mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-20 11:48:16 +00:00
New study status update
This commit is contained in:
Carlos Lopez
parent
de49397549
commit
5d23223e51
@ -1062,9 +1062,9 @@ components:
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user_uid:
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type: string
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example: dhf8r
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protocol_builder_status:
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status:
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type: string
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enum: ['incomplete', 'active', 'hold', 'open', 'abandoned']
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enum: ['in progress', 'hold', 'open for enrollment', 'abandoned']
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example: done
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sponsor:
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type: string
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@ -6,7 +6,7 @@ from sqlalchemy.exc import IntegrityError
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from crc import session
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from crc.api.common import ApiError, ApiErrorSchema
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from crc.models.protocol_builder import ProtocolBuilderStatus
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from crc.models.study import StudySchema, StudyModel, Study
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from crc.models.study import Study, StudyModel, StudySchema, StudyStatus
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from crc.services.study_service import StudyService
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@ -21,7 +21,7 @@ def add_study(body):
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title=body['title'],
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primary_investigator_id=body['primary_investigator_id'],
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last_updated=datetime.now(),
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protocol_builder_status=ProtocolBuilderStatus.active)
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status=StudyStatus.in_progress)
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session.add(study_model)
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errors = StudyService._add_all_workflow_specs_to_study(study_model)
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@ -17,6 +17,7 @@ class ProtocolBuilderInvestigatorType(enum.Enum):
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SCI = "Scientific Contact"
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# Deprecated: Marked for removal
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class ProtocolBuilderStatus(enum.Enum):
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# • Active: found in PB and no HSR number and not hold
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# • Hold: store boolean value in CR Connect (add to Study Model)
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@ -1,4 +1,5 @@
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import datetime
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import enum
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import json
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import marshmallow
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@ -14,12 +15,26 @@ from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, Workfl
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WorkflowModel
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class StudyStatus(enum.Enum):
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in_progress = 'in progress'
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hold = 'hold'
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open_for_enrollment = 'open for enrollment'
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abandoned = 'abandoned'
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class IrbStatus(enum.Enum):
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incomplete_in_protocol_builder = 'incomplete in protocol builder'
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completed_in_protocol_builder = 'completed in protocol builder'
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hsr_assigned = 'hsr number assigned'
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class StudyModel(db.Model):
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__tablename__ = 'study'
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id = db.Column(db.Integer, primary_key=True)
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title = db.Column(db.String)
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last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
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protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
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status = db.Column(db.Enum(StudyStatus))
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irb_status = db.Column(db.Enum(IrbStatus))
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primary_investigator_id = db.Column(db.String, nullable=True)
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sponsor = db.Column(db.String, nullable=True)
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hsr_number = db.Column(db.String, nullable=True)
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@ -29,7 +44,6 @@ class StudyModel(db.Model):
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requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
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on_hold = db.Column(db.Boolean, default=False)
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enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
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changes_history = db.Column(db.JSON, nullable=True)
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def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
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self.hsr_number = pbs.HSRNUMBER
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@ -37,11 +51,13 @@ class StudyModel(db.Model):
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self.user_uid = pbs.NETBADGEID
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self.last_updated = pbs.DATE_MODIFIED
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self.protocol_builder_status = ProtocolBuilderStatus.active
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self.irb_status = IrbStatus.incomplete_in_protocol_builder
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self.status = StudyStatus.in_progress
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if pbs.HSRNUMBER:
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self.protocol_builder_status = ProtocolBuilderStatus.open
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self.irb_status = IrbStatus.hsr_assigned
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self.status = StudyStatus.open_for_enrollment
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if self.on_hold:
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self.protocol_builder_status = ProtocolBuilderStatus.hold
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self.status = StudyStatus.hold
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class WorkflowMetadata(object):
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@ -112,15 +128,15 @@ class CategorySchema(ma.Schema):
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class Study(object):
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def __init__(self, title, last_updated, primary_investigator_id, user_uid,
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id=None,
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protocol_builder_status=None,
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id=None, status=None, irb_status=None,
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sponsor="", hsr_number="", ind_number="", categories=[],
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files=[], approvals=[], enrollment_date=None, **argsv):
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self.id = id
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self.user_uid = user_uid
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self.title = title
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self.last_updated = last_updated
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self.protocol_builder_status = protocol_builder_status
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self.status = status
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self.irb_status = irb_status
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self.primary_investigator_id = primary_investigator_id
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self.sponsor = sponsor
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self.hsr_number = hsr_number
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@ -142,25 +158,25 @@ class Study(object):
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"""As the case for update was very reduced, it's mostly and specifically
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updating only the study status and generating a history record
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"""
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pb_status = ProtocolBuilderStatus(self.protocol_builder_status)
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status = StudyStatus(self.status)
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study_model.last_updated = datetime.datetime.now()
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study_model.protocol_builder_status = pb_status
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study_model.status = status
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if pb_status == ProtocolBuilderStatus.open:
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if status == StudyStatus.open_for_enrollment:
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study_model.enrollment_date = self.enrollment_date
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change = {
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'status': ProtocolBuilderStatus(self.protocol_builder_status).value,
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'comment': '' if not hasattr(self, 'comment') else self.comment,
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'date': str(datetime.datetime.now())
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}
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# change = {
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# 'status': ProtocolBuilderStatus(self.protocol_builder_status).value,
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# 'comment': '' if not hasattr(self, 'comment') else self.comment,
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# 'date': str(datetime.datetime.now())
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# }
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if study_model.changes_history:
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changes_history = json.loads(study_model.changes_history)
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changes_history.append(change)
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else:
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changes_history = [change]
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study_model.changes_history = json.dumps(changes_history)
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# if study_model.changes_history:
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# changes_history = json.loads(study_model.changes_history)
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# changes_history.append(change)
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# else:
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# changes_history = [change]
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# study_model.changes_history = json.dumps(changes_history)
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def model_args(self):
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@ -174,7 +190,7 @@ class Study(object):
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class StudyForUpdateSchema(ma.Schema):
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id = fields.Integer(required=False, allow_none=True)
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protocol_builder_status = EnumField(ProtocolBuilderStatus, by_value=True)
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status = EnumField(StudyStatus, by_value=True)
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hsr_number = fields.String(allow_none=True)
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sponsor = fields.String(allow_none=True)
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ind_number = fields.String(allow_none=True)
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@ -196,7 +212,8 @@ class StudySchema(ma.Schema):
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id = fields.Integer(required=False, allow_none=True)
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categories = fields.List(fields.Nested(CategorySchema), dump_only=True)
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warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
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protocol_builder_status = EnumField(ProtocolBuilderStatus, by_value=True)
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protocol_builder_status = EnumField(StudyStatus, by_value=True)
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status = EnumField(StudyStatus, by_value=True)
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hsr_number = fields.String(allow_none=True)
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sponsor = fields.String(allow_none=True)
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ind_number = fields.String(allow_none=True)
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@ -12,7 +12,7 @@ from crc.api.common import ApiError
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from crc.models.file import FileModel, FileModelSchema, File
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from crc.models.ldap import LdapSchema
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from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
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from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
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from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata
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from crc.models.task_event import TaskEventModel, TaskEvent
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
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WorkflowStatus
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@ -64,7 +64,7 @@ class StudyService(object):
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# Calling this line repeatedly is very very slow. It creates the
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# master spec and runs it. Don't execute this for Abandoned studies, as
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# we don't have the information to process them.
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if study.protocol_builder_status != ProtocolBuilderStatus.abandoned:
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if study.status != StudyStatus.abandoned:
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status = StudyService.__get_study_status(study_model)
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study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
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@ -265,7 +265,7 @@ class StudyService(object):
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for study in db_studies:
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pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
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if not pb_study:
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study.protocol_builder_status = ProtocolBuilderStatus.abandoned
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study.status = StudyStatus.abandoned
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db.session.commit()
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36
migrations/versions/1c3f88dbccc3_.py
Normal file
36
migrations/versions/1c3f88dbccc3_.py
Normal file
@ -0,0 +1,36 @@
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"""empty message
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Revision ID: 1c3f88dbccc3
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Revises: 2e7b377cbc7b
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Create Date: 2020-07-30 18:51:01.816284
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"""
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from alembic import op
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import sqlalchemy as sa
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from sqlalchemy.dialects import postgresql
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# revision identifiers, used by Alembic.
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revision = '1c3f88dbccc3'
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down_revision = '2e7b377cbc7b'
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branch_labels = None
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depends_on = None
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def upgrade():
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op.execute("CREATE TYPE irbstatus AS ENUM('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned')")
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op.execute("CREATE TYPE studystatus AS ENUM('in_progress', 'hold', 'open_for_enrollment', 'abandoned')")
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# ### commands auto generated by Alembic - please adjust! ###
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op.add_column('study', sa.Column('irb_status', sa.Enum('incomplete_in_protocol_builder', 'completed_in_protocol_builder', 'hsr_assigned', name='irbstatus'), nullable=True))
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op.add_column('study', sa.Column('status', sa.Enum('in_progress', 'hold', 'open_for_enrollment', 'abandoned', name='studystatus'), nullable=True))
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op.drop_column('study', 'protocol_builder_status')
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.add_column('study', sa.Column('protocol_builder_status', postgresql.ENUM('incomplete', 'active', 'hold', 'open', 'abandoned', name='protocolbuilderstatus'), autoincrement=False, nullable=True))
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op.drop_column('study', 'status')
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op.drop_column('study', 'irb_status')
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# ### end Alembic commands ###
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op.execute('DROP TYPE studystatus')
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op.execute('DROP TYPE irbstatus')
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@ -1,28 +0,0 @@
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"""empty message
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Revision ID: 369d65dcb269
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Revises: c4ddb69e7ef4
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Create Date: 2020-07-27 20:05:29.524553
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"""
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from alembic import op
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import sqlalchemy as sa
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# revision identifiers, used by Alembic.
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revision = '369d65dcb269'
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down_revision = 'c4ddb69e7ef4'
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branch_labels = None
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depends_on = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.add_column('study', sa.Column('changes_history', sa.JSON(), nullable=True))
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# ### end Alembic commands ###
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def downgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.drop_column('study', 'changes_history')
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# ### end Alembic commands ###
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@ -15,9 +15,8 @@ from crc import app, db, session
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from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
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from crc.models.approval import ApprovalModel, ApprovalStatus
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from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
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from crc.models.protocol_builder import ProtocolBuilderStatus
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from crc.models.task_event import TaskEventModel
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from crc.models.study import StudyModel
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from crc.models.study import StudyModel, StudyStatus
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from crc.models.user import UserModel
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from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
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from crc.services.file_service import FileService
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@ -60,7 +59,7 @@ class BaseTest(unittest.TestCase):
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'id':0,
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'title':'The impact of fried pickles on beer consumption in bipedal software developers.',
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'last_updated':datetime.datetime.now(),
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'protocol_builder_status':ProtocolBuilderStatus.active,
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'status':StudyStatus.in_progress,
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'primary_investigator_id':'dhf8r',
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'sponsor':'Sartography Pharmaceuticals',
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'ind_number':'1234',
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@ -70,7 +69,7 @@ class BaseTest(unittest.TestCase):
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'id':1,
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'title':'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
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'last_updated':datetime.datetime.now(),
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'protocol_builder_status':ProtocolBuilderStatus.active,
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'status':StudyStatus.in_progress,
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'primary_investigator_id':'dhf8r',
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'sponsor':'Makerspace & Co.',
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'ind_number':'5678',
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@ -241,7 +240,7 @@ class BaseTest(unittest.TestCase):
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study = session.query(StudyModel).filter_by(user_uid=uid).filter_by(title=title).first()
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if study is None:
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user = self.create_user(uid=uid)
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study = StudyModel(title=title, protocol_builder_status=ProtocolBuilderStatus.active,
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study = StudyModel(title=title, status=StudyStatus.in_progress,
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user_uid=user.uid, primary_investigator_id=primary_investigator_id)
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db.session.add(study)
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db.session.commit()
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@ -11,7 +11,7 @@ from crc.models.protocol_builder import ProtocolBuilderStatus, \
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ProtocolBuilderStudySchema
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from crc.models.approval import ApprovalStatus
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from crc.models.task_event import TaskEventModel
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from crc.models.study import StudyModel, StudySchema
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from crc.models.study import StudyModel, StudySchema, StudyStatus
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from crc.models.workflow import WorkflowSpecModel, WorkflowModel
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from crc.services.file_service import FileService
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from crc.services.workflow_processor import WorkflowProcessor
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@ -30,7 +30,7 @@ class TestStudyApi(BaseTest):
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def add_test_study(self):
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study_schema = StudySchema().dump(self.TEST_STUDY)
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study_schema['protocol_builder_status'] = ProtocolBuilderStatus.active.value
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study_schema['status'] = StudyStatus.in_progress.value
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rv = self.app.post('/v1.0/study',
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content_type="application/json",
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headers=self.logged_in_headers(),
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@ -137,7 +137,7 @@ class TestStudyApi(BaseTest):
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study: StudyModel = session.query(StudyModel).first()
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study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
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study_schema = StudySchema().dump(study)
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study_schema['protocol_builder_status'] = ProtocolBuilderStatus.active.value
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study_schema['status'] = StudyStatus.in_progress.value
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rv = self.app.put('/v1.0/study/%i' % study.id,
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content_type="application/json",
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headers=self.logged_in_headers(),
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@ -145,7 +145,7 @@ class TestStudyApi(BaseTest):
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self.assert_success(rv)
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json_data = json.loads(rv.get_data(as_text=True))
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self.assertEqual(study.title, json_data['title'])
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self.assertEqual(study.protocol_builder_status.value, json_data['protocol_builder_status'])
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self.assertEqual(study.status.value, json_data['status'])
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
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@ -183,15 +183,15 @@ class TestStudyApi(BaseTest):
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num_incomplete = 0
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num_abandoned = 0
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num_active = 0
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num_in_progress = 0
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num_open = 0
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for study in json_data:
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if study['protocol_builder_status'] == 'abandoned': # One study does not exist in user_studies.json
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if study['status'] == 'abandoned': # One study does not exist in user_studies.json
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num_abandoned += 1
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if study['protocol_builder_status'] == 'active': # One study is marked complete without HSR Number
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num_active += 1
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if study['protocol_builder_status'] == 'open': # One study is marked complete and has an HSR Number
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if study['status'] == 'in progress': # One study is marked complete without HSR Number
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num_in_progress += 1
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if study['status'] == 'open for enrollment': # One study is marked complete and has an HSR Number
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num_open += 1
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db_studies_after = session.query(StudyModel).all()
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@ -199,10 +199,10 @@ class TestStudyApi(BaseTest):
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self.assertGreater(num_db_studies_after, num_db_studies_before)
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self.assertEqual(num_abandoned, 1)
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self.assertEqual(num_open, 1)
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self.assertEqual(num_active, 2)
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self.assertEqual(num_in_progress, 2)
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self.assertEqual(num_incomplete, 0)
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self.assertEqual(len(json_data), num_db_studies_after)
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self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)
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self.assertEqual(num_open + num_in_progress + num_incomplete + num_abandoned, num_db_studies_after)
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
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@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
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@ -230,7 +230,7 @@ class TestStudyApi(BaseTest):
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json_data = json.loads(rv.get_data(as_text=True))
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self.assertEqual(study.id, json_data['id'])
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self.assertEqual(study.title, json_data['title'])
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self.assertEqual(study.protocol_builder_status.value, json_data['protocol_builder_status'])
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self.assertEqual(study.status.value, json_data['status'])
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self.assertEqual(study.primary_investigator_id, json_data['primary_investigator_id'])
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self.assertEqual(study.sponsor, json_data['sponsor'])
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self.assertEqual(study.ind_number, json_data['ind_number'])
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|
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@ -6,7 +6,7 @@ from tests.base_test import BaseTest
|
||||
|
||||
from crc import db, app
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.study import StudyModel, StudyStatus
|
||||
from crc.models.user import UserModel
|
||||
from crc.models.workflow import WorkflowModel, WorkflowStatus, \
|
||||
WorkflowSpecCategoryModel
|
||||
@ -40,7 +40,7 @@ class TestStudyService(BaseTest):
|
||||
for study in db.session.query(StudyModel).all():
|
||||
StudyService().delete_study(study.id)
|
||||
|
||||
study = StudyModel(title="My title", protocol_builder_status=ProtocolBuilderStatus.active, user_uid=user.uid)
|
||||
study = StudyModel(title="My title", status=StudyStatus.in_progress, user_uid=user.uid)
|
||||
db.session.add(study)
|
||||
|
||||
self.load_test_spec("random_fact", category_id=cat.id)
|
||||
|
||||
@ -8,7 +8,7 @@ from tests.base_test import BaseTest
|
||||
from crc import db, app
|
||||
from crc.api.common import ApiError
|
||||
from crc.models.protocol_builder import ProtocolBuilderStatus
|
||||
from crc.models.study import StudySchema, StudyModel
|
||||
from crc.models.study import StudySchema, StudyModel, StudyStatus
|
||||
from crc.models.user import UserModel
|
||||
|
||||
|
||||
@ -220,7 +220,7 @@ class TestAuthentication(BaseTest):
|
||||
return {
|
||||
"title": "blah",
|
||||
"last_updated": datetime.now(tz=timezone.utc),
|
||||
"protocol_builder_status": ProtocolBuilderStatus.active,
|
||||
"status": StudyStatus.in_progress,
|
||||
"primary_investigator_id": uid,
|
||||
"user_uid": uid,
|
||||
}
|
||||
|
||||
Loading…
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Reference in New Issue
Block a user