                                    consent_date=date.today(),
+                                                    date_revoked=None))
+        else:
+            new_source = Source.build_source(source_id, account_id, body)
+
         source_repo.create_source(new_source)
+
         # Must pull from db to get creation_time, update_time
         s = source_repo.get_source(account_id, new_source.id)
         t.commit()
-        # TODO: What about 404 and 422 errors?
-        return jsonify(s.to_api()), 200
+
+    response = jsonify(s.to_api())
+    response.status_code = 201
+    response.headers['Location'] = '/api/accounts/%s/sources/%s' % \
+                                   (account_id, source_id)
+    return response
 
 
 def read_source(account_id, source_id):
@@ -223,36 +283,57 @@ def submit_answered_survey(account_id, source_id, language_tag, body):
     # TODO: Rename survey_text to survey_model/model to match Vue's naming?
     with Transaction() as t:
         survey_answers_repo = SurveyAnswersRepo(t)
-        success = survey_answers_repo.submit_answered_survey(
+        survey_answers_id = survey_answers_repo.submit_answered_survey(
             account_id,
             source_id,
             language_tag,
             body["survey_template_id"],
             body["survey_text"]
         )
-        if success:
-            t.commit()
-            return jsonify(''), 201
-        return jsonify(code=422,
-                       message="Could not submit answered survey"), 422
+        t.commit()
+
+        response = jsonify('')
+        response.status_code = 201
+        response.headers['Location'] = '/api/accounts/%s' \
+                                       '/sources/%s' \
+                                       '/surveys/%s' % \
+                                       (account_id,
+                                        source_id,
+                                        survey_answers_id)
+        return response
 
 
 def read_sample_associations(account_id, source_id):
-    return not_yet_implemented()
+    with Transaction() as t:
+        sample_repo = SampleRepo(t)
+        samples = sample_repo.get_samples_by_source(account_id, source_id)
+
+    api_samples = [x.to_api() for x in samples]
+    return jsonify(api_samples), 200
 
 
 def associate_sample(account_id, source_id, body):
-    return not_yet_implemented()
+    with Transaction() as t:
+        sample_repo = SampleRepo(t)
+        sample_repo.associate_sample(account_id,
+                                     source_id,
+                                     body['sample_id'])
+        t.commit()
+    response = jsonify('')
+    response.status_code = 201
+    response.headers['Location'] = '/api/accounts/%s/sources/%s/samples/%s' % \
+                                   (account_id, source_id, ['sample_id'])
+    return response
 
 
 def read_sample_association(account_id, source_id, sample_id):
     with Transaction() as t:
         sample_repo = SampleRepo(t)
-        sample = sample_repo.get_sample(sample_id)
+        sample = sample_repo.get_sample(account_id, source_id, sample_id)
         if sample is None:
             return jsonify(error=404, text="Sample not found"), 404
 
-        return jsonify(sample), 200
+        return jsonify(sample.to_api()), 200
 
 
 def update_sample_association(account_id, source_id, sample_id, body):
@@ -301,12 +382,33 @@ def render_consent_doc(account_id):
 
 
 def create_human_source_from_consent(account_id, body):
-    # A human source's participant name becomes the source name. Note pop
-    # removes the existing `participant_name` key if exists, else errors.
+    # Must convert consent form body into object processable by create_source.
+
     # Not adding any error handling here because if 'participant_name' isn't
     # here, we SHOULD be getting an error.
-    body['source_name'] = body.pop('participant_name')
+    source = {
+        'source_type': "human",
+        'source_name': body['participant_name'],
+        'consent': {
+            'participant_email': body['participant_email'],
+            'age_range': body['age_range']
+        }
+    }
+
+    child_keys = ['parent_1_name', 'parent_2_name',
+                  'deceased_parent', 'obtainer_name']
+
+    any_in = False
+    for key in child_keys:
+        if key in body:
+            any_in = True
+
+    if any_in:
+        source['consent']['child_info'] = {}
+        for key in child_keys:
+            if key in body:
+                source['consent']['child_info'][key] = body[key]
 
     # NB: Don't expect to handle errors 404, 422 in this function; expect to
     # farm out to `create_source`
-    return create_source(account_id, body)
+    return create_source(account_id, source)

microsetta_private_api/api/microsetta_private_api.yaml

@@ -45,6 +45,8 @@ paths:
                 $ref: '#/components/schemas/account'
         '401':
           $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
         '422':
           $ref: '#/components/responses/422UnprocessableEntity'
 
@@ -822,7 +824,7 @@ components:
       in: path
       description: Unique id specifying a sample associated with a source
       schema:
-        $ref: '#/components/schemas/survey_id'
+        $ref: '#/components/schemas/sample_id'
       required: true
     survey_id:
       name: survey_id
@@ -871,6 +873,12 @@ components:
   responses:
     401Unauthorized:   # Can be referenced as '#/components/responses/401Unauthorized'
       description: Invalid or missing token.
+    403Forbidden:      # Can be referenced as '#/components/responses/403Forbidden'
+      description: Incorrect required parameter.
+      content:
+        application/json:
+          schema:
+            $ref: '#/components/schemas/Error'
     404NotFound:       # Can be referenced as '#/components/responses/404NotFound'
       description: The specified resource was not found.
     422UnprocessableEntity:
@@ -1065,6 +1073,8 @@ components:
         source_type:
           type: string
           enum: [animal, environmental]
+        source_name:
+          type: string
         source_description:
           type: string
           nullable: true
@@ -1107,8 +1117,8 @@ components:
 
     # survey template section
     survey_template_id:
-      type: string
-      example: "e928f910-bf11-4cda-93b5-c34c8914b97f"
+      type: integer
+      example: 3
     survey_template_title:
       type: string
       example: "Personal Information"
@@ -1205,7 +1215,7 @@ components:
       example: "69f697cb-8e52-4a4f-8db2-efffcfa186a5"
     survey_text:
       # The contents of this string ARE structured, but their structure is not specified in THIS api.
-      type: string
+      type: object
       example: '{ |
                     "1": "Omnivore", |
                                           "2": "No", |