Merge pull request #14 from sartography/feature/protocol-builder

Feature/protocol builder

Pipfile

@@ -33,6 +33,7 @@ recommonmark = "*"
 psycopg2-binary = "*"
 docxtpl = "*"
 flask-sso = "*"
+python-dateutil = "*"
 
 [requires]
 python_version = "3.7"

Pipfile.lock

@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "4bcfdceb9683a7885711d4d96296d8ba78fd60bebd5ab56cd3bb1b5eb1dee7b2"
+            "sha256": "60e48d05048f627878a5c81377318bc2ff2a94b2574441c166fda3a523c789df"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -91,10 +91,10 @@
         },
         "billiard": {
             "hashes": [
-                "sha256:26fd494dc3251f8ce1f5559744f18aeed427fdaf29a75d7baae26752a5d3816f",
+                "sha256:bff575450859a6e0fbc2f9877d9b715b0bbc07c3565bb7ed2280526a0cdf5ede",
-                "sha256:f4e09366653aa3cb3ae8ed16423f9ba1665ff426f087bcdbbed86bf3664fe02c"
+                "sha256:d91725ce6425f33a97dfa72fb6bfef0e47d4652acd98a032bd1a7fbf06d5fa6a"
             ],
-            "version": "==3.6.2.0"
+            "version": "==3.6.3.0"
         },
         "blinker": {
             "hashes": [
@@ -597,6 +597,7 @@
                 "sha256:73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c",
                 "sha256:75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"
             ],
+            "index": "pypi",
             "version": "==2.8.1"
         },
         "python-docx": {
@@ -668,18 +669,18 @@
         },
         "soupsieve": {
             "hashes": [
-                "sha256:bdb0d917b03a1369ce964056fc195cfdff8819c40de04695a80bc813c3cfa1f5",
+                "sha256:e914534802d7ffd233242b785229d5ba0766a7f487385e3f714446a07bf540ae",
-                "sha256:e2c1c5dee4a1c36bcb790e0fabd5492d874b8ebd4617622c4f6a731701060dda"
+                "sha256:fcd71e08c0aee99aca1b73f45478549ee7e7fc006d51b37bec9e9def7dc22b69"
             ],
-            "version": "==1.9.5"
+            "version": "==2.0"
         },
         "sphinx": {
             "hashes": [
-                "sha256:525527074f2e0c2585f68f73c99b4dc257c34bbe308b27f5f8c7a6e20642742f",
+                "sha256:776ff8333181138fae52df65be733127539623bb46cc692e7fa0fcfc80d7aa88",
-                "sha256:543d39db5f82d83a5c1aa0c10c88f2b6cff2da3e711aa849b2c627b4b403bbd9"
+                "sha256:ca762da97c3b5107cbf0ab9e11d3ec7ab8d3c31377266fd613b962ed971df709"
             ],
             "index": "pypi",
-            "version": "==2.4.2"
+            "version": "==2.4.3"
         },
         "sphinxcontrib-applehelp": {
             "hashes": [
@@ -697,10 +698,10 @@
         },
         "sphinxcontrib-htmlhelp": {
             "hashes": [
-                "sha256:4670f99f8951bd78cd4ad2ab962f798f5618b17675c35c5ac3b2132a14ea8422",
+                "sha256:3c0bc24a2c41e340ac37c85ced6dafc879ab485c095b1d65d2461ac2f7cca86f",
-                "sha256:d4fd39a65a625c9df86d7fa8a2d9f3cd8299a3a4b15db63b50aac9e161d8eff7"
+                "sha256:e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b"
             ],
-            "version": "==1.0.2"
+            "version": "==1.0.3"
         },
         "sphinxcontrib-jsmath": {
             "hashes": [
@@ -726,7 +727,7 @@
         "spiffworkflow": {
             "editable": true,
             "git": "https://github.com/sartography/SpiffWorkflow.git",
-            "ref": "bab9a280f94b8a94ade5107c0bce104aade9ad04"
+            "ref": "0da57a83bfa0edaf1cfd5500f87757553621c412"
         },
         "sqlalchemy": {
             "hashes": [
@@ -788,11 +789,11 @@
         },
         "xlsxwriter": {
             "hashes": [
-                "sha256:18fe8f891a4adf7556c05d56059e136f9fbce5b19f9335f6d7b42c389c4592bc",
+                "sha256:488e1988ab16ff3a9cd58c7656d0a58f8abe46ee58b98eecea78c022db28656b",
-                "sha256:5d3630ff9b2a277c939bd5053d0e7466499593abebbab9ce1dc9b1481a8ebbb6"
+                "sha256:97ab487b81534415c5313154203f3e8a637d792b1e6a8201e8f7f71da0203c2a"
             ],
             "index": "pypi",
-            "version": "==1.2.7"
+            "version": "==1.2.8"
         },
         "zipp": {
             "hashes": [

crc/__init__.py

@@ -19,7 +19,7 @@ auth = HTTPTokenAuth('Bearer')
 
 if "TESTING" in os.environ and os.environ["TESTING"] == "true":
     app.config.from_object('config.testing')
-    app.config.from_pyfile('testing.py')
+    app.config.from_pyfile('../config/testing.py')
 else:
     app.config.root_path = app.instance_path
     app.config.from_pyfile('config.py', silent=True)

crc/api.yml

@@ -670,6 +670,9 @@ components:
           type: string
           enum: [out_of_date, in_process, complete, updating]
           example: done
+        user_uid:
+          type: string
+          example: dhf8r
         primary_investigator_id:
           type: string
           example: dhf8r

crc/api/file.py

@@ -8,7 +8,7 @@ from flask import send_file
 from crc import session
 from crc.api.common import ApiErrorSchema, ApiError
 from crc.models.file import FileModelSchema, FileModel, FileDataModel, FileType
-from crc.services.FileService import FileService
+from crc.services.file_service import FileService
 
 
 def get_files(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):

crc/api/study.py

@@ -1,29 +1,36 @@
-from connexion import NoContent
+from typing import List, Optional, Union, Tuple, Dict
 
-from crc import session
+from connexion import NoContent
+from flask import g
+
+from crc import session, auth
 from crc.api.common import ApiError, ApiErrorSchema
 from crc.api.workflow import __get_workflow_api_model
+from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
 from crc.models.study import StudyModelSchema, StudyModel
-from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
+from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel, WorkflowApi
 from crc.services.workflow_processor import WorkflowProcessor
+from crc.services.protocol_builder import ProtocolBuilderService
 
 
+@auth.login_required
 def all_studies():
-    # todo: Limit returned studies to a user
+    return update_from_protocol_builder()
-    schema = StudyModelSchema(many=True)
-    return schema.dump(session.query(StudyModel).all())
 
 
+@auth.login_required
 def add_study(body):
     study = StudyModelSchema().load(body, session=session)
     session.add(study)
     session.commit()
+
     # FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all.
     for spec in session.query(WorkflowSpecModel).all():
         WorkflowProcessor.create(study.id, spec.id)
     return StudyModelSchema().dump(study)
 
 
+@auth.login_required
 def update_study(study_id, body):
     if study_id is None:
         error = ApiError('unknown_study', 'Please provide a valid Study ID.')
@@ -35,12 +42,14 @@ def update_study(study_id, body):
         error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
         return ApiErrorSchema.dump(error), 404
 
-    study = StudyModelSchema().load(body, session=session, instance=study)
+    schema = StudyModelSchema()
+    study = schema.load(body, session=session, instance=study, partial=True)
     session.add(study)
     session.commit()
-    return StudyModelSchema().dump(study)
+    return schema.dump(study)
 
 
+@auth.login_required
 def get_study(study_id):
     study = session.query(StudyModel).filter_by(id=study_id).first()
     schema = StudyModelSchema()
@@ -48,28 +57,71 @@ def get_study(study_id):
         return NoContent, 404
     return schema.dump(study)
 
-def update_from_protocol_builder():
-    """Call the """
 
-def post_update_study_from_protocol_builder(study_id):
+@auth.login_required
-    """This will update the list of known studies based on data received from
+def update_from_protocol_builder():
+    """Updates the list of known studies for a given user based on data received from
     the protocol builder."""
 
-    # todo: Actually get data from an external service here
+    user = g.user
+    """:type: crc.models.user.UserModel"""
+
+    # Get studies matching this user from Protocol Builder
+    pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies()
+
+    # Get studies from the database
+    db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
+    db_study_ids = list(map(lambda s: s.id, db_studies))
+    pb_study_ids = list(map(lambda s: s['STUDYID'], pb_studies))
+
+    for pb_study in pb_studies:
+
+        # Update studies with latest data from Protocol Builder
+        if pb_study['STUDYID'] in db_study_ids:
+            update_study(pb_study['STUDYID'], map_pb_study_to_study(pb_study))
+
+        # Add studies from Protocol Builder that aren't in the database yet
+        else:
+            new_study = map_pb_study_to_study(pb_study)
+            add_study(new_study)
+
+    # Mark studies as inactive that are no longer in Protocol Builder
+    for study_id in db_study_ids:
+        if study_id not in pb_study_ids:
+            update_study(study_id=study_id, body={'inactive': True})
+
+    # Return updated studies
+    updated_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
+    results = StudyModelSchema(many=True).dump(updated_studies)
+    return results
+
+
+@auth.login_required
+def post_update_study_from_protocol_builder(study_id):
+    """Update a single study based on data received from
+    the protocol builder."""
+
+    pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies()
+    for pb_study in pb_studies:
+        if pb_study['STUDYID'] == study_id:
+            return update_study(study_id, map_pb_study_to_study(pb_study))
+
     return NoContent, 304
 
 
+@auth.login_required
 def get_study_workflows(study_id):
     workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all()
     api_models = []
     for workflow_model in workflow_models:
         processor = WorkflowProcessor(workflow_model.workflow_spec_id,
                                       workflow_model.bpmn_workflow_json)
-        api_models.append( __get_workflow_api_model(processor))
+        api_models.append(__get_workflow_api_model(processor))
     schema = WorkflowApiSchema(many=True)
     return schema.dump(api_models)
 
 
+@auth.login_required
 def add_workflow_to_study(study_id, body):
     workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
     if workflow_spec_model is None:
@@ -78,3 +130,37 @@ def add_workflow_to_study(study_id, body):
     processor = WorkflowProcessor.create(study_id, workflow_spec_model.id)
     return WorkflowApiSchema().dump(__get_workflow_api_model(processor))
 
+
+@auth.login_required
+def get_user_pb_studies() -> List[ProtocolBuilderStudy]:
+    """Get studies from Protocol Builder matching the given user"""
+
+    user = g.user
+    """:type: crc.models.user.UserModel"""
+
+    return ProtocolBuilderService.get_studies(user.uid)
+
+
+def map_pb_study_to_study(pb_study):
+    """Translates the given dict of ProtocolBuilderStudy properties to dict of StudyModel attributes"""
+    prop_map = {
+        'STUDYID': 'id',
+        'HSRNUMBER': 'hsr_number',
+        'TITLE': 'title',
+        'NETBADGEID': 'user_uid',
+        'DATE_MODIFIED': 'last_updated',
+    }
+    study_info = {}
+
+    # Translate Protocol Builder property names to Study attributes
+    for k, v in pb_study.items():
+        if k in prop_map:
+            study_info[prop_map[k]] = v
+
+    if pb_study['Q_COMPLETE']:
+        study_info['protocol_builder_status'] = ProtocolBuilderStatus.complete._value_
+    else:
+        study_info['protocol_builder_status'] = ProtocolBuilderStatus.in_process._value_
+
+    return study_info
+

crc/models/protocol_builder.py

@@ -0,0 +1,247 @@
+import enum
+
+from marshmallow import INCLUDE
+
+from crc import ma
+
+
+class ProtocolBuilderInvestigatorType(enum.Enum):
+    PI = "Primary Investigator"
+    SI = "Sub Investigator"
+    DC = "Department Contact"
+    SC_I = "Study Coordinator 1"
+    SC_II = "Study Coordinator 2"
+    AS_C = "Additional Study Coordinators"
+    DEPT_CH = "Department Chair"
+    IRBC = "IRB Coordinator"
+    SCI = "Scientific Contact"
+
+
+class ProtocolBuilderStatus(enum.Enum):
+    out_of_date = "out_of_date"
+    in_process = "in_process"
+    complete = "complete"
+    updating = "updating"
+
+
+class ProtocolBuilderStudy(object):
+    def __init__(
+            self, STUDYID: int, HSRNUMBER: str, TITLE: str, NETBADGEID: str,
+            Q_COMPLETE: bool, DATE_MODIFIED: str
+    ):
+        self.STUDYID = STUDYID
+        self.HSRNUMBER = HSRNUMBER
+        self.TITLE = TITLE
+        self.NETBADGEID = NETBADGEID
+        self.Q_COMPLETE = Q_COMPLETE
+        self.DATE_MODIFIED = DATE_MODIFIED
+
+
+class ProtocolBuilderStudySchema(ma.Schema):
+    class Meta:
+        model = ProtocolBuilderStudy
+        unknown = INCLUDE
+
+
+class ProtocolBuilderInvestigator(object):
+    def __init__(self, STUDYID: int, NETBADGEID: str, INVESTIGATORTYPE: str, INVESTIGATORTYPEFULL: str):
+        self.STUDYID = STUDYID
+        self.NETBADGEID = NETBADGEID
+        self.INVESTIGATORTYPE = INVESTIGATORTYPE
+        self.INVESTIGATORTYPEFULL = INVESTIGATORTYPEFULL
+
+
+class ProtocolBuilderInvestigatorSchema(ma.Schema):
+    class Meta:
+        model = ProtocolBuilderInvestigator
+        unknown = INCLUDE
+
+
+class ProtocolBuilderRequiredDocument(object):
+    DOC_TYPES = {
+        1: "Investigators Brochure",
+        6: "Cancer Center's PRC Approval Form",
+        8: "SOM CTO IND/IDE Review Letter",
+        9: "HIRE Approval",
+        10: "Cancer Center's PRC Approval Waiver",
+        12: "Certificate of Confidentiality Application",
+        14: "Institutional Biosafety Committee Approval",
+        18: "SOM CTO Approval Letter - UVA PI Multisite Trial",
+        20: "IRB Approval or Letter of Approval from Administration: Study Conducted at non- UVA Facilities ",
+        21: "New Medical Device Form",
+        22: "SOM CTO Review regarding need for IDE",
+        23: "SOM CTO Review regarding need for IND",
+        24: "InfoSec Approval",
+        25: "Scientific Pre-review Documentation",
+        26: "IBC Number",
+        32: "IDS - Investigational Drug Service Approval",
+        36: "RDRC Approval ",
+        40: "SBS/IRB Approval-FERPA",
+        41: "HIRE Standard Radiation Language",
+        42: "COI Management Plan ",
+        43: "SOM CTO Approval Letter-Non UVA, Non Industry PI MultiSite Study",
+        44: "GRIME Approval",
+        45: "GMEC Approval",
+        46: "IRB Reliance Agreement Request Form- IRB-HSR is IRB of Record",
+        47: "Non UVA IRB Approval - Initial and Last Continuation",
+        48: "MR Physicist Approval- Use of Gadolinium",
+        49: "SOM CTO Approval- Non- UVA Academia PI of IDE",
+        51: "IDS Waiver",
+        52: "Package Inserts",
+        53: "IRB Reliance Agreement Request Form- IRB-HSR Not IRB of Record",
+        54: "ESCRO Approval",
+        57: "Laser Safety Officer Approval",
+    }
+
+    def __init__(self, AUXDOCID: str, AUXDOC: str):
+        self.AUXDOCID = AUXDOCID
+        self.AUXDOC = AUXDOC
+
+
+class ProtocolBuilderRequiredDocumentSchema(ma.Schema):
+    class Meta:
+        model = ProtocolBuilderRequiredDocument
+        unknown = INCLUDE
+
+
+class ProtocolBuilderStudyDetails(object):
+
+    def __init__(
+            self,
+            STUDYID: int,
+            IS_IND: int,
+            IND_1: str,
+            IND_2: str,
+            IND_3: str,
+            IS_UVA_IND: int,
+            IS_IDE: int,
+            IS_UVA_IDE: int,
+            IDE: str,
+            IS_CHART_REVIEW: int,
+            IS_RADIATION: int,
+            GCRC_NUMBER: str,
+            IS_GCRC: int,
+            IS_PRC_DSMP: int,
+            IS_PRC: int,
+            PRC_NUMBER: str,
+            IS_IBC: int,
+            IBC_NUMBER: str,
+            SPONSORS_PROTOCOL_REVISION_DATE: int,
+            IS_SPONSOR_MONITORING: int,
+            IS_AUX: int,
+            IS_SPONSOR: int,
+            IS_GRANT: int,
+            IS_COMMITTEE_CONFLICT: int,
+            DSMB: int,
+            DSMB_FREQUENCY: int,
+            IS_DB: int,
+            IS_UVA_DB: int,
+            IS_CENTRAL_REG_DB: int,
+            IS_CONSENT_WAIVER: int,
+            IS_HGT: int,
+            IS_GENE_TRANSFER: int,
+            IS_TISSUE_BANKING: int,
+            IS_SURROGATE_CONSENT: int,
+            IS_ADULT_PARTICIPANT: int,
+            IS_MINOR_PARTICIPANT: int,
+            IS_MINOR: int,
+            IS_BIOMEDICAL: int,
+            IS_QUALITATIVE: int,
+            IS_PI_SCHOOL: int,
+            IS_PRISONERS_POP: int,
+            IS_PREGNANT_POP: int,
+            IS_FETUS_POP: int,
+            IS_MENTAL_IMPAIRMENT_POP: int,
+            IS_ELDERLY_POP: int,
+            IS_OTHER_VULNERABLE_POP: int,
+            OTHER_VULNERABLE_DESC: str,
+            IS_MULTI_SITE: int,
+            IS_UVA_LOCATION: int,
+            NON_UVA_LOCATION: str,
+            MULTI_SITE_LOCATIONS: str,
+            IS_OUTSIDE_CONTRACT: int,
+            IS_UVA_PI_MULTI: int,
+            IS_NOT_PRC_WAIVER: int,
+            IS_CANCER_PATIENT: int,
+            UPLOAD_COMPLETE: int,
+            IS_FUNDING_SOURCE: int,
+            IS_PI_INITIATED: int,
+            IS_ENGAGED_RESEARCH: int,
+            IS_APPROVED_DEVICE: int,
+            IS_FINANCIAL_CONFLICT: int,
+            IS_NOT_CONSENT_WAIVER: int,
+            IS_FOR_CANCER_CENTER: int,
+            IS_REVIEW_BY_CENTRAL_IRB: int,
+            IRBREVIEWERADMIN: str
+    ):
+        self.STUDYID = STUDYID
+        self.IS_IND = IS_IND
+        self.IND_1 = IND_1
+        self.IND_2 = IND_2
+        self.IND_3 = IND_3
+        self.IS_UVA_IND = IS_UVA_IND
+        self.IS_IDE = IS_IDE
+        self.IS_UVA_IDE = IS_UVA_IDE
+        self.IDE = IDE
+        self.IS_CHART_REVIEW = IS_CHART_REVIEW
+        self.IS_RADIATION = IS_RADIATION
+        self.GCRC_NUMBER = GCRC_NUMBER
+        self.IS_GCRC = IS_GCRC
+        self.IS_PRC_DSMP = IS_PRC_DSMP
+        self.IS_PRC = IS_PRC
+        self.PRC_NUMBER = PRC_NUMBER
+        self.IS_IBC = IS_IBC
+        self.IBC_NUMBER = IBC_NUMBER
+        self.SPONSORS_PROTOCOL_REVISION_DATE = SPONSORS_PROTOCOL_REVISION_DATE
+        self.IS_SPONSOR_MONITORING = IS_SPONSOR_MONITORING
+        self.IS_AUX = IS_AUX
+        self.IS_SPONSOR = IS_SPONSOR
+        self.IS_GRANT = IS_GRANT
+        self.IS_COMMITTEE_CONFLICT = IS_COMMITTEE_CONFLICT
+        self.DSMB = DSMB
+        self.DSMB_FREQUENCY = DSMB_FREQUENCY
+        self.IS_DB = IS_DB
+        self.IS_UVA_DB = IS_UVA_DB
+        self.IS_CENTRAL_REG_DB = IS_CENTRAL_REG_DB
+        self.IS_CONSENT_WAIVER = IS_CONSENT_WAIVER
+        self.IS_HGT = IS_HGT
+        self.IS_GENE_TRANSFER = IS_GENE_TRANSFER
+        self.IS_TISSUE_BANKING = IS_TISSUE_BANKING
+        self.IS_SURROGATE_CONSENT = IS_SURROGATE_CONSENT
+        self.IS_ADULT_PARTICIPANT = IS_ADULT_PARTICIPANT
+        self.IS_MINOR_PARTICIPANT = IS_MINOR_PARTICIPANT
+        self.IS_MINOR = IS_MINOR
+        self.IS_BIOMEDICAL = IS_BIOMEDICAL
+        self.IS_QUALITATIVE = IS_QUALITATIVE
+        self.IS_PI_SCHOOL = IS_PI_SCHOOL
+        self.IS_PRISONERS_POP = IS_PRISONERS_POP
+        self.IS_PREGNANT_POP = IS_PREGNANT_POP
+        self.IS_FETUS_POP = IS_FETUS_POP
+        self.IS_MENTAL_IMPAIRMENT_POP = IS_MENTAL_IMPAIRMENT_POP
+        self.IS_ELDERLY_POP = IS_ELDERLY_POP
+        self.IS_OTHER_VULNERABLE_POP = IS_OTHER_VULNERABLE_POP
+        self.OTHER_VULNERABLE_DESC = OTHER_VULNERABLE_DESC
+        self.IS_MULTI_SITE = IS_MULTI_SITE
+        self.IS_UVA_LOCATION = IS_UVA_LOCATION
+        self.NON_UVA_LOCATION = NON_UVA_LOCATION
+        self.MULTI_SITE_LOCATIONS = MULTI_SITE_LOCATIONS
+        self.IS_OUTSIDE_CONTRACT = IS_OUTSIDE_CONTRACT
+        self.IS_UVA_PI_MULTI = IS_UVA_PI_MULTI
+        self.IS_NOT_PRC_WAIVER = IS_NOT_PRC_WAIVER
+        self.IS_CANCER_PATIENT = IS_CANCER_PATIENT
+        self.UPLOAD_COMPLETE = UPLOAD_COMPLETE
+        self.IS_FUNDING_SOURCE = IS_FUNDING_SOURCE
+        self.IS_PI_INITIATED = IS_PI_INITIATED
+        self.IS_ENGAGED_RESEARCH = IS_ENGAGED_RESEARCH
+        self.IS_APPROVED_DEVICE = IS_APPROVED_DEVICE
+        self.IS_FINANCIAL_CONFLICT = IS_FINANCIAL_CONFLICT
+        self.IS_NOT_CONSENT_WAIVER = IS_NOT_CONSENT_WAIVER
+        self.IS_FOR_CANCER_CENTER = IS_FOR_CANCER_CENTER
+        self.IS_REVIEW_BY_CENTRAL_IRB = IS_REVIEW_BY_CENTRAL_IRB
+        self.IRBREVIEWERADMIN = IRBREVIEWERADMIN
+
+
+class ProtocolBuilderStudyDetailsSchema(ma.Schema):
+    class Meta:
+        model = ProtocolBuilderStudyDetails
+        unknown = INCLUDE

crc/models/study.py

@@ -1,17 +1,9 @@
-import enum
-
 from marshmallow_enum import EnumField
 from marshmallow_sqlalchemy import ModelSchema
 from sqlalchemy import func
 
 from crc import db
-
+from crc.models.protocol_builder import ProtocolBuilderStatus
-
-class ProtocolBuilderStatus(enum.Enum):
-    out_of_date = "out_of_date"
-    in_process = "in_process"
-    complete = "complete"
-    updating = "updating"
 
 
 class StudyModel(db.Model):
@@ -20,13 +12,21 @@ class StudyModel(db.Model):
     title = db.Column(db.String)
     last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
     protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
-    primary_investigator_id = db.Column(db.String)
+    primary_investigator_id = db.Column(db.String, nullable=True)
-    sponsor = db.Column(db.String)
+    sponsor = db.Column(db.String, nullable=True)
-    ind_number = db.Column(db.String)
+    hsr_number = db.Column(db.String, nullable=True)
+    ind_number = db.Column(db.String, nullable=True)
+    user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=False)
+    investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
+    inactive = db.Column(db.Boolean, default=False)
+    requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
 
 
 class StudyModelSchema(ModelSchema):
     class Meta:
         model = StudyModel
+        include_fk = True  # Includes foreign keys
 
     protocol_builder_status = EnumField(ProtocolBuilderStatus)
+
+

crc/scripts/CompleteTemplate.py

@@ -9,7 +9,7 @@ from crc.models.workflow import WorkflowSpecModel
 from docxtpl import DocxTemplate
 import jinja2
 
-from crc.services.FileService import FileService
+from crc.services.file_service import FileService
 from crc.services.workflow_processor import WorkflowProcessor
 
 
@@ -19,7 +19,6 @@ class CompleteTemplate(object):
     as much feedback as possible.  Some of this might move up to a higher level object or be
     passed into all tasks as we complete more work."""
 
-
     def do_task(self, task, *args, **kwargs):
         """Entry point, mostly worried about wiring it all up."""
         if len(args) != 1:
@@ -38,7 +37,6 @@ class CompleteTemplate(object):
             .filter(FileModel.name == file_name) \
             .filter(FileModel.workflow_spec_id == workflow_spec_model.id).first()
 
-
         if file_data_model is None:
             raise ApiError(code="file_missing",
                            message="Can not find a file called '%s' "

crc/services/file_service.py

@@ -11,7 +11,6 @@ class FileService(object):
 
     DOCX_MIME = "application/vnd.openxmlformats-officedocument.wordprocessingml.document"
 
-
     @staticmethod
     def add_workflow_spec_file(workflow_spec_id, name, content_type, binary_data):
         """Create a new file and associate it with a workflow spec."""

crc/services/protocol_builder.py

@@ -1,41 +1,52 @@
+import json
+from typing import List, Optional
+
 import requests
 
 from crc import app
-
+from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
-STUDY_URL = app.config['PB_USER_STUDIES_URL']
+    ProtocolBuilderRequiredDocument, ProtocolBuilderStudyDetails, ProtocolBuilderInvestigatorSchema, \
-INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
+    ProtocolBuilderRequiredDocumentSchema, ProtocolBuilderStudyDetailsSchema
-REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
-STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
 
 
+class ProtocolBuilderService(object):
+    STUDY_URL = app.config['PB_USER_STUDIES_URL']
+    INVESTIGATOR_URL = app.config['PB_INVESTIGATORS_URL']
+    REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
+    STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
 
-def get_studies(user_id):
+    @staticmethod
-    response = requests.get(STUDY_URL % user_id)
+    def get_studies(user_id) -> Optional[List[ProtocolBuilderStudy]]:
-    if response.ok:
+        response = requests.get(ProtocolBuilderService.STUDY_URL % user_id)
-        return response
+        if response.ok and response.text:
-    else:
+            pb_studies = ProtocolBuilderStudySchema(many=True).loads(response.text)
-        return None
+            return pb_studies
+        else:
+            return None
 
+    @staticmethod
+    def get_investigators(study_id) -> Optional[List[ProtocolBuilderInvestigator]]:
+        response = requests.get(ProtocolBuilderService.INVESTIGATOR_URL % study_id)
+        if response.ok and response.text:
+            pb_studies = ProtocolBuilderInvestigatorSchema(many=True).loads(response.text)
+            return pb_studies
+        else:
+            return None
 
-def get_investigators(study_id):
+    @staticmethod
-    response = requests.get(INVESTIGATOR_URL % study_id)
+    def get_required_docs(study_id) -> Optional[List[ProtocolBuilderRequiredDocument]]:
-    if response.ok:
+        response = requests.get(ProtocolBuilderService.REQUIRED_DOCS_URL % study_id)
-        return response
+        if response.ok and response.text:
-    else:
+            pb_studies = ProtocolBuilderRequiredDocumentSchema(many=True).loads(response.text)
-        return None
+            return pb_studies
+        else:
+            return None
 
-
+    @staticmethod
-def get_required_docs(study_id):
+    def get_study_details(study_id) -> Optional[ProtocolBuilderStudyDetails]:
-    response = requests.get(REQUIRED_DOCS_URL % study_id)
+        response = requests.get(ProtocolBuilderService.STUDY_DETAILS_URL % study_id)
-    if response.ok:
+        if response.ok and response.text:
-        return response
+            pb_study_details = ProtocolBuilderStudyDetailsSchema().loads(response.text)
-    else:
+            return pb_study_details
-        return None
+        else:
-
+            return None
-
-def get_study_details(study_id):
-    response = requests.get(STUDY_DETAILS_URL % study_id)
-    if response.ok:
-        return response
-    else:
-        return None

crc/services/workflow_processor.py

@@ -54,7 +54,6 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
                            'The expression you provided does not exist:' + expression)
 
 
-
 class MyCustomParser(BpmnDmnParser):
     """
     A BPMN and DMN parser that can also parse Camunda forms.
@@ -62,6 +61,7 @@ class MyCustomParser(BpmnDmnParser):
     OVERRIDE_PARSER_CLASSES = BpmnDmnParser.OVERRIDE_PARSER_CLASSES
     OVERRIDE_PARSER_CLASSES.update(CamundaParser.OVERRIDE_PARSER_CLASSES)
 
+
 class WorkflowProcessor(object):
     _script_engine = CustomBpmnScriptEngine()
     _serializer = BpmnSerializer()
@@ -171,9 +171,6 @@ class WorkflowProcessor(object):
             next_task = task
         return next_task
 
-
-
-
     def complete_task(self, task):
         self.bpmn_workflow.complete_task_from_id(task.id)
 

docker_push.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
-docker push sartography/cr-connect-workflow
+docker push sartography/cr-connect-workflow || true

example_data.py

@@ -1,16 +1,31 @@
 import datetime
 import glob
 import os
+import xml.etree.ElementTree as ElementTree
 
 from crc import app, db, session
 from crc.models.file import FileType, FileModel, FileDataModel
 from crc.models.study import StudyModel
+from crc.models.user import UserModel
 from crc.models.workflow import WorkflowSpecModel
-import xml.etree.ElementTree as ElementTree
 from crc.services.workflow_processor import WorkflowProcessor
 
+
 class ExampleDataLoader:
     def make_data(self):
+        users = [
+            UserModel(
+                uid='dhf8r',
+                email_address='dhf8r@virginia.EDU',
+                display_name='Daniel Harold Funk',
+                affiliation='staff@virginia.edu;member@virginia.edu',
+                eppn='dhf8r@virginia.edu',
+                first_name='Daniel',
+                last_name='Funk',
+                title='SOFTWARE ENGINEER V'
+            )
+        ]
+
         studies = [
             StudyModel(
                 id=1,
@@ -19,7 +34,8 @@ class ExampleDataLoader:
                 protocol_builder_status='in_process',
                 primary_investigator_id='dhf8r',
                 sponsor='Sartography Pharmaceuticals',
-                ind_number='1234'
+                ind_number='1234',
+                user_uid='dhf8r'
             ),
             StudyModel(
                 id=2,
@@ -28,7 +44,8 @@ class ExampleDataLoader:
                 protocol_builder_status='in_process',
                 primary_investigator_id='dhf8r',
                 sponsor='Makerspace & Co.',
-                ind_number='5678'
+                ind_number='5678',
+                user_uid='dhf8r'
             ),
         ]
 
@@ -69,11 +86,11 @@ class ExampleDataLoader:
                              description='How to take different paths based on input.')
         workflow_specifications += \
             self.create_spec(id="docx",
-                            name="docx",
+                             name="docx",
-                            display_name="Form with document generation",
+                             display_name="Form with document generation",
-                            description='the name says it all')
+                             description='the name says it all')
 
-        all_data = studies + workflow_specifications
+        all_data = users + studies + workflow_specifications
         return all_data
 
     def create_spec(self, id, name, display_name="", description="", filepath=None):
@@ -112,7 +129,7 @@ class ExampleDataLoader:
             try:
                 file = open(file_path, "rb")
                 data = file.read()
-                if(is_primary):
+                if (is_primary):
                     bpmn: ElementTree.Element = ElementTree.fromstring(data)
                     spec.primary_process_id = WorkflowProcessor.get_process_id(bpmn)
                     print("Locating Process Id for " + filename + "  " + spec.primary_process_id)
@@ -121,7 +138,6 @@ class ExampleDataLoader:
                 file.close()
         return models
 
-
     @staticmethod
     def clean_db():
         session.flush()  # Clear out any transactions before deleting it all to avoid spurious errors.

migrations/versions/0a6e0b829398_.py

@@ -1,36 +0,0 @@
-"""empty message
-
-Revision ID: 0a6e0b829398
-Revises: ad5483cb7f3b
-Create Date: 2020-02-20 15:42:16.473470
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '0a6e0b829398'
-down_revision = 'ad5483cb7f3b'
-branch_labels = None
-depends_on = None
-
-
-def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column('user', sa.Column('affiliation', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('eppn', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('first_name', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('last_name', sa.String(), nullable=True))
-    op.add_column('user', sa.Column('title', sa.String(), nullable=True))
-    # ### end Alembic commands ###
-
-
-def downgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column('user', 'title')
-    op.drop_column('user', 'last_name')
-    op.drop_column('user', 'first_name')
-    op.drop_column('user', 'eppn')
-    op.drop_column('user', 'affiliation')
-    # ### end Alembic commands ###

migrations/versions/ad5483cb7f3b_.py

@@ -1,35 +0,0 @@
-"""empty message
-
-Revision ID: ad5483cb7f3b
-Revises: 02fcf09d9085
-Create Date: 2020-02-19 11:59:09.948767
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = 'ad5483cb7f3b'
-down_revision = '02fcf09d9085'
-branch_labels = None
-depends_on = None
-
-
-def upgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('user',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('uid', sa.String(), nullable=True),
-    sa.Column('email_address', sa.String(), nullable=True),
-    sa.Column('display_name', sa.String(), nullable=True),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('uid')
-    )
-    # ### end Alembic commands ###
-
-
-def downgrade():
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_table('user')
-    # ### end Alembic commands ###

migrations/versions/cb3a03c10a0e_.py

@@ -1,8 +1,8 @@
 """empty message
 
-Revision ID: 02fcf09d9085
+Revision ID: cb3a03c10a0e
 Revises: 
-Create Date: 2020-02-05 17:18:35.324675
+Create Date: 2020-02-28 11:12:56.150837
 
 """
 from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.
-revision = '02fcf09d9085'
+revision = 'cb3a03c10a0e'
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -18,15 +18,18 @@ depends_on = None
 
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('study',
+    op.create_table('user',
     sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('uid', sa.String(), nullable=True),
+    sa.Column('email_address', sa.String(), nullable=True),
+    sa.Column('display_name', sa.String(), nullable=True),
+    sa.Column('affiliation', sa.String(), nullable=True),
+    sa.Column('eppn', sa.String(), nullable=True),
+    sa.Column('first_name', sa.String(), nullable=True),
+    sa.Column('last_name', sa.String(), nullable=True),
     sa.Column('title', sa.String(), nullable=True),
-    sa.Column('last_updated', sa.DateTime(timezone=True), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
-    sa.Column('protocol_builder_status', sa.Enum('out_of_date', 'in_process', 'complete', 'updating', name='protocolbuilderstatus'), nullable=True),
+    sa.UniqueConstraint('uid')
-    sa.Column('primary_investigator_id', sa.String(), nullable=True),
-    sa.Column('sponsor', sa.String(), nullable=True),
-    sa.Column('ind_number', sa.String(), nullable=True),
-    sa.PrimaryKeyConstraint('id')
     )
     op.create_table('workflow_spec',
     sa.Column('id', sa.String(), nullable=False),
@@ -36,6 +39,22 @@ def upgrade():
     sa.Column('primary_process_id', sa.String(), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
+    op.create_table('study',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(), nullable=True),
+    sa.Column('last_updated', sa.DateTime(timezone=True), nullable=True),
+    sa.Column('protocol_builder_status', sa.Enum('out_of_date', 'in_process', 'complete', 'updating', name='protocolbuilderstatus'), nullable=True),
+    sa.Column('primary_investigator_id', sa.String(), nullable=True),
+    sa.Column('sponsor', sa.String(), nullable=True),
+    sa.Column('hsr_number', sa.String(), nullable=True),
+    sa.Column('ind_number', sa.String(), nullable=True),
+    sa.Column('user_uid', sa.String(), nullable=False),
+    sa.Column('investigator_uids', sa.ARRAY(sa.String()), nullable=True),
+    sa.Column('inactive', sa.Boolean(), nullable=True),
+    sa.Column('requirements', sa.ARRAY(sa.Integer()), nullable=True),
+    sa.ForeignKeyConstraint(['user_uid'], ['user.uid'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
     op.create_table('workflow',
     sa.Column('id', sa.Integer(), nullable=False),
     sa.Column('bpmn_workflow_json', sa.JSON(), nullable=True),
@@ -79,6 +98,7 @@ def downgrade():
     op.drop_table('file_data')
     op.drop_table('file')
     op.drop_table('workflow')
-    op.drop_table('workflow_spec')
     op.drop_table('study')
+    op.drop_table('workflow_spec')
+    op.drop_table('user')
     # ### end Alembic commands ###

tests/base_test.py

@@ -3,11 +3,13 @@
 import json
 import os
 import unittest
+import urllib.parse
+
+os.environ["TESTING"] = "true"
 
 from crc.models.file import FileModel, FileDataModel
 from crc.models.workflow import WorkflowSpecModel
-
+from crc.models.user import UserModel
-os.environ["TESTING"] = "true"
 
 from crc import app, db, session
 from example_data import ExampleDataLoader
@@ -18,14 +20,13 @@ from example_data import ExampleDataLoader
 # logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
 
 
-
-
-
-# Great class to inherit from, as it sets up and tears down
-# classes efficiently when we have a database in place.
 class BaseTest(unittest.TestCase):
+    """ Great class to inherit from, as it sets up and tears down classes
+        efficiently when we have a database in place.
+    """
 
     auths = {}
+    test_uid = "dhf8r"
 
     @classmethod
     def setUpClass(cls):
@@ -48,6 +49,25 @@ class BaseTest(unittest.TestCase):
         self.ctx.pop()
         self.auths = {}
 
+    def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
+        if user is None:
+            uid = self.test_uid
+            user_info = {'uid': self.test_uid, 'first_name': 'Daniel', 'last_name': 'Funk',
+                         'email_address': 'dhf8r@virginia.edu'}
+        else:
+            uid = user.uid
+            user_info = {'uid': user.uid, 'first_name': user.first_name, 'last_name': user.last_name,
+                         'email_address': user.email_address}
+
+        query_string = self.user_info_to_query_string(user_info, redirect_url)
+        rv = self.app.get("/v1.0/sso_backdoor%s" % query_string, follow_redirects=False)
+        self.assertTrue(rv.status_code == 302)
+        self.assertTrue(str.startswith(rv.location, redirect_url))
+
+        user_model = session.query(UserModel).filter_by(uid=uid).first()
+        self.assertIsNotNone(user_model.display_name)
+        return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
+
     def load_example_data(self):
         from example_data import ExampleDataLoader
         ExampleDataLoader.clean_db()
@@ -66,7 +86,8 @@ class BaseTest(unittest.TestCase):
                 self.assertIsNotNone(file_data)
                 self.assertGreater(len(file_data), 0)
 
-    def load_test_spec(self, dir_name):
+    @staticmethod
+    def load_test_spec(dir_name):
         """Loads a spec into the database based on a directory in /tests/data"""
         if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
             return
@@ -81,7 +102,8 @@ class BaseTest(unittest.TestCase):
         session.flush()
         return spec
 
-    def protocol_builder_response(self, file_name):
+    @staticmethod
+    def protocol_builder_response(file_name):
         filepath = os.path.join(app.root_path, '..', 'tests', 'data', 'pb_responses', file_name)
         with open(filepath, 'r') as myfile:
             data = myfile.read()
@@ -102,3 +124,16 @@ class BaseTest(unittest.TestCase):
                          "Incorrect Valid Response:" + rv.status + ".")
         if code != 0:
             self.assertEqual(code, rv.status_code)
+
+    @staticmethod
+    def user_info_to_query_string(user_info, redirect_url):
+        query_string_list = []
+        items = user_info.items()
+        for key, value in items:
+            query_string_list.append('%s=%s' % (key, urllib.parse.quote(value)))
+
+        query_string_list.append('redirect_url=%s' % redirect_url)
+
+        return '?%s' % '&'.join(query_string_list)
+
+

tests/test_authentication.py

@@ -1,31 +1,9 @@
-import urllib.parse
-
 from crc import db
 from crc.models.user import UserModel
 from tests.base_test import BaseTest
 
 
 class TestAuthentication(BaseTest):
-    test_uid = "dhf8r"
-
-    def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
-        if user is None:
-            uid = self.test_uid
-            user_info = {'uid': self.test_uid, 'first_name': 'Daniel', 'last_name': 'Funk',
-                       'email_address': 'dhf8r@virginia.edu'}
-        else:
-            uid = user.uid
-            user_info = {'uid': user.uid, 'first_name': user.first_name, 'last_name': user.last_name,
-                       'email_address': user.email_address}
-
-        query_string = self.user_info_to_query_string(user_info, redirect_url)
-        rv = self.app.get("/v1.0/sso_backdoor%s" % query_string, follow_redirects=False)
-        self.assertTrue(rv.status_code == 302)
-        self.assertTrue(str.startswith(rv.location, redirect_url))
-
-        user_model = UserModel.query.filter_by(uid=uid).first()
-        self.assertIsNotNone(user_model.display_name)
-        return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
 
     def test_auth_token(self):
         self.load_example_data()
@@ -35,12 +13,13 @@ class TestAuthentication(BaseTest):
         self.assertEqual("dhf8r", user.decode_auth_token(auth_token))
 
     def test_auth_creates_user(self):
+        new_uid = 'czn1z';
         self.load_example_data()
-        user = db.session.query(UserModel).filter(UserModel.uid == self.test_uid).first()
+        user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
         self.assertIsNone(user)
 
-        user_info = {'uid': self.test_uid, 'first_name': 'Daniel', 'last_name': 'Funk',
+        user_info = {'uid': new_uid, 'first_name': 'Cordi', 'last_name': 'Nator',
-                   'email_address': 'dhf8r@virginia.edu'}
+                   'email_address': 'czn1z@virginia.edu'}
         redirect_url = 'http://worlds.best.website/admin'
         query_string = self.user_info_to_query_string(user_info, redirect_url)
         url = '/v1.0/sso_backdoor%s' % query_string
@@ -48,7 +27,7 @@ class TestAuthentication(BaseTest):
         self.assertTrue(rv_1.status_code == 302)
         self.assertTrue(str.startswith(rv_1.location, redirect_url))
 
-        user = db.session.query(UserModel).filter(UserModel.uid == self.test_uid).first()
+        user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
         self.assertIsNotNone(user)
         self.assertIsNotNone(user.display_name)
         self.assertIsNotNone(user.email_address)
@@ -69,15 +48,3 @@ class TestAuthentication(BaseTest):
         user = UserModel(uid="ajl2j", first_name='Aaron', last_name='Louie', email_address='ajl2j@virginia.edu')
         rv = self.app.get('/v1.0/user', headers=self.logged_in_headers(user, redirect_url='http://omg.edu/lolwut'))
         self.assert_success(rv)
-
-    def user_info_to_query_string(self, user_info, redirect_url):
-        query_string_list = []
-        items = user_info.items()
-        for key, value in items:
-            query_string_list.append('%s=%s' % (key, urllib.parse.quote(value)))
-
-        query_string_list.append('redirect_url=%s' % redirect_url)
-
-        return '?%s' % '&'.join(query_string_list)
-
-

tests/test_protocol_builder.py

@@ -1,40 +1,37 @@
 from unittest.mock import patch
 
-from crc import db
+from crc.services.protocol_builder import ProtocolBuilderService
-from crc.models.user import UserModel
-from crc.services import protocol_builder
 from tests.base_test import BaseTest
 
 
 class TestProtocolBuilder(BaseTest):
-
     test_uid = "dhf8r"
     test_study_id = 1
 
     @patch('crc.services.protocol_builder.requests.get')
     def test_get_studies(self, mock_get):
         mock_get.return_value.ok = True
-        mock_get.return_value.json.return_value = self.protocol_builder_response('study_details.json')
+        mock_get.return_value.text = self.protocol_builder_response('user_studies.json')
-        response = protocol_builder.get_studies(self.test_uid)
+        response = ProtocolBuilderService.get_studies(self.test_uid)
         self.assertIsNotNone(response)
 
     @patch('crc.services.protocol_builder.requests.get')
     def test_get_investigators(self, mock_get):
         mock_get.return_value.ok = True
-        mock_get.return_value.json.return_value = self.protocol_builder_response('investigators.json')
+        mock_get.return_value.text = self.protocol_builder_response('investigators.json')
-        response = protocol_builder.get_studies(self.test_study_id)
+        response = ProtocolBuilderService.get_investigators(self.test_study_id)
-        self.assertIsNotNone(response)
-
-    @patch('crc.services.protocol_builder.requests.get')
-    def test_get_details(self, mock_get):
-        mock_get.return_value.ok = True
-        mock_get.return_value.json.return_value = self.protocol_builder_response('study_details.json')
-        response = protocol_builder.get_studies(self.test_study_id)
         self.assertIsNotNone(response)
 
     @patch('crc.services.protocol_builder.requests.get')
     def test_get_required_docs(self, mock_get):
         mock_get.return_value.ok = True
-        mock_get.return_value.json.return_value = self.protocol_builder_response('required_docs.json')
+        mock_get.return_value.text = self.protocol_builder_response('required_docs.json')
-        response = protocol_builder.get_studies(self.test_study_id)
+        response = ProtocolBuilderService.get_required_docs(self.test_study_id)
+        self.assertIsNotNone(response)
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_get_details(self, mock_get):
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('study_details.json')
+        response = ProtocolBuilderService.get_study_details(self.test_study_id)
         self.assertIsNotNone(response)

tests/test_study_api.py

@@ -1,9 +1,9 @@
 import json
-from datetime import datetime, tzinfo, timezone
+from datetime import datetime, timezone
 
 from crc import session
-from crc.models.file import FileModel
+from crc.models.study import StudyModel, StudyModelSchema
-from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
+from crc.models.protocol_builder import ProtocolBuilderStatus
 from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
     WorkflowApiSchema
 from tests.base_test import BaseTest
@@ -20,15 +20,18 @@ class TestStudyApi(BaseTest):
         self.load_example_data()
         study = {
             "id": 12345,
-            "title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents for Interstellar Spacecraft",
+            "title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
+                     "for Interstellar Spacecraft",
             "last_updated": datetime.now(tz=timezone.utc),
             "protocol_builder_status": ProtocolBuilderStatus.in_process,
             "primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
             "sponsor": "Sirius Cybernetics Corporation",
             "ind_number": "567890",
+            "user_uid": "dhf8r",
         }
         rv = self.app.post('/v1.0/study',
                            content_type="application/json",
+                           headers=self.logged_in_headers(),
                            data=json.dumps(StudyModelSchema().dump(study)))
         self.assert_success(rv)
         db_study = session.query(StudyModel).filter_by(id=12345).first()
@@ -39,8 +42,7 @@ class TestStudyApi(BaseTest):
         self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id)
         self.assertEqual(study["sponsor"], db_study.sponsor)
         self.assertEqual(study["ind_number"], db_study.ind_number)
-
+        self.assertEqual(study["user_uid"], db_study.user_uid)
-
 
     def test_update_study(self):
         self.load_example_data()
@@ -48,8 +50,9 @@ class TestStudyApi(BaseTest):
         study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
         study.protocol_builder_status = ProtocolBuilderStatus.complete
         rv = self.app.put('/v1.0/study/%i' % study.id,
-                           content_type="application/json",
+                          content_type="application/json",
-                           data=json.dumps(StudyModelSchema().dump(study)))
+                          headers=self.logged_in_headers(),
+                          data=json.dumps(StudyModelSchema().dump(study)))
         self.assert_success(rv)
         db_study = session.query(StudyModel).filter_by(id=study.id).first()
         self.assertIsNotNone(db_study)
@@ -61,6 +64,7 @@ class TestStudyApi(BaseTest):
         study = session.query(StudyModel).first()
         rv = self.app.get('/v1.0/study/%i' % study.id,
                           follow_redirects=True,
+                          headers=self.logged_in_headers(),
                           content_type="application/json")
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
@@ -79,7 +83,9 @@ class TestStudyApi(BaseTest):
         study = session.query(StudyModel).first()
         self.assertEqual(0, session.query(WorkflowModel).count())
         spec = session.query(WorkflowSpecModel).first()
-        rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
+        rv = self.app.post('/v1.0/study/%i/workflows' % study.id,
+                           content_type="application/json",
+                           headers=self.logged_in_headers(),
                            data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
         self.assert_success(rv)
         self.assertEqual(1, session.query(WorkflowModel).count())
@@ -97,7 +103,9 @@ class TestStudyApi(BaseTest):
         self.load_example_data()
         study = session.query(StudyModel).first()
         spec = session.query(WorkflowSpecModel).first()
-        rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
+        rv = self.app.post('/v1.0/study/%i/workflows' % study.id,
+                           content_type="application/json",
+                           headers=self.logged_in_headers(),
                            data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
         self.assertEqual(1, session.query(WorkflowModel).count())
         json_data = json.loads(rv.get_data(as_text=True))

tests/test_tasks_api.py

@@ -13,8 +13,12 @@ class TestTasksApi(BaseTest):
     def create_workflow(self, workflow_name):
         study = session.query(StudyModel).first()
         spec = session.query(WorkflowSpecModel).filter_by(id=workflow_name).first()
-        self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
+        rv = self.app.post(
-                      data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
+            '/v1.0/study/%i/workflows' % study.id,
+            headers=self.logged_in_headers(),
+            content_type="application/json",
+            data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
+        self.assert_success(rv)
         workflow = session.query(WorkflowModel).filter_by(study_id=study.id, workflow_spec_id=workflow_name).first()
         return workflow
 

tests/test_workflow_spec_api.py

@@ -1,11 +1,8 @@
 import json
-from datetime import datetime, tzinfo, timezone
 
 from crc import session
 from crc.models.file import FileModel
-from crc.models.study import StudyModel, StudyModelSchema, ProtocolBuilderStatus
+from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
-from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
-    WorkflowApiSchema
 from tests.base_test import BaseTest