Merge pull request #375 from sartography/study-info-adds-463
Study info adds #463
This commit is contained in:
Dan Funk
GitHub
commit
e672d46dd0
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@ -53,6 +53,8 @@ class StudyModel(db.Model):
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enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
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#events = db.relationship("TaskEventModel")
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events_history = db.relationship("StudyEvent", cascade="all, delete, delete-orphan")
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short_name = db.Column(db.String, nullable=True)
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proposal_name = db.Column(db.String, nullable=True)
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def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
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self.title = pbs.TITLE
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@ -168,7 +170,7 @@ class CategorySchema(ma.Schema):
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class Study(object):
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def __init__(self, title, short_title, last_updated, primary_investigator_id, user_uid,
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id=None, status=None, irb_status=None, comment="",
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id=None, status=None, irb_status=None, short_name=None, proposal_name=None, comment="",
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sponsor="", ind_number="", categories=[],
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files=[], approvals=[], enrollment_date=None, events_history=[],
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last_activity_user="",last_activity_date =None,create_user_display="", **argsv):
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@ -192,6 +194,8 @@ class Study(object):
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self.files = files
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self.enrollment_date = enrollment_date
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self.events_history = events_history
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self.short_name = short_name
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self.proposal_name = proposal_name
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@classmethod
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def from_model(cls, study_model: StudyModel):
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@ -253,13 +257,15 @@ class StudySchema(ma.Schema):
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files = fields.List(fields.Nested(FileSchema), dump_only=True)
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enrollment_date = fields.Date(allow_none=True)
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events_history = fields.List(fields.Nested('StudyEventSchema'), dump_only=True)
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short_name = fields.String(allow_none=True)
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proposal_name = fields.String(allow_none=True)
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class Meta:
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model = Study
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additional = ["id", "title", "short_title", "last_updated", "primary_investigator_id", "user_uid",
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"sponsor", "ind_number", "files", "enrollment_date",
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"create_user_display", "last_activity_date","last_activity_user",
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"events_history"]
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"create_user_display", "last_activity_date", "last_activity_user",
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"events_history", "short_name", "proposal_name"]
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unknown = INCLUDE
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@marshmallow.post_load
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@ -44,6 +44,10 @@ update_study(title=PIComputingID.label, short_title="Really Short Name")
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study.title = kwargs[arg]
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elif arg.lower() == "short_title":
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study.short_title = kwargs[arg]
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elif arg.lower() == "short_name":
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study.short_name = kwargs[arg]
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elif arg.lower() == "proposal_name":
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study.proposal_name = kwargs[arg]
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elif arg.lower() == "pi":
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study.primary_investigator_id = kwargs[arg]
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else:
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@ -0,0 +1,26 @@
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"""new study info data points
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Revision ID: 9afbd55082a0
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Revises: 981156283cb9
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Create Date: 2021-09-17 10:31:05.094062
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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 = '9afbd55082a0'
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down_revision = '981156283cb9'
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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.add_column('study', sa.Column('short_name', sa.String(), nullable=True))
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op.add_column('study', sa.Column('proposal_name', sa.String(), nullable=True))
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def downgrade():
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op.drop_column('study', 'short_name')
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op.drop_column('study', 'proposal_name')
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@ -0,0 +1,85 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_3435c8d" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
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<bpmn:process id="Process_3435c8d" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>Flow_0g8e1jy</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="Flow_0g8e1jy" sourceRef="StartEvent_1" targetRef="Activity_GetData" />
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<bpmn:userTask id="Activity_GetData" name="Get Data" camunda:formKey="GetDataForm">
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<bpmn:extensionElements>
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<camunda:formData>
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<camunda:formField id="short_name" label="Short Name" type="string" />
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<camunda:formField id="proposal_name" label="Proposal Name" type="string" />
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</camunda:formData>
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</bpmn:extensionElements>
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<bpmn:incoming>Flow_0g8e1jy</bpmn:incoming>
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<bpmn:outgoing>Flow_09flr91</bpmn:outgoing>
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</bpmn:userTask>
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<bpmn:sequenceFlow id="Flow_09flr91" sourceRef="Activity_GetData" targetRef="Activity_UpdateStudy" />
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<bpmn:scriptTask id="Activity_UpdateStudy" name="Update Study">
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<bpmn:incoming>Flow_09flr91</bpmn:incoming>
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<bpmn:outgoing>Flow_0xf0u0k</bpmn:outgoing>
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<bpmn:script>update_study(short_name=short_name, proposal_name=proposal_name)</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="Flow_0xf0u0k" sourceRef="Activity_UpdateStudy" targetRef="Activity_GetStudyInfo" />
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<bpmn:scriptTask id="Activity_GetStudyInfo" name="Get Study Info">
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<bpmn:incoming>Flow_0xf0u0k</bpmn:incoming>
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<bpmn:outgoing>Flow_0tzamxo</bpmn:outgoing>
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<bpmn:script>study_info = study_info("info")</bpmn:script>
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</bpmn:scriptTask>
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<bpmn:sequenceFlow id="Flow_0tzamxo" sourceRef="Activity_GetStudyInfo" targetRef="Activity_DisplayInfo" />
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<bpmn:manualTask id="Activity_DisplayInfo" name="Display Study Info">
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<bpmn:documentation># Info
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{{ study_info }}
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</bpmn:documentation>
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<bpmn:incoming>Flow_0tzamxo</bpmn:incoming>
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<bpmn:outgoing>Flow_0x5ex3d</bpmn:outgoing>
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</bpmn:manualTask>
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<bpmn:endEvent id="Event_05xjsir">
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<bpmn:incoming>Flow_0x5ex3d</bpmn:incoming>
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</bpmn:endEvent>
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<bpmn:sequenceFlow id="Flow_0x5ex3d" sourceRef="Activity_DisplayInfo" targetRef="Event_05xjsir" />
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</bpmn:process>
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<bpmndi:BPMNDiagram id="BPMNDiagram_1">
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<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_3435c8d">
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<bpmndi:BPMNEdge id="Flow_0x5ex3d_di" bpmnElement="Flow_0x5ex3d">
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<di:waypoint x="850" y="177" />
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<di:waypoint x="912" y="177" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0tzamxo_di" bpmnElement="Flow_0tzamxo">
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<di:waypoint x="690" y="177" />
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<di:waypoint x="750" y="177" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0xf0u0k_di" bpmnElement="Flow_0xf0u0k">
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<di:waypoint x="530" y="177" />
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<di:waypoint x="590" y="177" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_09flr91_di" bpmnElement="Flow_09flr91">
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<di:waypoint x="370" y="177" />
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<di:waypoint x="430" y="177" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="Flow_0g8e1jy_di" bpmnElement="Flow_0g8e1jy">
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<di:waypoint x="215" y="177" />
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<di:waypoint x="270" y="177" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
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<dc:Bounds x="179" y="159" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_06lg3xc_di" bpmnElement="Activity_GetData">
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<dc:Bounds x="270" y="137" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_0ulzpsr_di" bpmnElement="Activity_UpdateStudy">
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<dc:Bounds x="430" y="137" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_15xfbrf_di" bpmnElement="Activity_GetStudyInfo">
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<dc:Bounds x="590" y="137" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Activity_1yteq9j_di" bpmnElement="Activity_DisplayInfo">
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<dc:Bounds x="750" y="137" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="Event_05xjsir_di" bpmnElement="Event_05xjsir">
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<dc:Bounds x="912" y="159" width="36" height="36" />
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</bpmndi:BPMNShape>
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</bpmndi:BPMNPlane>
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</bpmndi:BPMNDiagram>
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</bpmn:definitions>
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@ -14,9 +14,12 @@ class TestUpdateStudyScript(BaseTest):
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processor = WorkflowProcessor(workflow)
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task = processor.next_task()
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details = Box({
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"label": "My New Title",
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"short": "My New Short Title",
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"value": "dhf8r"})
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"title": "My New Title",
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"short_title": "My New Short Title",
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"pi": "dhf8r",
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"short_name": "My Short Name",
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"proposal_name": "My Proposal Name"
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})
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script = UpdateStudy()
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@ -26,9 +29,14 @@ class TestUpdateStudyScript(BaseTest):
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# evaluated before they are passed to the script -
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# this allows us to do a lot more things like strings, functions, etc.
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# and it makes the arguments less confusing to use.
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script.do_task(task, workflow.study_id, workflow.id, title = details.label,
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short_title = details.short,
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pi = details.value)
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self.assertEqual("My New Title", workflow.study.title)
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self.assertEqual("My New Short Title", workflow.study.short_title)
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self.assertEqual("dhf8r", workflow.study.primary_investigator_id)
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script.do_task(task, workflow.study_id, workflow.id,
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title=details.title,
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short_title=details.short_title,
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pi=details.pi,
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short_name=details.short_name,
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proposal_name=details.proposal_name)
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self.assertEqual(details.title, workflow.study.title)
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self.assertEqual(details.short_title, workflow.study.short_title)
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self.assertEqual(details.pi, workflow.study.primary_investigator_id)
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self.assertEqual(details.short_name, workflow.study.short_name)
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self.assertEqual(details.proposal_name, workflow.study.proposal_name)
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@ -33,6 +33,25 @@ class TestStudyInfoScript(BaseTest):
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self.assertEqual(study_info['primary_investigator_id'], second_task.data['info']['primary_investigator_id'])
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self.assertIn(study_info['title'], second_task.documentation)
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def test_info_script_updated_study_info(self):
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self.load_example_data()
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short_name = "My Short Name"
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proposal_name = "My Proposal Name"
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workflow = self.create_workflow('update_study_info')
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workflow_api = self.get_workflow_api(workflow)
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task = workflow_api.next_task
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workflow_api = self.complete_form(workflow, task, {'short_name': short_name, 'proposal_name': proposal_name})
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task = workflow_api.next_task
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# The workflow calls study_info('info') and puts the result in Element Documentation
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# I create a dictionary of that info with `eval` to make the asserts easier to read
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study_info = eval(task.documentation)
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self.assertIn('short_name', study_info.keys())
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self.assertEqual(short_name, study_info['short_name'])
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self.assertIn('proposal_name', study_info.keys())
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self.assertIn(proposal_name, study_info['proposal_name'])
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@patch('crc.services.protocol_builder.requests.get')
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def test_info_script_investigators(self, mock_get):
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app.config['PB_ENABLED'] = True
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