merge conflicts

2019-12-27 13:53:29 -05:00 · 2019-12-27 13:53:29 -05:00 · 2ac2514e32
parent 12953fc991 2afd3015be
commit 2ac2514e32
6 changed files with 237 additions and 42 deletions
--- a/26
+++ b/26
@ -0,0 +1,26 @@
+FROM python:3.6-stretch
+
+ENV PATH=/root/.local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
+
+# install node and yarn
+RUN apt-get update
+RUN apt-get -y install postgresql-client
+
+# config project dir
+RUN mkdir /crc-workflow
+WORKDIR /crc-workflow
+
+# install python requirements
+RUN pip install pipenv
+ADD Pipfile /crc-workflow/
+ADD Pipfile.lock /crc-workflow/
+RUN pipenv install --dev
+
+# include rejoiner code (gets overriden by local changes)
+COPY . /crc-workflow/
+
+# run webserver by default
+CMD ["pipenv", "run", "python", "/crc-workflow/run.py"]
+
+# expose ports
+EXPOSE 5000
--- a/crc/api.yml
+++ b/crc/api.yml
@ -1,4 +1,4 @@
-openapi: "3.0.0"
+openapi: "3.0.2"
 info:
  version: 1.0.0
  title: Workflow Microservice
@ -525,58 +525,156 @@ components:
      properties:
        id:
          readOnly: true
-          type: integer
-          format: int64
+          type: string
        name:
          type: string
+        title:
+          type: string
        type:
          type: string
-        status:
+        state:
          type: string
        form:
          $ref: "#/components/schemas/Form"
+        documentation:
+          type: string
      example:
-        {
-          id: study_identification,
-          name: "Study Identification",
-          state: "ready",
-          type: "form",
-          form: {
-            key: "oncology_form",
-            field: {
-              id: "is_adult_patient",
-              type: enum,
-              label: "Is this study treating adult oncology patients?",
-              options: ["yes", "no"],
-              value: "yes"
-            }
-          }
-        }
+        id: study_identification
+        name: Study Identification
+        title: IRB Review
+        documentation: "# Heading 1\n\nMarkdown documentation text goes here"
+        type: form
+        state: ready
+        form:
+          "key": "irb_review_form"
+          "fields":
+            - "id": "irb_review_type"
+              "type": "enum"
+              "label": "Select IRB Review Type"
+              "options":
+                - id: "emergency_use"
+                  name: "Emergency Use"
+                - id: "humanitarian_device"
+                  name: "Humanitarian Device"
+                - id: "non_human"
+                  name: "Non-Human"
+                - id: "non_uva_agent"
+                  name: "Non-UVA Agent"
+                - id: "exempt"
+                  name: "Exempt"
+                - id: "non_engaged"
+                  name: "Non-Engaged"
+                - id: "expedited"
+                  name: "Expedited"
+                - id: "full_board"
+                  name: "Full Board"
+              "defaultValue": "Full Board"
+              "validation":
+                - name: "required"
+                  config: "true"
+              "properties":
+                - id: "description"
+                  value: "Description text goes here"
+                - id: "help"
+                  value: "# Heading 1\n\nMarkdown help text goes here"
+                - id: "required_expression"
+                  value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
+                - id: "hide_expression"
+                  value: "model.my_enum_field_value === 'something'"
    Form:
      properties:
+        key:
+          type: string
        fields:
          type: array
          items:
            $ref: "#/components/schemas/Field"
+      example:
+        "key": "irb_review_form"
+        "fields":
+          - "id": "irb_review_type"
+            "type": "enum"
+            "label": "Select IRB Review Type"
+            "options":
+              - id: "emergency_use"
+                name: "Emergency Use"
+              - id: "humanitarian_device"
+                name: "Humanitarian Device"
+              - id: "non_human"
+                name: "Non-Human"
+              - id: "non_uva_agent"
+                name: "Non-UVA Agent"
+              - id: "exempt"
+                name: "Exempt"
+              - id: "non_engaged"
+                name: "Non-Engaged"
+              - id: "expedited"
+                name: "Expedited"
+              - id: "full_board"
+                name: "Full Board"
+            "defaultValue": "Full Board"
+            "validation":
+              - name: "required"
+                config: "true"
+            "properties":
+              - id: "description"
+                value: "Description text goes here"
+              - id: "help"
+                value: "# Heading 1\n\nMarkdown help text goes here"
+              - id: "required_expression"
+                value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
+              - id: "hide_expression"
+                value: "model.my_enum_field_value === 'something'"
    Field:
      properties:
        id:
          type: string
          readOnly: true
-        label:
-          type: string
-          readOnly: true
        type:
          type: enum
-          enum: ['text','number', 'enum']
+          enum: ['string', 'long', 'boolean', 'date', 'enum']
+          readOnly: true
+        label:
+          type: string
          readOnly: true
        options:
          type: array
          items:
-            type: string
+            $ref: "#/components/schemas/EnumFieldOption"
          readOnly: true
+        defaultValue:
+          type: string
+        validation:
+          type: array
+          items:
+            $ref: "#/components/schemas/FieldValidation"
+          readOnly: true
+        "properties":
+          type: array
+          items:
+            $ref: "#/components/schemas/FieldProperty"
+          readOnly: true
+    EnumFieldOption:
+      properties:
+        id:
+          type: string
+        name:
+          type: string
+    FieldValidation:
+      properties:
+        name:
+          type: string
+        config:
+          type: string
+    FieldProperty:
+      properties:
+        id:
+          type: string
        value:
          type: string
+      example:
+        id: "required_expression"
+        value: "model.should_require"
    Error:
      required:
        - code
--- a/crc/models.py
+++ b/crc/models.py
@ -2,7 +2,7 @@ import enum

 from SpiffWorkflow import Task
 from flask_marshmallow.sqla import ModelSchema
-from marshmallow import post_load, fields, Schema
+from marshmallow import post_load, fields
 from marshmallow_enum import EnumField
 from sqlalchemy import func

@ -30,6 +30,7 @@ class StudyModel(db.Model):
 class StudySchema(ModelSchema):
    class Meta:
        model = StudyModel
+
    protocol_builder_status = EnumField(ProtocolBuilderStatus)


@ -95,24 +96,29 @@ class WorkflowModel(db.Model):
 class WorkflowSchema(ModelSchema):
    class Meta:
        model = WorkflowModel
+
    status = EnumField(WorkflowStatus)


 class Task:
-    def __init__(self, id, name, type, state, form):
+    def __init__(self, id, name, title, type, state, form, documentation):
        self.id = id
        self.name = name
+        self.title = title
        self.type = type
        self.state = state
        self.form = form
+        self.documentation = documentation

    @classmethod
    def from_spiff(cls, spiff_task):
        instance = cls(spiff_task.id,
                       spiff_task.task_spec.name,
+                       spiff_task.task_spec.description,
                       spiff_task.get_state_name(),
                       "task",
-                       {})
+                       {},
+                       spiff_task.task_spec.documentation)
        if hasattr(spiff_task.task_spec, "form"):
            instance.type = "form"
            instance.form = spiff_task.task_spec.form
@ -124,25 +130,40 @@ class OptionSchema(ma.Schema):
        fields = ["id", "name"]


+class ValidationSchema(ma.Schema):
+    class Meta:
+        fields = ["name", "config"]
+
+
+class PropertiesSchema(ma.Schema):
+    class Meta:
+        fields = ["id", "value"]
+
+
 class FieldSchema(ma.Schema):
    class Meta:
-        fields = ["id", "type", "label", "defaultValue", "options"]
+        fields = [
+            "id", "type", "label", "defaultValue", "options", "validation", "properties"
+        ]
+
    options = fields.List(fields.Nested(OptionSchema))
+    validation = fields.List(fields.Nested(ValidationSchema))
+    properties = fields.List(fields.Nested(PropertiesSchema))


 class FormSchema(ma.Schema):
    class Meta:
        fields = ["key", "fields"]
+
    fields = fields.List(fields.Nested(FieldSchema))


 class TaskSchema(ma.Schema):
    class Meta:
-        fields = ["id", "name", "type", "state", "form"]
+        fields = ["id", "name", "title", "type", "state", "form", "documentation"]

    form = fields.Nested(FormSchema)
+
    @post_load
    def make_task(self, data, **kwargs):
        return Task(**data)
-
-
--- a/crc/static/bpmn/random_fact/random_fact.bpmn
+++ b/crc/static/bpmn/random_fact/random_fact.bpmn
@ -1,11 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<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_1gjhqt9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
+<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_1gjhqt9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.6.0-dev">
  <bpmn:process id="Process_1ds61df" isExecutable="true">
    <bpmn:startEvent id="StartEvent_1">
      <bpmn:outgoing>SequenceFlow_0ik56h0</bpmn:outgoing>
    </bpmn:startEvent>
    <bpmn:sequenceFlow id="SequenceFlow_0ik56h0" sourceRef="StartEvent_1" targetRef="Task_User_Select_Type" />
-    <bpmn:userTask id="Task_User_Select_Type" name="Set Type" camunda:formKey="Fact">
+    <bpmn:userTask id="Task_User_Select_Type" name="Set Type" camunda:formKey="Get A Random Fun Fact">
+      <bpmn:documentation>Here's some documentation</bpmn:documentation>
      <bpmn:extensionElements>
        <camunda:formData>
          <camunda:formField id="type" label="Type" type="enum" defaultValue="cat">
@ -13,6 +14,42 @@
            <camunda:value id="cat" name="Cat Fact" />
            <camunda:value id="buzzword" name="Business Buzzword" />
          </camunda:formField>
+          <camunda:formField id="is_anonymous" label="Do you want to remain anonymous?" type="boolean">
+            <camunda:properties>
+              <camunda:property id="description" value="Choose &#34;yes&#34; if you don&#39;t want us to use your name" />
+              <camunda:property id="help" value="# Heading 1\n\nOh hey, it&#39;s Markdown text." />
+            </camunda:properties>
+            <camunda:validation>
+              <camunda:constraint name="required" config="true" />
+            </camunda:validation>
+          </camunda:formField>
+          <camunda:formField id="name" label="Your full name" type="string">
+            <camunda:properties>
+              <camunda:property id="description" value="Please enter your first and last name." />
+              <camunda:property id="help" value="# Heading 1\n\nLook, it&#39;s some Markdown!" />
+              <camunda:property id="hide_expression" value="model.is_anonymous" />
+            </camunda:properties>
+            <camunda:validation>
+              <camunda:constraint name="required" config="true" />
+            </camunda:validation>
+          </camunda:formField>
+          <camunda:formField id="should_send_greeting" label="Say hi to user?" type="enum" defaultValue="yes">
+            <camunda:properties>
+              <camunda:property id="label_expression" value="model.name ? &#39;Say hi to &#39; + model.name + &#39;?&#39; : &#39;Say hi?&#39;" />
+              <camunda:property id="hide_expression" value="model.is_anonymous" />
+            </camunda:properties>
+            <camunda:value id="no" name="No!" />
+            <camunda:value id="yes" name="Yes!" />
+            <camunda:value id="maybe" name="Meh." />
+          </camunda:formField>
+          <camunda:formField id="random_num" label="Pick a number, any number." type="enum">
+            <camunda:properties>
+              <camunda:property id="enum_type" value="checkbox" />
+            </camunda:properties>
+            <camunda:value id="Value_190fel2" name="42" />
+            <camunda:value id="Value_2mknvfh" name="21" />
+            <camunda:value id="Value_1atqgco" name="7" />
+          </camunda:formField>
        </camunda:formData>
        <camunda:properties>
          <camunda:property name="type" value="string" />
--- a/example_data.py
+++ b/example_data.py
@ -6,13 +6,26 @@ from crc.models import StudyModel, WorkflowSpecModel, FileType, FileModel, FileD


 class ExampleDataLoader:
-    studies = [StudyModel(id=1,
-                          title='The impact of fried pickles on beer consumption in bipedal software developers.',
-                          last_updated=datetime.datetime.now(),
-                          protocol_builder_status='in_process',
-                          primary_investigator_id='dhf8r',
-                          sponsor='Sartography Pharmaceuticals',
-                          ind_number='1234')]
+    studies = [
+        StudyModel(
+            id=1,
+            title='The impact of fried pickles on beer consumption in bipedal software developers.',
+            last_updated=datetime.datetime.now(),
+            protocol_builder_status='in_process',
+            primary_investigator_id='dhf8r',
+            sponsor='Sartography Pharmaceuticals',
+            ind_number='1234'
+        ),
+        StudyModel(
+            id=2,
+            title='Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
+            last_updated=datetime.datetime.now(),
+            protocol_builder_status='in_process',
+            primary_investigator_id='dhf8r',
+            sponsor='Makerspace & Co.',
+            ind_number='5678'
+        ),
+    ]

    workflow_specs = [WorkflowSpecModel(
        id="random_fact",
--- a/run.py
+++ b/run.py
@ -1,3 +1,3 @@
 from crc import app
 if __name__ == "__main__":
-    app.run()
+    app.run(host='0.0.0.0')