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updating readme
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README.md
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README.md
@ -95,9 +95,65 @@ and primary investigator to dhf8r - which is a user in the mock ldap service, an
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fire up the interface.
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### Configuration
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1. `instance/config.py`: This will configure the application for your local instance, overriding the configuration
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in config/default
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This covers both local configurations for development, and production settings.
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We will cover all the settings below, but perhaps the most important part of the configuration is setting
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the location of your workflow specifications. If you start up without setting a path, then it will
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use a few testing workflows as a default.
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For CRConnect, there is a private repository that contains all the workflow specifications, so get this
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checked out, then in a file called /instance/config.py add the following setting:
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SYNC_FILE_ROOT = '/path/to/my/git/dir/crconnect-workflow-specs'
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#### Local Configuration
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`instance/config.py`: This will configure the application for your local instance, overriding the configuration
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in config/default. Very handy for setting
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#### Production Configuration
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We use environment variables with identical names to the variables in the default configuration file to configure the
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application for production deplyment in a docker container
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#### Common Configuration Settings
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While these can be set in instance/config.py or as environment settings in docker, I'll present this as how you would
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define the Docker Container, as /config/default.py offers a good example of the former.
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```yaml
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cr-connect-backend-testing:
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container_name: cr-connect-backend-testing
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image: ghcr.io/sartography/cr-connect-workflow:master # We use GitHub's actions to publish images
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volumes:
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- /home/sartography/docker-volumes/testing:/var/lib/cr-connect/specs # where specs are located.
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ports:
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environment:
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- PRODUCTION=true # Should be set to true if you aren't running locally for development.
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- DEVELOPMENT=false # Should be the opposite of production.
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- PB_ENABLED=true # Generally true, we should connect to Protocol Builder
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- PREFERRED_URL_SCHEME=https # Generally you want to run on SSL, should be https
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- SERVER_NAME=testing.crconnect.uvadcos.io # The url used to access this app.
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- TOKEN_AUTH_SECRET_KEY=-0-0-0- TESTING SUPER SECURE -0-0-0- # Some random characters that seed our key gen.
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- APPLICATION_ROOT=/api # Appended to SERVER_NAME, is the full path to this service
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- ADMIN_UIDS=dhf8r,cah3us # A comma delimited list of people who can preform administrative tasks.
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- CORS_ALLOW_ORIGINS=testing.crconnect.uvadcos.io,shibidp.its.virginia.edu,sp.uvadcos.io # CORS stuff
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- FRONTEND=testing.crconnect.uvadcos.io # URL to reach the front end application.
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- BPMN=testing.crconnect.uvadcos.io/bpmn # URL to reach the configuration interface.
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- PB_BASE_URL=http://10.250.124.174:11022/pb/v2.0/ # URL for Protocol Builder
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- UPGRADE_DB=true # Will run all migrations on startup if set to true. Generally a good idea for production.
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- DB_USER=crc_user # Database user name
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- DB_NAME=crc_testing # Database passwprd
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- DB_HOST=10.250.124.186 # Domain/IP of database server.
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- DB_PORT=15432 # Port of database server.
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- DB_PASSWORD=XXXXX # Passwword for the database
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- MAIL_PASSWORD=XXXX # Mail Password
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- MAIL_USERNAME=XXXXX # Mail username
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- LDAP_URL=privopenldap.its.virginia.edu # URL for the LDAP Server
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- LDAP_PASS=XXXX # Password for the ldap server
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- LDAP_USER=cn=crcconnect,ou=Special Users,o=University of Virginia,c=US #LDAP settings for search, likely these.
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- SENTRY_ENVIRONMENT=testing.crconnect.uvadcos.io # Configuration for Sentry
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- GITHUB_TOKEN=XXXX # A token for GitHub so we can push and pull changes.
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- PORT0=11021 # The port on the server where this sytem should be avialable, could be 80, but we are behind a proxy.
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- SYNC_FILE_ROOT=/var/lib/cr-connect/specs # This should be the same as the volumes above, a location where the specs are checked out in git.
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```
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### Project Initialization
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1. Clone this repository.
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@ -1,26 +0,0 @@
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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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="empty_workflow" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
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<bpmn:endEvent id="EndEvent_0q4qzl9">
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<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
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</bpmn:endEvent>
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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="empty_workflow">
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<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="432" y="117" />
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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="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
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<dc:Bounds x="432" y="99" 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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@ -1,12 +0,0 @@
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{
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"library": false,
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"standalone": false,
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"display_order": 2,
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"id": "workflow_one",
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"description": "Workflow One, is a workflow.",
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"is_master_spec": false,
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"libraries": [],
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"display_name": "Workflow One",
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"primary_file_name": "empty_workflow.bpmn",
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"primary_process_id": "empty_workflow"
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}
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@ -1,26 +0,0 @@
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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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="empty_workflow" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
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<bpmn:endEvent id="EndEvent_0q4qzl9">
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<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
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</bpmn:endEvent>
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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="empty_workflow">
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<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="432" y="117" />
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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="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
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<dc:Bounds x="432" y="99" 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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@ -1,12 +0,0 @@
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{
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"library": false,
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"standalone": false,
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"display_order": 3,
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"id": "workflow_three",
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"description": "Workflow Three, is a workflow.",
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"is_master_spec": false,
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"libraries": [],
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"display_name": "Workflow Three",
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"primary_file_name": "empty_workflow.bpmn",
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"primary_process_id": "empty_workflow"
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}
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@ -1,26 +0,0 @@
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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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="empty_workflow" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
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<bpmn:endEvent id="EndEvent_0q4qzl9">
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<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
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</bpmn:endEvent>
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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="empty_workflow">
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<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="432" y="117" />
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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="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
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<dc:Bounds x="432" y="99" 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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@ -1,12 +0,0 @@
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{
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"library": false,
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"standalone": false,
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"display_order": 3,
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"id": "workflow_two",
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"description": "Workflow Two, is a workflow.",
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"is_master_spec": false,
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"libraries": [],
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"display_name": "Workflow Two",
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"primary_file_name": "empty_workflow.bpmn",
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"primary_process_id": "empty_workflow"
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}
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@ -1,26 +0,0 @@
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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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="empty_workflow_library" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
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<bpmn:endEvent id="EndEvent_0q4qzl9">
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<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
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</bpmn:endEvent>
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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="empty_workflow">
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<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="432" y="117" />
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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="99" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
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<dc:Bounds x="432" y="99" 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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@ -1,26 +0,0 @@
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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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
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<bpmn:process id="empty_workflow" isExecutable="true">
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<bpmn:startEvent id="StartEvent_1">
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<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
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</bpmn:startEvent>
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<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
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<bpmn:endEvent id="EndEvent_0q4qzl9">
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<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
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</bpmn:endEvent>
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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="empty_workflow">
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<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
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<di:waypoint x="215" y="117" />
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<di:waypoint x="432" y="117" />
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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="99" width="36" height="36" />
|
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</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
|
||||
<dc:Bounds x="432" y="99" 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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@ -1,12 +0,0 @@
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{
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"library": false,
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"standalone": false,
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"is_master_spec": true,
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"display_name": "Top Level Workflow",
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"description": "Determines the status of other workflows in a study",
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"primary_file_name": "empty_workflow.bpmn",
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"primary_process_id": "empty_workflow",
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"libraries": [
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{ "id": "library_one" }
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]
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}
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@ -1,23 +0,0 @@
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{
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"libraries": [
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{
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"id": "library_one",
|
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"description": "The One Library",
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"primary_file_name": "empty_workflow_library.bpmn",
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"primary_process_id": "empty_workflow_library",
|
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"display_name": "The One Library"
|
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}
|
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],
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"categories": [
|
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{
|
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"admin": false,
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"display_order": 0,
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"display_name": "Category Number One",
|
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},
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{
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"admin": false,
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"display_order": 1,
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"display_name": "Category Number Two",
|
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}
|
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]
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}
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@ -97,4 +97,4 @@ MAIL_USERNAME = environ.get('MAIL_USERNAME', default='')
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MAIL_PASSWORD = environ.get('MAIL_PASSWORD', default='')
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# Local file path
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SYNC_FILE_ROOT = './SPECS'
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SYNC_FILE_ROOT = 'tests/data/IMPORT_TEST'
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@ -2,5 +2,121 @@
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# loop over all the categories in the database
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# assure we have a directory with the correct name
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# assure it contains a valid json file called categories.json
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import json
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import os
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import pathlib
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import re
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import shutil
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categories = db.
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from crc import db, app
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from crc.models.file import FileModel
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowSpecCategoryModelSchema, WorkflowSpecModelSchema, \
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WorkflowSpecModel
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LIBRARY_SPECS = "Library Specs"
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STAND_ALONE_SPECS = "Stand Alone"
|
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MASTER_SPECIFICATION = "Master Specification"
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REFERENCE_FILES = "Reference Files"
|
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SPECIAL_FOLDERS = [LIBRARY_SPECS, MASTER_SPECIFICATION, REFERENCE_FILES]
|
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CAT_JSON_FILE = "category.json"
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WF_JSON_FILE = "workflow.json"
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|
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|
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base_dir = '../SPECS'
|
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app_root = app.root_path
|
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path = os.path.join(app_root, '..', 'SPECS')
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CAT_SCHEMA = WorkflowSpecCategoryModelSchema()
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SPEC_SCHEMA = WorkflowSpecModelSchema()
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def remove_all_json_files(path):
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for json_file in pathlib.Path(path).glob('*.json'):
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print("removing ", json_file)
|
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os.remove(json_file)
|
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def update_workflows_for_category(path, schemas, category_id):
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for schema in schemas:
|
||||
orig_path = os.path.join(path, schema.display_name)
|
||||
new_path = os.path.join(path, schema.id)
|
||||
if (os.path.exists(orig_path)):
|
||||
os.rename(orig_path, new_path)
|
||||
print(new_path)
|
||||
update_spec(new_path, schema, category_id)
|
||||
|
||||
|
||||
def update_spec(path, schema, category_id):
|
||||
json_data = SPEC_SCHEMA.dump(schema)
|
||||
remove_all_json_files(path)
|
||||
|
||||
# Fixup the libraries
|
||||
lib_ids = list(map(lambda x: x['id'], json_data['libraries']))
|
||||
|
||||
# calculate the primary process id, and primary file name
|
||||
file = db.session.query(FileModel).\
|
||||
filter(FileModel.workflow_spec_id == schema.id).\
|
||||
filter(FileModel.primary == True).first()
|
||||
if(file):
|
||||
json_data['primary_file_name'] = file.name
|
||||
json_data['primary_process_id'] = file.primary_process_id
|
||||
else:
|
||||
print("This workflow doesn't have a primary process:", json_data)
|
||||
|
||||
json_data['category_id'] = category_id
|
||||
json_data.pop('category', None)
|
||||
json_data.pop('parents', None)
|
||||
if json_data['library'] is None:
|
||||
json_data['library'] = False
|
||||
|
||||
json_data['libraries'] = lib_ids
|
||||
if not os.path.exists(path):
|
||||
os.makedirs(path)
|
||||
json_file_name = os.path.join(path, 'workflow.json')
|
||||
with open(json_file_name, 'w') as wf_handle:
|
||||
json.dump(json_data, wf_handle, indent=4)
|
||||
|
||||
# Clean up json files
|
||||
remove_all_json_files(path)
|
||||
|
||||
# Clean up libraries
|
||||
lib_path = os.path.join(path, LIBRARY_SPECS)
|
||||
remove_all_json_files(lib_path)
|
||||
workflows = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.library == True)
|
||||
update_workflows_for_category(lib_path, workflows, "")
|
||||
|
||||
# Clean up reference Files
|
||||
ref_path = os.path.join(path, REFERENCE_FILES)
|
||||
old_ref_path = os.path.join(path,'Reference')
|
||||
if os.path.exists(old_ref_path):
|
||||
os.rename(old_ref_path, ref_path)
|
||||
remove_all_json_files(ref_path)
|
||||
|
||||
# Clean up the master spec
|
||||
tlw = os.path.join(path, MASTER_SPECIFICATION, "Top Level Workflow")
|
||||
master_path = os.path.join(path, MASTER_SPECIFICATION)
|
||||
if os.path.exists(tlw):
|
||||
for src_file in pathlib.Path(tlw).glob('*.*'):
|
||||
shutil.copy(src_file, master_path)
|
||||
remove_all_json_files(master_path)
|
||||
schema = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.is_master_spec == True).first()
|
||||
update_spec(master_path, schema, "")
|
||||
|
||||
|
||||
# Fix all the categories
|
||||
categories = db.session.query(WorkflowSpecCategoryModel).all()
|
||||
for category in categories:
|
||||
json_data = CAT_SCHEMA.dump(category)
|
||||
orig_path = os.path.join(path, category.display_name)
|
||||
new_name = re.sub(r'[^A-Za-z0-9]', '_', category.display_name).lower()
|
||||
new_path = os.path.join(path, new_name)
|
||||
json_data['id'] = new_name
|
||||
if (os.path.exists(orig_path)):
|
||||
os.rename(orig_path, new_path)
|
||||
|
||||
remove_all_json_files(new_path)
|
||||
json_file_name = os.path.join(new_path, 'category.json')
|
||||
with open(json_file_name, 'w') as f_handle:
|
||||
json.dump(json_data, f_handle, indent=4)
|
||||
|
||||
workflows = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.category_id == category.id)
|
||||
update_workflows_for_category(new_path, workflows, new_name)
|
||||
6
tests/data/IMPORT_TEST/Library Specs/category.json
Normal file
6
tests/data/IMPORT_TEST/Library Specs/category.json
Normal file
@ -0,0 +1,6 @@
|
||||
{
|
||||
"admin": false,
|
||||
"display_name": "Library Specs",
|
||||
"id": "Library Specs",
|
||||
"display_order": 10000
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user