Adding Data and Bio Consent through DB

microsetta_private_api/api/__init__.py

@@ -5,11 +5,13 @@
 )
 from ._consent import (
     render_consent_doc,
+    check_consent_signature,
+    sign_consent_doc
 )
 from ._source import (
     create_source, read_source, update_source, delete_source,
     read_sources, create_human_source_from_consent,
-    check_duplicate_source_name
+    check_duplicate_source_name, scrub_source
 )
 from ._survey import (
     read_survey_template, read_survey_templates, read_answered_survey,
@@ -71,9 +73,12 @@
     'read_source',
     'update_source',
     'delete_source',
+    'scrub_source',
     'read_sources',
     'check_duplicate_source_name',
     'create_human_source_from_consent',
+    'check_consent_signature',
+    'sign_consent_doc',
     'read_survey_template',
     'read_survey_templates',
     'read_answered_survey',

microsetta_private_api/api/_consent.py

@@ -1,18 +1,73 @@
 from flask import jsonify
-
+import uuid
 from microsetta_private_api import localization
 from microsetta_private_api.api._account import \
     _validate_account_access
+from microsetta_private_api.model.consent import ConsentSignature
+from microsetta_private_api.repo.consent_repo import ConsentRepo
+from microsetta_private_api.repo.transaction import Transaction
+from microsetta_private_api.api.literals import CONSENT_DOC_NOT_FOUND_MSG
 
 
 def render_consent_doc(account_id, language_tag, token_info):
     _validate_account_access(token_info, account_id)
 
-    # NB: Do NOT need to explicitly pass account_id into template for
-    # integration into form submission URL because form submit URL builds on
-    # the base of the URL that called it (which includes account_id)
+    consent_form = {}
 
     localization_info = localization.LANG_SUPPORT[language_tag]
     content = localization_info[localization.NEW_PARTICIPANT_KEY]
+    consent_form["PARTICIPANT_FORM"] = content
+
+    with Transaction() as t:
+        consent_repo = ConsentRepo(t)
+        documents = consent_repo.get_all_consent_documents(language_tag)
+        data = [x.to_api() for x in documents]
+        consent_form["CONSENT_DOCS"] = data
+
+    return jsonify(consent_form), 200
+
+
+def get_consent_doc(account_id, consent_id, token_info):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        consent_repo = ConsentRepo(t)
+        document = consent_repo.get_consent_document(consent_id)
+
+    if document:
+        data = document.to_api()
+        return jsonify(data), 200
+    else:
+        return jsonify(code=404, message=CONSENT_DOC_NOT_FOUND_MSG), 404
+
+
+def check_consent_signature(account_id, source_id, consent_type, token_info):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        consent_repo = ConsentRepo(t)
+        res = consent_repo.is_consent_required(source_id, consent_type)
+
+    return jsonify({"result": res}), 200
+
+
+def sign_consent_doc(account_id, source_id, consent_type, body, token_info):
+
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        consent_repo = ConsentRepo(t)
+        sign_id = str(uuid.uuid4())
+        consent_sign = ConsentSignature.from_dict(body, source_id, sign_id)
+        try:
+            consent_repo.sign_consent(account_id, consent_sign)
+            t.commit()
+        except Exception:
+            return jsonify(code=404, message=CONSENT_DOC_NOT_FOUND_MSG), 404
+
+    response = jsonify({"result": True})
+    response.status_code = 201
+    response.headers['Location'] = '/api/accounts/%s' % \
+        (account_id)
 
-    return jsonify(content), 200
+    return response

microsetta_private_api/api/_source.py

@@ -1,13 +1,14 @@
 import uuid
 from datetime import date
-
 from flask import jsonify
 
 from microsetta_private_api.api._account import _validate_account_access
 from microsetta_private_api.api.literals import SRC_NOT_FOUND_MSG
 from microsetta_private_api.exceptions import RepoException
 from microsetta_private_api.model.source import Source, HumanInfo, NonHumanInfo
 from microsetta_private_api.repo.source_repo import SourceRepo
+from microsetta_private_api.repo.consent_repo import ConsentRepo
+from microsetta_private_api.repo.sample_repo import SampleRepo
 from microsetta_private_api.repo.survey_answers_repo import SurveyAnswersRepo
 from microsetta_private_api.repo.transaction import Transaction
 
@@ -109,20 +110,60 @@ def delete_source(account_id, source_id, token_info):
     with Transaction() as t:
         source_repo = SourceRepo(t)
         survey_answers_repo = SurveyAnswersRepo(t)
+        consent_repo = ConsentRepo(t)
+        samp_repo = SampleRepo(t)
+
+        samples = samp_repo.get_samples_by_source(account_id, source_id)
+        for sample in samples:
+            # we scrub rather than disassociate in the event that the
+            # sample is in our freezers but not with an up-to-date scan
+            samp_repo.dissociate_sample(account_id, source_id, sample.id)
 
         answers = survey_answers_repo.list_answered_surveys(account_id,
                                                             source_id)
         for survey_id in answers:
             survey_answers_repo.delete_answered_survey(account_id,
                                                        survey_id)
 
+        # delete all consents accosiated with source
+        consent_repo.delete_signatures(account_id, source_id)
+
         if not source_repo.delete_source(account_id, source_id):
             return jsonify(code=404, message=SRC_NOT_FOUND_MSG), 404
         # TODO: 422?
         t.commit()
         return '', 204
 
 
+def scrub_source(account_id, source_id, token_info):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        source_repo = SourceRepo(t)
+        consent_repo = ConsentRepo(t)
+        samp_repo = SampleRepo(t)
+        sur_repo = SurveyAnswersRepo(t)
+
+        samples = samp_repo.get_samples_by_source(account_id, source_id)
+        for sample in samples:
+            # we scrub rather than disassociate in the event that the
+            # sample is in our freezers but not with an up-to-date scan
+            samp_repo.scrub(account_id, source_id, sample.id)
+
+        # fetch and scrub all surveys
+        surveys = sur_repo.list_answered_surveys(account_id, source_id)
+        for survey_id in surveys:
+            sur_repo.scrub(account_id, source_id, survey_id)
+
+        # scrub all consents accosiated with source
+        consent_repo.scrub(account_id, source_id)
+
+        # scrub the source
+        source_repo.scrub(account_id, source_id)
+        t.commit()
+        return jsonify({"result": True}), 200
+
+
 def create_human_source_from_consent(account_id, body, token_info):
     _validate_account_access(token_info, account_id)
 

microsetta_private_api/api/literals.py

@@ -14,3 +14,4 @@
 ACCT_NOT_FOUND_MSG = "Account not found"
 SRC_NOT_FOUND_MSG = "Source not found"
 INVALID_TOKEN_MSG = "Invalid token"
+CONSENT_DOC_NOT_FOUND_MSG = "Consent not found"