diff --git a/Pipfile b/Pipfile index 34cc883d..94b56e3d 100644 --- a/Pipfile +++ b/Pipfile @@ -41,6 +41,7 @@ gunicorn = "*" werkzeug = "*" sentry-sdk = {extras = ["flask"],version = "==0.14.4"} flask-mail = "*" +flask-admin = "*" markdown = "*" [requires] diff --git a/Pipfile.lock b/Pipfile.lock index fc4fba3e..5a76e529 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "f5c922e74e296622c19ecfdd5c22cdcc71841fe81cdd95f407a2eb2ba475e615" + "sha256": "deb9e257fe8240d12bf82940ff22f5ddb338b305491f33655a82adda9438990f" }, "pipfile-spec": 6, "requires": { @@ -104,17 +104,17 @@ }, "celery": { "hashes": [ - "sha256:c3f4173f83ceb5a5c986c5fdaefb9456de3b0729a72a5776e46bd405fda7b647", - "sha256:d1762d6065522879f341c3d67c2b9fe4615eb79756d59acb1434601d4aca474b" + "sha256:ef17d7dffde7fc73ecab3a3b6389d93d3213bac53fa7f28e68e33647ad50b916", + "sha256:fd77e4248bb1b7af5f7922dd8e81156f540306e3a5c4b1c24167c1f5f06025da" ], - "version": "==4.4.5" + "version": "==4.4.6" }, "certifi": { "hashes": [ - "sha256:5ad7e9a056d25ffa5082862e36f119f7f7cec6457fa07ee2f8c339814b80c9b1", - "sha256:9cd41137dc19af6a5e03b630eefe7d1f458d964d406342dd3edf625839b944cc" + "sha256:5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3", + "sha256:8fc0819f1f30ba15bdb34cceffb9ef04d99f420f68eb75d901e9560b8749fc41" ], - "version": "==2020.4.5.2" + "version": "==2020.6.20" }, "cffi": { "hashes": [ @@ -261,6 +261,13 @@ "index": "pypi", "version": "==1.1.2" }, + "flask-admin": { + "hashes": [ + "sha256:68c761d8582d59b1f7702013e944a7ad11d7659a72f3006b89b68b0bd8df61b8" + ], + "index": "pypi", + "version": "==1.5.6" + }, "flask-bcrypt": { "hashes": [ "sha256:d71c8585b2ee1c62024392ebdbc447438564e2c8c02b4e57b56a4cafd8d13c5f" @@ -394,10 +401,10 @@ }, "kombu": { "hashes": [ - "sha256:437b9cdea193cc2ed0b8044c85fd0f126bb3615ca2f4d4a35b39de7cacfa3c1a", - "sha256:dc282bb277197d723bccda1a9ba30a27a28c9672d0ab93e9e51bb05a37bd29c3" + "sha256:be48cdffb54a2194d93ad6533d73f69408486483d189fe9f5990ee24255b0e0a", + "sha256:ca1b45faac8c0b18493d02a8571792f3c40291cf2bcf1f55afed3d8f3aa7ba74" ], - "version": "==4.6.10" + "version": "==4.6.11" }, "ldap3": { "hashes": [ @@ -518,29 +525,34 @@ }, "numpy": { "hashes": [ - "sha256:0172304e7d8d40e9e49553901903dc5f5a49a703363ed756796f5808a06fc233", - "sha256:34e96e9dae65c4839bd80012023aadd6ee2ccb73ce7fdf3074c62f301e63120b", - "sha256:3676abe3d621fc467c4c1469ee11e395c82b2d6b5463a9454e37fe9da07cd0d7", - "sha256:3dd6823d3e04b5f223e3e265b4a1eae15f104f4366edd409e5a5e413a98f911f", - "sha256:4064f53d4cce69e9ac613256dc2162e56f20a4e2d2086b1956dd2fcf77b7fac5", - "sha256:4674f7d27a6c1c52a4d1aa5f0881f1eff840d2206989bae6acb1c7668c02ebfb", - "sha256:7d42ab8cedd175b5ebcb39b5208b25ba104842489ed59fbb29356f671ac93583", - "sha256:965df25449305092b23d5145b9bdaeb0149b6e41a77a7d728b1644b3c99277c1", - "sha256:9c9d6531bc1886454f44aa8f809268bc481295cf9740827254f53c30104f074a", - "sha256:a78e438db8ec26d5d9d0e584b27ef25c7afa5a182d1bf4d05e313d2d6d515271", - "sha256:a7acefddf994af1aeba05bbbafe4ba983a187079f125146dc5859e6d817df824", - "sha256:a87f59508c2b7ceb8631c20630118cc546f1f815e034193dc72390db038a5cb3", - 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"version": "==1.18.5" + "version": "==1.19.0" }, "openapi-spec-validator": { "hashes": [ @@ -552,10 +564,10 @@ }, "openpyxl": { "hashes": [ - "sha256:547a9fc6aafcf44abe358b89ed4438d077e9d92e4f182c87e2dc294186dc4b64" + "sha256:6e62f058d19b09b95d20ebfbfb04857ad08d0833190516c1660675f699c6186f" ], "index": "pypi", - "version": "==3.0.3" + "version": "==3.0.4" }, "packaging": { "hashes": [ @@ -566,25 +578,25 @@ }, "pandas": { "hashes": [ - "sha256:034185bb615dc96d08fa13aacba8862949db19d5e7804d6ee242d086f07bcc46", - "sha256:0c9b7f1933e3226cc16129cf2093338d63ace5c85db7c9588e3e1ac5c1937ad5", - "sha256:1f6fcf0404626ca0475715da045a878c7062ed39bc859afc4ccf0ba0a586a0aa", - "sha256:1fc963ba33c299973e92d45466e576d11f28611f3549469aec4a35658ef9f4cc", - "sha256:29b4cfee5df2bc885607b8f016e901e63df7ffc8f00209000471778f46cc6678", - "sha256:2a8b6c28607e3f3c344fe3e9b3cd76d2bf9f59bc8c0f2e582e3728b80e1786dc", - "sha256:2bc2ff52091a6ac481cc75d514f06227dc1b10887df1eb72d535475e7b825e31", - "sha256:415e4d52fcfd68c3d8f1851cef4d947399232741cc994c8f6aa5e6a9f2e4b1d8", - "sha256:519678882fd0587410ece91e3ff7f73ad6ded60f6fcb8aa7bcc85c1dc20ecac6", - "sha256:51e0abe6e9f5096d246232b461649b0aa627f46de8f6344597ca908f2240cbaa", - "sha256:698e26372dba93f3aeb09cd7da2bb6dd6ade248338cfe423792c07116297f8f4", - "sha256:83af85c8e539a7876d23b78433d90f6a0e8aa913e37320785cf3888c946ee874", - "sha256:982cda36d1773076a415ec62766b3c0a21cdbae84525135bdb8f460c489bb5dd", - "sha256:a647e44ba1b3344ebc5991c8aafeb7cca2b930010923657a273b41d86ae225c4", - "sha256:b35d625282baa7b51e82e52622c300a1ca9f786711b2af7cbe64f1e6831f4126", - "sha256:bab51855f8b318ef39c2af2c11095f45a10b74cbab4e3c8199efcc5af314c648" + "sha256:02f1e8f71cd994ed7fcb9a35b6ddddeb4314822a0e09a9c5b2d278f8cb5d4096", + "sha256:13f75fb18486759da3ff40f5345d9dd20e7d78f2a39c5884d013456cec9876f0", + "sha256:35b670b0abcfed7cad76f2834041dcf7ae47fd9b22b63622d67cdc933d79f453", + "sha256:4c73f373b0800eb3062ffd13d4a7a2a6d522792fa6eb204d67a4fad0a40f03dc", + "sha256:5759edf0b686b6f25a5d4a447ea588983a33afc8a0081a0954184a4a87fd0dd7", + "sha256:5a7cf6044467c1356b2b49ef69e50bf4d231e773c3ca0558807cdba56b76820b", + "sha256:69c5d920a0b2a9838e677f78f4dde506b95ea8e4d30da25859db6469ded84fa8", + "sha256:8778a5cc5a8437a561e3276b85367412e10ae9fff07db1eed986e427d9a674f8", + "sha256:9871ef5ee17f388f1cb35f76dc6106d40cb8165c562d573470672f4cdefa59ef", + "sha256:9c31d52f1a7dd2bb4681d9f62646c7aa554f19e8e9addc17e8b1b20011d7522d", + "sha256:ab8173a8efe5418bbe50e43f321994ac6673afc5c7c4839014cf6401bbdd0705", + "sha256:ae961f1f0e270f1e4e2273f6a539b2ea33248e0e3a11ffb479d757918a5e03a9", + "sha256:b3c4f93fcb6e97d993bf87cdd917883b7dab7d20c627699f360a8fb49e9e0b91", + "sha256:c9410ce8a3dee77653bc0684cfa1535a7f9c291663bd7ad79e39f5ab58f67ab3", + "sha256:f69e0f7b7c09f1f612b1f8f59e2df72faa8a6b41c5a436dde5b615aaf948f107", + "sha256:faa42a78d1350b02a7d2f0dbe3c80791cf785663d6997891549d0f86dc49125e" ], "index": "pypi", - "version": "==1.0.4" + "version": "==1.0.5" }, "psycopg2-binary": { "hashes": [ @@ -810,7 +822,7 @@ "spiffworkflow": { "editable": true, "git": "https://github.com/sartography/SpiffWorkflow.git", - "ref": "b8a064a0bb76c705a1be04ee9bb8ac7beee56eb0" + "ref": "5450dc0463a95811d386b7de063d950bf6179d2b" }, "sqlalchemy": { "hashes": [ @@ -898,6 +910,13 @@ "index": "pypi", "version": "==1.0.1" }, + "wtforms": { + "hashes": [ + "sha256:6ff8635f4caeed9f38641d48cfe019d0d3896f41910ab04494143fc027866e1b", + "sha256:861a13b3ae521d6700dac3b2771970bd354a63ba7043ecc3a82b5288596a1972" + ], + "version": "==2.3.1" + }, "xlrd": { "hashes": [ "sha256:546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2", @@ -1035,10 +1054,10 @@ }, "wcwidth": { "hashes": [ - "sha256:79375666b9954d4a1a10739315816324c3e73110af9d0e102d906fdb0aec009f", - "sha256:8c6b5b6ee1360b842645f336d9e5d68c55817c26d3050f46b235ef2bc650e48f" + "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784", + "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83" ], - "version": "==0.2.4" + "version": "==0.2.5" }, "zipp": { "hashes": [ diff --git a/crc/__init__.py b/crc/__init__.py index 1ac2678f..59ffeac7 100644 --- a/crc/__init__.py +++ b/crc/__init__.py @@ -4,6 +4,8 @@ import sentry_sdk import connexion from jinja2 import Environment, FileSystemLoader +from flask_admin import Admin +from flask_admin.contrib.sqla import ModelView from flask_cors import CORS from flask_marshmallow import Marshmallow from flask_mail import Mail @@ -37,13 +39,16 @@ ma = Marshmallow(app) from crc import models from crc import api +from crc.api import admin connexion_app.add_api('api.yml', base_path='/v1.0') + # Convert list of allowed origins to list of regexes origins_re = [r"^https?:\/\/%s(.*)" % o.replace('.', '\.') for o in app.config['CORS_ALLOW_ORIGINS']] cors = CORS(connexion_app.app, origins=origins_re) +# Sentry error handling if app.config['ENABLE_SENTRY']: sentry_sdk.init( dsn="https://25342ca4e2d443c6a5c49707d68e9f40@o401361.ingest.sentry.io/5260915", @@ -88,3 +93,10 @@ def clear_db(): """Load example data into the database.""" from example_data import ExampleDataLoader ExampleDataLoader.clean_db() + +@app.cli.command() +def rrt_data_fix(): + """Finds all the empty task event logs, and populates + them with good wholesome data.""" + from crc.services.workflow_service import WorkflowService + WorkflowService.fix_legacy_data_model_for_rrt() diff --git a/crc/api/admin.py b/crc/api/admin.py new file mode 100644 index 00000000..37532c38 --- /dev/null +++ b/crc/api/admin.py @@ -0,0 +1,72 @@ +# Admin app +import json + +from flask import url_for +from flask_admin import Admin +from flask_admin.contrib import sqla +from flask_admin.contrib.sqla import ModelView +from werkzeug.utils import redirect +from jinja2 import Markup + +from crc import db, app +from crc.api.user import verify_token, verify_token_admin +from crc.models.approval import ApprovalModel +from crc.models.file import FileModel +from crc.models.stats import TaskEventModel +from crc.models.study import StudyModel +from crc.models.user import UserModel +from crc.models.workflow import WorkflowModel + + +class AdminModelView(sqla.ModelView): + can_create = False + can_edit = False + can_delete = False + page_size = 50 # the number of entries to display on the list view + column_exclude_list = ['bpmn_workflow_json', ] + column_display_pk = True + can_export = True + + def is_accessible(self): + return verify_token_admin() + + def inaccessible_callback(self, name, **kwargs): + # redirect to login page if user doesn't have access + return redirect(url_for('home')) + +class UserView(AdminModelView): + column_filters = ['uid'] + +class StudyView(AdminModelView): + column_filters = ['id', 'primary_investigator_id'] + column_searchable_list = ['title'] + +class ApprovalView(AdminModelView): + column_filters = ['study_id', 'approver_uid'] + +class WorkflowView(AdminModelView): + column_filters = ['study_id', 'id'] + +class FileView(AdminModelView): + column_filters = ['workflow_id'] + +def json_formatter(view, context, model, name): + value = getattr(model, name) + json_value = json.dumps(value, ensure_ascii=False, indent=2) + return Markup('
{}
'.format(json_value)) + +class TaskEventView(AdminModelView): + column_filters = ['workflow_id', 'action'] + column_list = ['study_id', 'user_id', 'workflow_id', 'action', 'task_title', 'form_data', 'date'] + column_formatters = { + 'form_data': json_formatter, + } + +admin = Admin(app) + +admin.add_view(StudyView(StudyModel, db.session)) +admin.add_view(ApprovalView(ApprovalModel, db.session)) +admin.add_view(UserView(UserModel, db.session)) +admin.add_view(WorkflowView(WorkflowModel, db.session)) +admin.add_view(FileView(FileModel, db.session)) +admin.add_view(TaskEventView(TaskEventModel, db.session)) diff --git a/crc/api/workflow.py b/crc/api/workflow.py index 655a85e7..9e1dffc2 100644 --- a/crc/api/workflow.py +++ b/crc/api/workflow.py @@ -1,7 +1,7 @@ import uuid +from SpiffWorkflow.util.deep_merge import DeepMerge from flask import g - from crc import session, app from crc.api.common import ApiError, ApiErrorSchema from crc.models.api_models import WorkflowApi, WorkflowApiSchema, NavigationItem, NavigationItemSchema @@ -96,59 +96,10 @@ def delete_workflow_specification(spec_id): session.commit() -def __get_workflow_api_model(processor: WorkflowProcessor, next_task = None): - """Returns an API model representing the state of the current workflow, if requested, and - possible, next_task is set to the current_task.""" - - nav_dict = processor.bpmn_workflow.get_nav_list() - navigation = [] - for nav_item in nav_dict: - spiff_task = processor.bpmn_workflow.get_task(nav_item['task_id']) - if 'description' in nav_item: - nav_item['title'] = nav_item.pop('description') - # fixme: duplicate code from the workflow_service. Should only do this in one place. - if ' ' in nav_item['title']: - nav_item['title'] = nav_item['title'].partition(' ')[2] - else: - nav_item['title'] = "" - if spiff_task: - nav_item['task'] = WorkflowService.spiff_task_to_api_task(spiff_task, add_docs_and_forms=False) - nav_item['title'] = nav_item['task'].title # Prefer the task title. - else: - nav_item['task'] = None - if not 'is_decision' in nav_item: - nav_item['is_decision'] = False - - navigation.append(NavigationItem(**nav_item)) - NavigationItemSchema().dump(nav_item) - - spec = session.query(WorkflowSpecModel).filter_by(id=processor.workflow_spec_id).first() - workflow_api = WorkflowApi( - id=processor.get_workflow_id(), - status=processor.get_status(), - next_task=None, - navigation=navigation, - workflow_spec_id=processor.workflow_spec_id, - spec_version=processor.get_version_string(), - is_latest_spec=processor.is_latest_spec, - total_tasks=len(navigation), - completed_tasks=processor.workflow_model.completed_tasks, - last_updated=processor.workflow_model.last_updated, - title=spec.display_name - ) - if not next_task: # The Next Task can be requested to be a certain task, useful for parallel tasks. - # This may or may not work, sometimes there is no next task to complete. - next_task = processor.next_task() - if next_task: - workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True) - - return workflow_api - - def get_workflow(workflow_id, soft_reset=False, hard_reset=False): workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first() processor = WorkflowProcessor(workflow_model, soft_reset=soft_reset, hard_reset=hard_reset) - workflow_api_model = __get_workflow_api_model(processor) + workflow_api_model = WorkflowService.processor_to_workflow_api(processor) return WorkflowApiSchema().dump(workflow_api_model) @@ -161,17 +112,20 @@ def set_current_task(workflow_id, task_id): user_uid = __get_user_uid(workflow_model.study.user_uid) processor = WorkflowProcessor(workflow_model) task_id = uuid.UUID(task_id) - task = processor.bpmn_workflow.get_task(task_id) - if task.state != task.COMPLETED and task.state != task.READY: + spiff_task = processor.bpmn_workflow.get_task(task_id) + if spiff_task.state != spiff_task.COMPLETED and spiff_task.state != spiff_task.READY: raise ApiError("invalid_state", "You may not move the token to a task who's state is not " "currently set to COMPLETE or READY.") # Only reset the token if the task doesn't already have it. - if task.state == task.COMPLETED: - task.reset_token(reset_data=False) # we could optionally clear the previous data. + if spiff_task.state == spiff_task.COMPLETED: + spiff_task.reset_token(reset_data=True) # Don't try to copy the existing data back into this task. + processor.save() - WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_TOKEN_RESET) - workflow_api_model = __get_workflow_api_model(processor, task) + WorkflowService.log_task_action(user_uid, workflow_model, spiff_task, + WorkflowService.TASK_ACTION_TOKEN_RESET, + version=processor.get_version_string()) + workflow_api_model = WorkflowService.processor_to_workflow_api(processor, spiff_task) return WorkflowApiSchema().dump(workflow_api_model) @@ -187,17 +141,19 @@ def update_task(workflow_id, task_id, body): user_uid = __get_user_uid(workflow_model.study.user_uid) processor = WorkflowProcessor(workflow_model) task_id = uuid.UUID(task_id) - task = processor.bpmn_workflow.get_task(task_id) - if task.state != task.READY: + spiff_task = processor.bpmn_workflow.get_task(task_id) + if spiff_task.state != spiff_task.READY: raise ApiError("invalid_state", "You may not update a task unless it is in the READY state. " "Consider calling a token reset to make this task Ready.") - task.update_data(body) - processor.complete_task(task) + if body: # IF and only if we get the body back, update the task data with the content. + spiff_task.data = body # Accept the data from the front end as complete. Do not merge it in, as then it is impossible to remove items. + processor.complete_task(spiff_task) processor.do_engine_steps() processor.save() - WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_COMPLETE) - workflow_api_model = __get_workflow_api_model(processor) + WorkflowService.log_task_action(user_uid, workflow_model, spiff_task, WorkflowService.TASK_ACTION_COMPLETE, + version=processor.get_version_string()) + workflow_api_model = WorkflowService.processor_to_workflow_api(processor) return WorkflowApiSchema().dump(workflow_api_model) diff --git a/crc/models/api_models.py b/crc/models/api_models.py index 53706a75..361b9183 100644 --- a/crc/models/api_models.py +++ b/crc/models/api_models.py @@ -36,6 +36,7 @@ class Task(object): PROP_OPTIONS_FILE = "spreadsheet.name" PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column" PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column" + PROP_OPTIONS_READ_ONLY = "read_only" PROP_LDAP_LOOKUP = "ldap.lookup" VALIDATION_REQUIRED = "required" FIELD_TYPE_AUTO_COMPLETE = "autocomplete" diff --git a/crc/models/stats.py b/crc/models/stats.py index c72df7d4..0a2e69b7 100644 --- a/crc/models/stats.py +++ b/crc/models/stats.py @@ -17,6 +17,7 @@ class TaskEventModel(db.Model): task_title = db.Column(db.String) task_type = db.Column(db.String) task_state = db.Column(db.String) + form_data = db.Column(db.JSON) # And form data submitted when the task was completed. mi_type = db.Column(db.String) mi_count = db.Column(db.Integer) mi_index = db.Column(db.Integer) diff --git a/crc/services/workflow_processor.py b/crc/services/workflow_processor.py index f04fb332..dde14bb5 100644 --- a/crc/services/workflow_processor.py +++ b/crc/services/workflow_processor.py @@ -102,14 +102,15 @@ class WorkflowProcessor(object): def __init__(self, workflow_model: WorkflowModel, soft_reset=False, hard_reset=False, validate_only=False): """Create a Workflow Processor based on the serialized information available in the workflow model. - If soft_reset is set to true, it will try to use the latest version of the workflow specification. - If hard_reset is set to true, it will create a new Workflow, but embed the data from the last - completed task in the previous workflow. + If soft_reset is set to true, it will try to use the latest version of the workflow specification + without resetting to the beginning of the workflow. This will work for some minor changes to the spec. + If hard_reset is set to true, it will use the latest spec, and start the workflow over from the beginning. + which should work in casees where a soft reset fails. If neither flag is set, it will use the same version of the specification that was used to originally create the workflow model. """ self.workflow_model = workflow_model - if soft_reset or len(workflow_model.dependencies) == 0: + if soft_reset or len(workflow_model.dependencies) == 0: # Depenencies of 0 means the workflow was never started. self.spec_data_files = FileService.get_spec_data_files( workflow_spec_id=workflow_model.workflow_spec_id) else: @@ -216,8 +217,6 @@ class WorkflowProcessor(object): full_version = "v%s (%s)" % (version, files) return full_version - - def update_dependencies(self, spec_data_files): existing_dependencies = FileService.get_spec_data_files( workflow_spec_id=self.workflow_model.workflow_spec_id, @@ -299,25 +298,12 @@ class WorkflowProcessor(object): return WorkflowStatus.waiting def hard_reset(self): - """Recreate this workflow, but keep the data from the last completed task and add - it back into the first task. This may be useful when a workflow specification changes, - and users need to review all the prior steps, but they don't need to reenter all the previous data. - - Returns the new version. + """Recreate this workflow. This will be useful when a workflow specification changes. """ - - # Create a new workflow based on the latest specs. self.spec_data_files = FileService.get_spec_data_files(workflow_spec_id=self.workflow_spec_id) new_spec = WorkflowProcessor.get_spec(self.spec_data_files, self.workflow_spec_id) new_bpmn_workflow = BpmnWorkflow(new_spec, script_engine=self._script_engine) new_bpmn_workflow.data = self.bpmn_workflow.data - - # Reset the current workflow to the beginning - which we will consider to be the first task after the root - # element. This feels a little sketchy, but I think it is safe to assume root will have one child. - first_task = self.bpmn_workflow.task_tree.children[0] - first_task.reset_token(reset_data=False) - for task in new_bpmn_workflow.get_tasks(SpiffTask.READY): - task.data = first_task.data new_bpmn_workflow.do_engine_steps() self.bpmn_workflow = new_bpmn_workflow diff --git a/crc/services/workflow_service.py b/crc/services/workflow_service.py index 48abdbd9..8d81a908 100644 --- a/crc/services/workflow_service.py +++ b/crc/services/workflow_service.py @@ -1,3 +1,4 @@ +import copy import string from datetime import datetime import random @@ -5,25 +6,26 @@ import random import jinja2 from SpiffWorkflow import Task as SpiffTask, WorkflowException from SpiffWorkflow.bpmn.specs.ManualTask import ManualTask +from SpiffWorkflow.bpmn.specs.MultiInstanceTask import MultiInstanceTask from SpiffWorkflow.bpmn.specs.ScriptTask import ScriptTask from SpiffWorkflow.bpmn.specs.UserTask import UserTask from SpiffWorkflow.dmn.specs.BusinessRuleTask import BusinessRuleTask from SpiffWorkflow.specs import CancelTask, StartTask -from flask import g +from SpiffWorkflow.util.deep_merge import DeepMerge from jinja2 import Template from crc import db, app from crc.api.common import ApiError -from crc.models.api_models import Task, MultiInstanceType +from crc.models.api_models import Task, MultiInstanceType, NavigationItem, NavigationItemSchema, WorkflowApi from crc.models.file import LookupDataModel from crc.models.stats import TaskEventModel from crc.models.study import StudyModel from crc.models.user import UserModel -from crc.models.workflow import WorkflowModel, WorkflowStatus +from crc.models.workflow import WorkflowModel, WorkflowStatus, WorkflowSpecModel from crc.services.file_service import FileService from crc.services.lookup_service import LookupService from crc.services.study_service import StudyService -from crc.services.workflow_processor import WorkflowProcessor, CustomBpmnScriptEngine +from crc.services.workflow_processor import WorkflowProcessor class WorkflowService(object): @@ -186,6 +188,77 @@ class WorkflowService(object): letters = string.ascii_lowercase return ''.join(random.choice(letters) for i in range(string_length)) + @staticmethod + def processor_to_workflow_api(processor: WorkflowProcessor, next_task=None): + """Returns an API model representing the state of the current workflow, if requested, and + possible, next_task is set to the current_task.""" + + nav_dict = processor.bpmn_workflow.get_nav_list() + navigation = [] + for nav_item in nav_dict: + spiff_task = processor.bpmn_workflow.get_task(nav_item['task_id']) + if 'description' in nav_item: + nav_item['title'] = nav_item.pop('description') + # fixme: duplicate code from the workflow_service. Should only do this in one place. + if ' ' in nav_item['title']: + nav_item['title'] = nav_item['title'].partition(' ')[2] + else: + nav_item['title'] = "" + if spiff_task: + nav_item['task'] = WorkflowService.spiff_task_to_api_task(spiff_task, add_docs_and_forms=False) + nav_item['title'] = nav_item['task'].title # Prefer the task title. + else: + nav_item['task'] = None + if not 'is_decision' in nav_item: + nav_item['is_decision'] = False + + navigation.append(NavigationItem(**nav_item)) + NavigationItemSchema().dump(nav_item) + + spec = db.session.query(WorkflowSpecModel).filter_by(id=processor.workflow_spec_id).first() + workflow_api = WorkflowApi( + id=processor.get_workflow_id(), + status=processor.get_status(), + next_task=None, + navigation=navigation, + workflow_spec_id=processor.workflow_spec_id, + spec_version=processor.get_version_string(), + is_latest_spec=processor.is_latest_spec, + total_tasks=len(navigation), + completed_tasks=processor.workflow_model.completed_tasks, + last_updated=processor.workflow_model.last_updated, + title=spec.display_name + ) + if not next_task: # The Next Task can be requested to be a certain task, useful for parallel tasks. + # This may or may not work, sometimes there is no next task to complete. + next_task = processor.next_task() + if next_task: + previous_form_data = WorkflowService.get_previously_submitted_data(processor.workflow_model.id, next_task) + DeepMerge.merge(next_task.data, previous_form_data) + workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True) + + return workflow_api + + @staticmethod + def get_previously_submitted_data(workflow_id, task): + """ If the user has completed this task previously, find the form data for the last submission.""" + latest_event = db.session.query(TaskEventModel) \ + .filter_by(workflow_id=workflow_id) \ + .filter_by(task_name=task.task_spec.name) \ + .filter_by(action=WorkflowService.TASK_ACTION_COMPLETE) \ + .order_by(TaskEventModel.date.desc()).first() + if latest_event: + if latest_event.form_data is not None: + return latest_event.form_data + else: + app.logger.error("missing_form_dat", "We have lost data for workflow %i, task %s, it is not " + "in the task event model, " + "and it should be." % (workflow_id, task.task_spec.name)) + return {} + else: + return {} + + @staticmethod def spiff_task_to_api_task(spiff_task, add_docs_and_forms=False): task_type = spiff_task.task_spec.__class__.__name__ @@ -317,21 +390,22 @@ class WorkflowService(object): field.options.append({"id": d.value, "name": d.label}) @staticmethod - def log_task_action(user_uid, processor, spiff_task, action): + def log_task_action(user_uid, workflow_model, spiff_task, action, version): task = WorkflowService.spiff_task_to_api_task(spiff_task) - workflow_model = processor.workflow_model + form_data = WorkflowService.extract_form_data(spiff_task.data, spiff_task) task_event = TaskEventModel( study_id=workflow_model.study_id, user_uid=user_uid, workflow_id=workflow_model.id, workflow_spec_id=workflow_model.workflow_spec_id, - spec_version=processor.get_version_string(), + spec_version=version, action=action, task_id=task.id, task_name=task.name, task_title=task.title, task_type=str(task.type), task_state=task.state, + form_data=form_data, mi_type=task.multi_instance_type.value, # Some tasks have a repeat behavior. mi_count=task.multi_instance_count, # This is the number of times the task could repeat. mi_index=task.multi_instance_index, # And the index of the currently repeating task. @@ -341,3 +415,64 @@ class WorkflowService(object): db.session.add(task_event) db.session.commit() + @staticmethod + def fix_legacy_data_model_for_rrt(): + """ Remove this after use! This is just to fix RRT so the data is handled correctly. + + Utility that is likely called via the flask command line, it will loop through all the + workflows in the system and attempt to add the right data into the task action log so that + users do not have to re fill out all of the forms if they start over or go back in the workflow. + Viciously inefficient, but should only have to run one time for RRT""" + workflows = db.session.query(WorkflowModel).all() + for workflow_model in workflows: + task_logs = db.session.query(TaskEventModel) \ + .filter(TaskEventModel.workflow_id == workflow_model.id) \ + .filter(TaskEventModel.action == WorkflowService.TASK_ACTION_COMPLETE) \ + .order_by(TaskEventModel.date.desc()).all() + + processor = WorkflowProcessor(workflow_model) + # Grab all the data from last task completed, which will be everything in this + # rrt situation because of how we were keeping all the data at the time. + latest_data = processor.next_task().data + + # Move forward in the task spec tree, dropping any data that would have been + # added in subsequent tasks, just looking at form data, will not track the automated + # task data additions, hopefully this doesn't hang us. + for log in task_logs: +# if log.task_data is not None: # Only do this if the task event does not have data populated in it. +# continue + data = copy.deepcopy(latest_data) # Or you end up with insane crazy issues. + # In the simple case of RRT, there is exactly one task for the given task_spec + task = processor.bpmn_workflow.get_tasks_from_spec_name(log.task_name)[0] + data = WorkflowService.extract_form_data(data, task) + log.form_data = data + db.session.add(log) + + db.session.commit() + + @staticmethod + def extract_form_data(latest_data, task): + """Removes data from latest_data that would be added by the child task or any of it's children.""" + data = {} + + if hasattr(task.task_spec, 'form'): + for field in task.task_spec.form.fields: + if field.has_property(Task.PROP_OPTIONS_READ_ONLY) and \ + field.get_property(Task.PROP_OPTIONS_READ_ONLY).lower().strip() == "true": + continue # Don't add read-only data + elif field.has_property(Task.PROP_OPTIONS_REPEAT): + group = field.get_property(Task.PROP_OPTIONS_REPEAT) + if group in latest_data: + data[group] = latest_data[group] + elif isinstance(task.task_spec, MultiInstanceTask): + group = task.task_spec.elementVar + if group in latest_data: + data[group] = latest_data[group] + else: + if field.id in latest_data: + data[field.id] = latest_data[field.id] + + return data + + + diff --git a/docker_run.sh b/docker_run.sh index 6bc3c90b..8ad66274 100755 --- a/docker_run.sh +++ b/docker_run.sh @@ -23,8 +23,16 @@ if [ "$RESET_DB_RRT" = "true" ]; then pipenv run flask load-example-rrt-data fi +if [ "$FIX_RRT_DATA" = "true" ]; then + echo 'Fixing RRT data...' + pipenv run flask rrt-data-fix +fi + + +# THIS MUST BE THE LAST COMMAND! if [ "$APPLICATION_ROOT" = "/" ]; then pipenv run gunicorn --bind 0.0.0.0:$PORT0 wsgi:app else pipenv run gunicorn -e SCRIPT_NAME="$APPLICATION_ROOT" --bind 0.0.0.0:$PORT0 wsgi:app fi + diff --git a/migrations/versions/1fdd1bdb600e_.py b/migrations/versions/1fdd1bdb600e_.py new file mode 100644 index 00000000..dff1fdae --- /dev/null +++ b/migrations/versions/1fdd1bdb600e_.py @@ -0,0 +1,28 @@ +"""empty message + +Revision ID: 1fdd1bdb600e +Revises: 17597692d0b0 +Create Date: 2020-06-17 16:44:16.427988 + +""" +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision = '1fdd1bdb600e' +down_revision = '17597692d0b0' +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('task_event', sa.Column('task_data', sa.JSON(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('task_event', 'task_data') + # ### end Alembic commands ### diff --git a/migrations/versions/de30304ff5e6_.py b/migrations/versions/de30304ff5e6_.py new file mode 100644 index 00000000..46a43f18 --- /dev/null +++ b/migrations/versions/de30304ff5e6_.py @@ -0,0 +1,30 @@ +"""empty message + +Revision ID: de30304ff5e6 +Revises: 1fdd1bdb600e +Create Date: 2020-06-18 16:19:11.133665 + +""" +from alembic import op +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision = 'de30304ff5e6' +down_revision = '1fdd1bdb600e' +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('task_event', sa.Column('form_data', sa.JSON(), nullable=True)) + op.drop_column('task_event', 'task_data') + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('task_event', sa.Column('task_data', postgresql.JSON(astext_type=sa.Text()), autoincrement=False, nullable=True)) + op.drop_column('task_event', 'form_data') + # ### end Alembic commands ### diff --git a/tests/test_tasks_api.py b/tests/test_tasks_api.py index 654b777e..1b35434c 100644 --- a/tests/test_tasks_api.py +++ b/tests/test_tasks_api.py @@ -4,14 +4,86 @@ import random from unittest.mock import patch from tests.base_test import BaseTest + from crc import session, app from crc.models.api_models import WorkflowApiSchema, MultiInstanceType, TaskSchema from crc.models.file import FileModelSchema from crc.models.workflow import WorkflowStatus - +from crc.services.workflow_service import WorkflowService +from crc.models.stats import TaskEventModel class TestTasksApi(BaseTest): + def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False): + rv = self.app.get('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' % + (workflow.id, str(soft_reset), str(hard_reset)), + headers=self.logged_in_headers(), + content_type="application/json") + self.assert_success(rv) + json_data = json.loads(rv.get_data(as_text=True)) + workflow_api = WorkflowApiSchema().load(json_data) + self.assertEqual(workflow.workflow_spec_id, workflow_api.workflow_spec_id) + return workflow_api + + def complete_form(self, workflow_in, task_in, dict_data, error_code = None): + prev_completed_task_count = workflow_in.completed_tasks + if isinstance(task_in, dict): + task_id = task_in["id"] + else: + task_id = task_in.id + rv = self.app.put('/v1.0/workflow/%i/task/%s/data' % (workflow_in.id, task_id), + headers=self.logged_in_headers(), + content_type="application/json", + data=json.dumps(dict_data)) + if error_code: + self.assert_failure(rv, error_code=error_code) + return + + self.assert_success(rv) + json_data = json.loads(rv.get_data(as_text=True)) + + # Assure stats are updated on the model + workflow = WorkflowApiSchema().load(json_data) + # The total number of tasks may change over time, as users move through gateways + # branches may be pruned. As we hit parallel Multi-Instance new tasks may be created... + self.assertIsNotNone(workflow.total_tasks) + self.assertEquals(prev_completed_task_count + 1, workflow.completed_tasks) + # Assure a record exists in the Task Events + task_events = session.query(TaskEventModel) \ + .filter_by(workflow_id=workflow.id) \ + .filter_by(task_id=task_id) \ + .order_by(TaskEventModel.date.desc()).all() + self.assertGreater(len(task_events), 0) + event = task_events[0] + self.assertIsNotNone(event.study_id) + self.assertEquals("dhf8r", event.user_uid) + self.assertEquals(workflow.id, event.workflow_id) + self.assertEquals(workflow.workflow_spec_id, event.workflow_spec_id) + self.assertEquals(workflow.spec_version, event.spec_version) + self.assertEquals(WorkflowService.TASK_ACTION_COMPLETE, event.action) + self.assertEquals(task_in.id, task_id) + self.assertEquals(task_in.name, event.task_name) + self.assertEquals(task_in.title, event.task_title) + self.assertEquals(task_in.type, event.task_type) + self.assertEquals("COMPLETED", event.task_state) + # Not sure what vodoo is happening inside of marshmallow to get me in this state. + if isinstance(task_in.multi_instance_type, MultiInstanceType): + self.assertEquals(task_in.multi_instance_type.value, event.mi_type) + else: + self.assertEquals(task_in.multi_instance_type, event.mi_type) + + self.assertEquals(task_in.multi_instance_count, event.mi_count) + self.assertEquals(task_in.multi_instance_index, event.mi_index) + self.assertEquals(task_in.process_name, event.process_name) + self.assertIsNotNone(event.date) + + # Assure that there is data in the form_data + self.assertIsNotNone(event.form_data) + + workflow = WorkflowApiSchema().load(json_data) + return workflow + + def test_get_current_user_tasks(self): self.load_example_data() workflow = self.create_workflow('random_fact') @@ -299,13 +371,13 @@ class TestTasksApi(BaseTest): self.assertEqual("UserTask", task.type) self.assertEqual("Activity_A", task.name) self.assertEqual("My Sub Process", task.process_name) - workflow_api = self.complete_form(workflow, task, {"name": "Dan"}) + workflow_api = self.complete_form(workflow, task, {"FieldA": "Dan"}) task = workflow_api.next_task self.assertIsNotNone(task) self.assertEqual("Activity_B", task.name) self.assertEqual("Sub Workflow Example", task.process_name) - workflow_api = self.complete_form(workflow, task, {"name": "Dan"}) + workflow_api = self.complete_form(workflow, task, {"FieldB": "Dan"}) self.assertEqual(WorkflowStatus.complete, workflow_api.status) def test_update_task_resets_token(self): @@ -373,7 +445,9 @@ class TestTasksApi(BaseTest): for i in random.sample(range(9), 9): task = TaskSchema().load(ready_items[i]['task']) - self.complete_form(workflow, task, {"investigator":{"email": "dhf8r@virginia.edu"}}) + data = workflow_api.next_task.data + data['investigator']['email'] = "dhf8r@virginia.edu" + self.complete_form(workflow, task, data) #tasks = self.get_workflow_api(workflow).user_tasks workflow = self.get_workflow_api(workflow) diff --git a/tests/workflow/test_workflow_processor.py b/tests/workflow/test_workflow_processor.py index b3f6c374..30f9150b 100644 --- a/tests/workflow/test_workflow_processor.py +++ b/tests/workflow/test_workflow_processor.py @@ -270,53 +270,6 @@ class TestWorkflowProcessor(BaseTest): processor = self.get_processor(study, workflow_spec_model) self.assertTrue(processor.get_version_string().startswith('v2.1.1')) - def test_restart_workflow(self): - self.load_example_data() - study = session.query(StudyModel).first() - workflow_spec_model = self.load_test_spec("two_forms") - processor = self.get_processor(study, workflow_spec_model) - self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id) - task = processor.next_task() - task.data = {"key": "Value"} - processor.complete_task(task) - task_before_restart = processor.next_task() - processor.hard_reset() - task_after_restart = processor.next_task() - - self.assertNotEqual(task.get_name(), task_before_restart.get_name()) - self.assertEqual(task.get_name(), task_after_restart.get_name()) - self.assertEqual(task.data, task_after_restart.data) - - def test_soft_reset(self): - self.load_example_data() - - # Start the two_forms workflow, and enter some data in the first form. - study = session.query(StudyModel).first() - workflow_spec_model = self.load_test_spec("two_forms") - processor = self.get_processor(study, workflow_spec_model) - self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id) - task = processor.next_task() - task.data = {"color": "blue"} - processor.complete_task(task) - - # Modify the specification, with a minor text change. - file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'two_forms', 'mods', 'two_forms_text_mod.bpmn') - self.replace_file("two_forms.bpmn", file_path) - - # Setting up another processor should not error out, but doesn't pick up the update. - processor.workflow_model.bpmn_workflow_json = processor.serialize() - processor2 = WorkflowProcessor(processor.workflow_model) - self.assertEqual("Step 1", processor2.bpmn_workflow.last_task.task_spec.description) - self.assertNotEqual("# This is some documentation I wanted to add.", - processor2.bpmn_workflow.last_task.task_spec.documentation) - - # You can do a soft update and get the right response. - processor3 = WorkflowProcessor(processor.workflow_model, soft_reset=True) - self.assertEqual("Step 1", processor3.bpmn_workflow.last_task.task_spec.description) - self.assertEqual("# This is some documentation I wanted to add.", - processor3.bpmn_workflow.last_task.task_spec.documentation) - - def test_hard_reset(self): self.load_example_data() @@ -344,8 +297,10 @@ class TestWorkflowProcessor(BaseTest): # Do a hard reset, which should bring us back to the beginning, but retain the data. processor3 = WorkflowProcessor(processor.workflow_model, hard_reset=True) self.assertEqual("Step 1", processor3.next_task().task_spec.description) - self.assertEqual({"color": "blue"}, processor3.next_task().data) - processor3.complete_task(processor3.next_task()) + self.assertTrue(processor3.is_latest_spec) # Now at version 2. + task = processor3.next_task() + task.data = {"color": "blue"} + processor3.complete_task(task) self.assertEqual("New Step", processor3.next_task().task_spec.description) self.assertEqual("blue", processor3.next_task().data["color"]) diff --git a/tests/workflow/test_workflow_service.py b/tests/workflow/test_workflow_service.py index 9f3ceda1..6b1b5c58 100644 --- a/tests/workflow/test_workflow_service.py +++ b/tests/workflow/test_workflow_service.py @@ -1,7 +1,14 @@ +import json + from tests.base_test import BaseTest from crc.services.workflow_processor import WorkflowProcessor from crc.services.workflow_service import WorkflowService +from SpiffWorkflow import Task as SpiffTask, WorkflowException +from example_data import ExampleDataLoader +from crc import db +from crc.models.stats import TaskEventModel +from crc.models.api_models import Task class TestWorkflowService(BaseTest): @@ -78,4 +85,50 @@ class TestWorkflowService(BaseTest): task = processor.next_task() task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True) WorkflowService.populate_form_with_random_data(task, task_api, required_only=False) - self.assertTrue(isinstance(task.data["sponsor"], dict)) \ No newline at end of file + self.assertTrue(isinstance(task.data["sponsor"], dict)) + + def test_fix_legacy_data_model_for_rrt(self): + ExampleDataLoader().load_rrt() # Make sure the research_rampup is loaded, as it's not a test spec. + workflow = self.create_workflow('research_rampup') + processor = WorkflowProcessor(workflow, validate_only=True) + + # Use the test spec code to complete the workflow of research rampup. + while not processor.bpmn_workflow.is_completed(): + processor.bpmn_workflow.do_engine_steps() + tasks = processor.bpmn_workflow.get_tasks(SpiffTask.READY) + for task in tasks: + task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True) + WorkflowService.populate_form_with_random_data(task, task_api, False) + task.complete() + # create the task events + WorkflowService.log_task_action('dhf8r', workflow, task, + WorkflowService.TASK_ACTION_COMPLETE, + version=processor.get_version_string()) + processor.save() + db.session.commit() + + WorkflowService.fix_legacy_data_model_for_rrt() + + # All tasks should now have data associated with them. + task_logs = db.session.query(TaskEventModel) \ + .filter(TaskEventModel.workflow_id == workflow.id) \ + .filter(TaskEventModel.action == WorkflowService.TASK_ACTION_COMPLETE) \ + .order_by(TaskEventModel.date).all() # Get them back in order. + + self.assertEqual(17, len(task_logs)) + for log in task_logs: + task = processor.bpmn_workflow.get_tasks_from_spec_name(log.task_name)[0] + self.assertIsNotNone(log.form_data) + # Each task should have the data in the form for that task in the task event. + if hasattr(task.task_spec, 'form'): + for field in task.task_spec.form.fields: + if field.has_property(Task.PROP_OPTIONS_REPEAT): + self.assertIn(field.get_property(Task.PROP_OPTIONS_REPEAT), log.form_data) + else: + self.assertIn(field.id, log.form_data) + + # Some spot checks: + # The first task should be empty, with all the data removed. + self.assertEqual({}, task_logs[0].form_data) + +