cr-connect-workflow/crc/models/approval.py

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import enum
import marshmallow
from marshmallow import INCLUDE
Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval Added the following columns: * date_created - so we know when the file was created * renamed workflow_version to just "version", because everything has a version, this is the version of the request. * workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out. * study - a quick relationship link to the study, so that this model is easier to use. * workflow - ditto * approval_files - these is a list from a new link table that links an approval to specific files and versions. The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram. Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as users modify their submission - adding new files or replacing existing ones. Deleting files worries me, and I will need to revisit this. The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently. Lots more tests around the file service to make sure it is versioning user uploaded files correctly. The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system. So it should just "do the right thing".
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from sqlalchemy import func
from ldap3.core.exceptions import LDAPSocketOpenError
from crc import db, ma
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from crc.api.common import ApiError
Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval Added the following columns: * date_created - so we know when the file was created * renamed workflow_version to just "version", because everything has a version, this is the version of the request. * workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out. * study - a quick relationship link to the study, so that this model is easier to use. * workflow - ditto * approval_files - these is a list from a new link table that links an approval to specific files and versions. The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram. Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as users modify their submission - adding new files or replacing existing ones. Deleting files worries me, and I will need to revisit this. The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently. Lots more tests around the file service to make sure it is versioning user uploaded files correctly. The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system. So it should just "do the right thing".
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from crc.models.file import FileModel
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowModel
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from crc.services.ldap_service import LdapService
class ApprovalStatus(enum.Enum):
WAITING = "WAITING" # no one has done jack.
APPROVED = "APPROVED" # approved by the reviewer
DECLINED = "DECLINED" # rejected by the reviewer
CANCELED = "CANCELED" # The document was replaced with a new version and this review is no longer needed.
Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval Added the following columns: * date_created - so we know when the file was created * renamed workflow_version to just "version", because everything has a version, this is the version of the request. * workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out. * study - a quick relationship link to the study, so that this model is easier to use. * workflow - ditto * approval_files - these is a list from a new link table that links an approval to specific files and versions. The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram. Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as users modify their submission - adding new files or replacing existing ones. Deleting files worries me, and I will need to revisit this. The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently. Lots more tests around the file service to make sure it is versioning user uploaded files correctly. The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system. So it should just "do the right thing".
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class ApprovalFile(db.Model):
id = db.Column(db.Integer, primary_key=True)
file_id = db.Column(db.Integer, db.ForeignKey(FileModel.id), nullable=False)
approval_id = db.Column(db.Integer, db.ForeignKey("approval.id"), nullable=False)
file_version = db.Column(db.Integer, nullable=False)
approval = db.relationship("ApprovalModel")
file = db.relationship(FileModel)
class ApprovalModel(db.Model):
__tablename__ = 'approval'
id = db.Column(db.Integer, primary_key=True)
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
study = db.relationship(StudyModel, backref='approval', cascade='all,delete')
workflow_id = db.Column(db.Integer, db.ForeignKey(WorkflowModel.id), nullable=False)
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workflow = db.relationship(WorkflowModel)
approver_uid = db.Column(db.String) # Not linked to user model, as they may not have logged in yet.
status = db.Column(db.String)
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message = db.Column(db.String, default='')
Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval Added the following columns: * date_created - so we know when the file was created * renamed workflow_version to just "version", because everything has a version, this is the version of the request. * workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out. * study - a quick relationship link to the study, so that this model is easier to use. * workflow - ditto * approval_files - these is a list from a new link table that links an approval to specific files and versions. The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram. Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as users modify their submission - adding new files or replacing existing ones. Deleting files worries me, and I will need to revisit this. The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently. Lots more tests around the file service to make sure it is versioning user uploaded files correctly. The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system. So it should just "do the right thing".
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date_created = db.Column(db.DateTime(timezone=True), default=func.now())
version = db.Column(db.Integer) # Incremented integer, so 1,2,3 as requests are made.
workflow_hash = db.Column(db.String) # A hash of the workflow at the moment the approval was created.
approval_files = db.relationship(ApprovalFile, back_populates="approval")
class Approval(object):
def __init__(self, **kwargs):
self.__dict__.update(kwargs)
@classmethod
def from_model(cls, model: ApprovalModel):
# TODO: Reduce the code by iterating over model's dict keys
instance = cls()
instance.id = model.id
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instance.study_id = model.study_id
instance.workflow_id = model.workflow_id
Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval Added the following columns: * date_created - so we know when the file was created * renamed workflow_version to just "version", because everything has a version, this is the version of the request. * workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out. * study - a quick relationship link to the study, so that this model is easier to use. * workflow - ditto * approval_files - these is a list from a new link table that links an approval to specific files and versions. The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram. Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as users modify their submission - adding new files or replacing existing ones. Deleting files worries me, and I will need to revisit this. The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently. Lots more tests around the file service to make sure it is versioning user uploaded files correctly. The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system. So it should just "do the right thing".
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instance.version = model.version
instance.approver_uid = model.approver_uid
instance.status = model.status
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instance.message = model.message
instance.date_created = model.date_created
instance.version = model.version
instance.workflow_hash = model.workflow_hash
instance.title = ''
if model.study:
instance.title = model.study.title
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instance.approver = {}
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try:
ldap_service = LdapService()
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principal_investigator_id = model.study.primary_investigator_id
user_info = ldap_service.user_info(principal_investigator_id)
except (ApiError, LDAPSocketOpenError) as exception:
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user_info = None
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instance.approver['display_name'] = 'Primary Investigator details'
instance.approver['department'] = 'currently not available'
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if user_info:
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# TODO: Rename approver to primary investigator
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instance.approver['uid'] = model.approver_uid
instance.approver['display_name'] = user_info.display_name
instance.approver['title'] = user_info.title
instance.approver['department'] = user_info.department
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instance.associated_files = []
for approval_file in model.approval_files:
associated_file = {}
associated_file['id'] = approval_file.file.id
associated_file['name'] = approval_file.file.name
associated_file['content_type'] = approval_file.file.content_type
instance.associated_files.append(associated_file)
return instance
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def update_model(self, approval_model: ApprovalModel):
approval_model.status = self.status
approval_model.message = self.message
class ApprovalSchema(ma.Schema):
class Meta:
model = Approval
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fields = ["id", "study_id", "workflow_id", "version", "title",
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"version", "status", "message", "approver", "associated_files"]
unknown = INCLUDE
@marshmallow.post_load
def make_approval(self, data, **kwargs):
"""Loads the basic approval data for updates to the database"""
return Approval(**data)
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# Carlos: Here is the data structure I was trying to imagine.
# If I were to continue down my current traing of thought, I'd create
# another class called just "Approval" that can take an ApprovalModel from the
# database and construct a data structure like this one, that can
# be provided to the API at an /approvals endpoint with GET and PUT
# dat = { "approvals": [
# {"id": 1,
# "study_id": 20,
# "workflow_id": 454,
# "study_title": "Dan Funk (dhf8r)", # Really it's just the name of the Principal Investigator
# "workflow_version": "21",
# "approver": { # Pulled from ldap
# "uid": "bgb22",
# "display_name": "Billy Bob (bgb22)",
# "title": "E42:He's a hoopy frood",
# "department": "E0:EN-Eng Study of Parallel Universes",
# },
# "files": [
# {
# "id": 124,
# "name": "ResearchRestart.docx",
# "content_type": "docx-something-whatever"
# }
# ]
# }
# ...
# ]