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cr-connect-workflow
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Merge branch 'dev' into bug/navigation

This commit is contained in:
Dan 2020-12-14 11:46:44 -05:00
parent bcb78de225 4268d0f482
commit 1f9bf72c59
14 changed files with 1207 additions and 51 deletions
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8
config/default.py
View File

@ -6,6 +6,14 @@ basedir = os.path.abspath(os.path.dirname(__file__))
JSON_SORT_KEYS = False # CRITICAL. Do not sort the data when returning values to the front end.
# The API_TOKEN is used to ensure that the
# workflow synch can work without a lot of
# back and forth.
# you may want to change this to something simple for testing!!
# NB, if you change this in the local endpoint,
# it needs to be changed in the remote endpoint as well
API_TOKEN = environ.get('API_TOKEN', default = 'af95596f327c9ecc007b60414fc84b61')
NAME = "CR Connect Workflow"
FLASK_PORT = environ.get('PORT0') or environ.get('FLASK_PORT', default="5000")
CORS_ALLOW_ORIGINS = re.split(r',\s*', environ.get('CORS_ALLOW_ORIGINS', default="localhost:4200, localhost:5002"))

310
crc/api.yml
View File

@ -100,6 +100,200 @@ paths:
type: array
items:
$ref: "#/components/schemas/Study"
/workflow_sync/pullall:
get:
operationId: crc.api.workflow_sync.sync_all_changed_workflows
summary: Sync all workflows that have changed on the remote side and provide a list of the results
security:
- ApiKeyAuth : []
# in the endpoint
parameters:
- name: remote
in: query
required: true
description: The remote endpoint
schema:
type: string
tags:
- Workflow Sync API
responses:
'200':
description: An array of workflow specs that were synced from remote.
content:
application/json:
schema:
type: array
items:
type: string
example : ['top_level_workflow','3b495037-f7d4-4509-bf58-cee41c0c6b0e']
/workflow_sync/diff:
get:
operationId: crc.api.workflow_sync.get_changed_workflows
summary: Provides a list of workflow that differ from remote and if it is new or not
security :
- ApiKeyAuth : []
# in the endpoint
parameters:
- name: remote
in: query
required: true
description: The remote endpoint
schema:
type: string
tags:
- Workflow Sync API
responses:
'200':
description: An array of workflow specs, with last touched date and which one is most recent.
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpecDiffList"
/workflow_sync/{workflow_spec_id}/spec:
parameters:
- name: workflow_spec_id
in: path
required: false
description: The unique id of an existing workflow specification to modify.
schema:
type: string
get:
operationId: crc.api.workflow_sync.get_sync_workflow_specification
summary: Returns a single workflow specification
security:
- ApiKeyAuth: []
tags:
- Workflow Sync API
responses:
'200':
description: Workflow specification.
content:
application/json:
schema:
$ref: "#/components/schemas/WorkflowSpec"
/workflow_sync/{workflow_spec_id}/files:
get:
operationId: crc.api.workflow_sync.get_workflow_spec_files
summary: Provides a list of files for a workflow spec on this machine.
security :
- ApiKeyAuth : []
parameters:
- name: workflow_spec_id
in: path
required: true
description: The workflow_spec id
schema:
type: string
tags:
- Workflow Sync API
responses:
'200':
description: An array of files for a workflow spec on the local system, with details.
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpecFilesList"
/workflow_sync/{workflow_spec_id}/files/sync:
get:
operationId: crc.api.workflow_sync.sync_changed_files
summary: Syncs files from a workflow on a remote system and provides a list of files that were updated
security :
- ApiKeyAuth : []
parameters:
- name: workflow_spec_id
in: path
required: true
description: The workflow_spec id
schema:
type: string
- name: remote
in: query
required: true
description: The remote endpoint
schema:
type: string
tags:
- Workflow Sync API
responses:
'200':
description: A list of files that were synced for the workflow.
content:
application/json:
schema:
type: array
items:
type : string
example : ["data_security_plan.dmn",'some_other_file.xml']
/workflow_sync/{workflow_spec_id}/files/diff:
get:
operationId: crc.api.workflow_sync.get_changed_files
summary: Provides a list of files for a workflow specs that differ from remote and their signature.
security :
- ApiKeyAuth : []
parameters:
- name: workflow_spec_id
in: path
required: true
description: The workflow_spec id
schema:
type: string
- name: remote
in: query
required: true
description: The remote endpoint
schema:
type: string
tags:
- Workflow Sync API
responses:
'200':
description: An array of files that are different from remote, with last touched date and file signature.
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpecFilesDiff"
/workflow_sync/all:
get:
operationId: crc.api.workflow_sync.get_all_spec_state
summary: Provides a list of workflow specs, last update date and thumbprint
security:
- ApiKeyAuth : []
tags:
- Workflow Sync API
responses:
'200':
description: An array of workflow specs, with last touched date and file signature.
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpecAll"
/study/all:
get:
operationId: crc.api.study.all_studies
@ -474,6 +668,30 @@ paths:
responses:
'204':
description: The file has been removed.
/file/{md5_hash}/hash_data:
parameters:
- name: md5_hash
in: path
required: true
description: The md5 hash of the file requested
schema:
type: string
get:
operationId: crc.api.file.get_file_data_by_hash
summary: Returns only the file contents
security:
- ApiKeyAuth: []
tags:
- Files
responses:
'200':
description: Returns the actual file
content:
application/octet-stream:
schema:
type: string
format: binary
example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
/file/{file_id}/data:
parameters:
- name: file_id
@ -1154,6 +1372,12 @@ components:
scheme: bearer
bearerFormat: JWT
x-bearerInfoFunc: crc.api.user.verify_token_admin
ApiKeyAuth :
type : apiKey
in : header
name : X-CR-API-KEY
x-apikeyInfoFunc: crc.api.workflow_sync.verify_token
schemas:
User:
properties:
@ -1177,6 +1401,92 @@ components:
properties:
id:
type: string
WorkflowSpecDiffList:
properties:
workflow_spec_id:
type: string
example : top_level_workflow
date_created :
type: string
example : 2020-12-09 16:55:12.951500+00:00
location :
type : string
example : remote
new :
type : boolean
example : false
WorkflowSpecFilesList:
properties:
file_model_id:
type : integer
example : 171
workflow_spec_id :
type: string
example : top_level_workflow
filename :
type: string
example : data_security_plan.dmn
date_created :
type: string
example : 2020-12-01 13:58:12.420333+00:00
type:
type : string
example : dmn
primary :
type : boolean
example : false
content_type:
type: string
example : text/xml
primary_process_id:
type : string
example : null
md5_hash:
type: string
example: f12e2bbd-a20c-673b-ccb8-a8a1ea9c5b7b
WorkflowSpecFilesDiff:
properties:
filename :
type: string
example : data_security_plan.dmn
date_created :
type: string
example : 2020-12-01 13:58:12.420333+00:00
type:
type : string
example : dmn
primary :
type : boolean
example : false
content_type:
type: string
example : text/xml
primary_process_id:
type : string
example : null
md5_hash:
type: string
example: f12e2bbd-a20c-673b-ccb8-a8a1ea9c5b7b
location:
type : string
example : remote
new:
type: boolean
example : false
WorkflowSpecAll:
properties:
workflow_spec_id :
type: string
example : acaf1258-43b4-437e-8846-f612afa66811
date_created :
type: string
example : 2020-12-01 13:58:12.420333+00:00
md5_hash:
type: string
example: c30fd597f21715018eab12f97f9d4956
Study:
properties:
id:

5
crc/api/file.py
View File

@ -6,7 +6,7 @@ from flask import send_file
from crc import session
from crc.api.common import ApiError
from crc.models.file import FileSchema, FileModel, File, FileModelSchema
from crc.models.file import FileSchema, FileModel, File, FileModelSchema, FileDataModel
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
@ -99,6 +99,9 @@ def update_file_data(file_id):
file_model = FileService.update_file(file_model, file.stream.read(), file.content_type)
return FileSchema().dump(to_file_api(file_model))
def get_file_data_by_hash(md5_hash):
filedatamodel = session.query(FileDataModel).filter(FileDataModel.md5_hash == md5_hash).first()
return get_file_data(filedatamodel.file_model_id,version=filedatamodel.version)
def get_file_data(file_id, version=None):
file_data = FileService.get_file_data(file_id, version)

313
crc/api/workflow_sync.py Normal file
View File

@ -0,0 +1,313 @@
import hashlib
import json
import pandas as pd
import requests
from crc import session, app
from crc.api.common import ApiError
from crc.models.file import FileModel, FileDataModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel
from crc.services.file_service import FileService
from crc.services.workflow_sync import WorkflowSyncService
from crc.api.workflow import get_workflow_specification
def get_sync_workflow_specification(workflow_spec_id):
return get_workflow_specification(workflow_spec_id)
def join_uuids(uuids):
"""Joins a pandas Series of uuids and combines them in one hash"""
combined_uuids = ''.join([str(uuid) for uuid in uuids.sort_values()]) # ensure that values are always
# in the same order
return hashlib.md5(combined_uuids.encode('utf8')).hexdigest() # make a hash of the hashes
def verify_token(token, required_scopes):
if token == app.config['API_TOKEN']:
return {'scope':['any']}
else:
raise ApiError("permission_denied", "API Token information is not correct")
def get_changed_workflows(remote,as_df=False):
"""
gets a remote endpoint - gets the workflows and then
determines what workflows are different from the remote endpoint
"""
remote_workflows_list = WorkflowSyncService.get_all_remote_workflows(remote)
remote_workflows = pd.DataFrame(remote_workflows_list)
# get the local thumbprints & make sure that 'workflow_spec_id' is a column, not an index
local = get_all_spec_state_dataframe().reset_index()
# merge these on workflow spec id and hash - this will
# make two different date columns date_x and date_y
different = remote_workflows.merge(local,
right_on=['workflow_spec_id','md5_hash'],
left_on=['workflow_spec_id','md5_hash'],
how = 'outer' ,
indicator=True).loc[lambda x : x['_merge']!='both']
if len(different)==0:
return []
# each line has a tag on it - if was in the left or the right,
# label it so we know if that was on the remote or local machine
different.loc[different['_merge']=='left_only','location'] = 'remote'
different.loc[different['_merge']=='right_only','location'] = 'local'
# this takes the different date_created_x and date-created_y columns and
# combines them back into one date_created column
index = different['date_created_x'].isnull()
different.loc[index,'date_created_x'] = different[index]['date_created_y']
different = different[['workflow_spec_id','date_created_x','location']].copy()
different.columns=['workflow_spec_id','date_created','location']
# our different list will have multiple entries for a workflow if there is a version on either side
# we want to grab the most recent one, so we sort and grab the most recent one for each workflow
changedfiles = different.sort_values('date_created',ascending=False).groupby('workflow_spec_id').first()
# get an exclusive or list of workflow ids - that is we want lists of files that are
# on one machine or the other, but not both
remote_spec_ids = remote_workflows[['workflow_spec_id']]
local_spec_ids = local[['workflow_spec_id']]
left = remote_spec_ids[~remote_spec_ids['workflow_spec_id'].isin(local_spec_ids['workflow_spec_id'])]
right = local_spec_ids[~local_spec_ids['workflow_spec_id'].isin(remote_spec_ids['workflow_spec_id'])]
# flag files as new that are only on the remote box and remove the files that are only on the local box
changedfiles['new'] = False
changedfiles.loc[changedfiles.index.isin(left['workflow_spec_id']), 'new'] = True
output = changedfiles[~changedfiles.index.isin(right['workflow_spec_id'])]
# return the list as a dict, let swagger convert it to json
if as_df:
return output
else:
return output.reset_index().to_dict(orient='records')
def sync_all_changed_workflows(remote):
workflowsdf = get_changed_workflows(remote,as_df=True)
if len(workflowsdf) ==0:
return []
workflows = workflowsdf.reset_index().to_dict(orient='records')
for workflow in workflows:
sync_changed_files(remote,workflow['workflow_spec_id'])
return [x['workflow_spec_id'] for x in workflows]
def sync_changed_files(remote,workflow_spec_id):
# make sure that spec is local before syncing files
specdict = WorkflowSyncService.get_remote_workflow_spec(remote,workflow_spec_id)
localspec = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.id == workflow_spec_id).first()
if localspec is None:
localspec = WorkflowSpecModel()
localspec.id = workflow_spec_id
if specdict['category'] == None:
localspec.category = None
else:
localcategory = session.query(WorkflowSpecCategoryModel).filter(WorkflowSpecCategoryModel.name
== specdict['category']['name']).first()
if localcategory == None:
#category doesn't exist - lets make it
localcategory = WorkflowSpecCategoryModel()
localcategory.name = specdict['category']['name']
localcategory.display_name = specdict['category']['display_name']
localcategory.display_order = specdict['category']['display_order']
session.add(localcategory)
localspec.category = localcategory
localspec.display_order = specdict['display_order']
localspec.display_name = specdict['display_name']
localspec.name = specdict['name']
localspec.description = specdict['description']
session.add(localspec)
changedfiles = get_changed_files(remote,workflow_spec_id,as_df=True)
if len(changedfiles)==0:
return []
updatefiles = changedfiles[~((changedfiles['new']==True) & (changedfiles['location']=='local'))]
updatefiles = updatefiles.reset_index().to_dict(orient='records')
deletefiles = changedfiles[((changedfiles['new']==True) & (changedfiles['location']=='local'))]
deletefiles = deletefiles.reset_index().to_dict(orient='records')
for delfile in deletefiles:
currentfile = session.query(FileModel).filter(FileModel.workflow_spec_id==workflow_spec_id,
FileModel.name == delfile['filename']).first()
# it is more appropriate to archive the file than delete
# due to the fact that we might have workflows that are using the
# file data
currentfile.archived = True
session.add(currentfile)
for updatefile in updatefiles:
currentfile = session.query(FileModel).filter(FileModel.workflow_spec_id==workflow_spec_id,
FileModel.name == updatefile['filename']).first()
if not currentfile:
currentfile = FileModel()
currentfile.name = updatefile['filename']
currentfile.workflow_spec_id = workflow_spec_id
currentfile.date_created = updatefile['date_created']
currentfile.type = updatefile['type']
currentfile.primary = updatefile['primary']
currentfile.content_type = updatefile['content_type']
currentfile.primary_process_id = updatefile['primary_process_id']
session.add(currentfile)
content = WorkflowSyncService.get_remote_file_by_hash(remote,updatefile['md5_hash'])
FileService.update_file(currentfile,content,updatefile['type'])
session.commit()
return [x['filename'] for x in updatefiles]
def get_changed_files(remote,workflow_spec_id,as_df=False):
"""
gets a remote endpoint - gets the files for a workflow_spec on both
local and remote and determines what files have been change and returns a list of those
files
"""
remote_file_list = WorkflowSyncService.get_remote_workflow_spec_files(remote,workflow_spec_id)
remote_files = pd.DataFrame(remote_file_list)
# get the local thumbprints & make sure that 'workflow_spec_id' is a column, not an index
local = get_workflow_spec_files_dataframe(workflow_spec_id).reset_index()
local['md5_hash'] = local['md5_hash'].astype('str')
remote_files['md5_hash'] = remote_files['md5_hash'].astype('str')
different = remote_files.merge(local,
right_on=['filename','md5_hash'],
left_on=['filename','md5_hash'],
how = 'outer' ,
indicator=True).loc[lambda x : x['_merge']!='both']
if len(different) == 0:
if as_df:
return different
else:
return []
# each line has a tag on it - if was in the left or the right,
# label it so we know if that was on the remote or local machine
different.loc[different['_merge']=='left_only','location'] = 'remote'
different.loc[different['_merge']=='right_only','location'] = 'local'
# this takes the different date_created_x and date-created_y columns and
# combines them back into one date_created column
dualfields = ['date_created','type','primary','content_type','primary_process_id']
for merge in dualfields:
index = different[merge+'_x'].isnull()
different.loc[index,merge+'_x'] = different[index][merge+'_y']
fieldlist = [fld+'_x' for fld in dualfields]
different = different[ fieldlist + ['md5_hash','filename','location']].copy()
different.columns=dualfields+['md5_hash','filename','location']
# our different list will have multiple entries for a workflow if there is a version on either side
# we want to grab the most recent one, so we sort and grab the most recent one for each workflow
changedfiles = different.sort_values('date_created',ascending=False).groupby('filename').first()
# get an exclusive or list of workflow ids - that is we want lists of files that are
# on one machine or the other, but not both
remote_spec_ids = remote_files[['filename']]
local_spec_ids = local[['filename']]
left = remote_spec_ids[~remote_spec_ids['filename'].isin(local_spec_ids['filename'])]
right = local_spec_ids[~local_spec_ids['filename'].isin(remote_spec_ids['filename'])]
changedfiles['new'] = False
changedfiles.loc[changedfiles.index.isin(left['filename']), 'new'] = True
changedfiles.loc[changedfiles.index.isin(right['filename']),'new'] = True
changedfiles = changedfiles.replace({pd.np.nan: None})
# return the list as a dict, let swagger convert it to json
if as_df:
return changedfiles
else:
return changedfiles.reset_index().to_dict(orient='records')
def get_all_spec_state():
"""
Return a list of all workflow specs along with last updated date and a
thumbprint of all of the files that are used for that workflow_spec
Convert into a dict list from a dataframe
"""
df = get_all_spec_state_dataframe()
return df.reset_index().to_dict(orient='records')
def get_workflow_spec_files(workflow_spec_id):
"""
Return a list of all workflow specs along with last updated date and a
thumbprint of all of the files that are used for that workflow_spec
Convert into a dict list from a dataframe
"""
df = get_workflow_spec_files_dataframe(workflow_spec_id)
return df.reset_index().to_dict(orient='records')
def get_workflow_spec_files_dataframe(workflowid):
"""
Return a list of all files for a workflow_spec along with last updated date and a
hash so we can determine file differences for a changed workflow on a box.
Return a dataframe
"""
x = session.query(FileDataModel).join(FileModel).filter(FileModel.workflow_spec_id==workflowid)
# there might be a cleaner way of getting a data frome from some of the
# fields in the ORM - but this works OK
filelist = []
for file in x:
filelist.append({'file_model_id':file.file_model_id,
'workflow_spec_id': file.file_model.workflow_spec_id,
'md5_hash':file.md5_hash,
'filename':file.file_model.name,
'type':file.file_model.type.name,
'primary':file.file_model.primary,
'content_type':file.file_model.content_type,
'primary_process_id':file.file_model.primary_process_id,
'date_created':file.date_created})
if len(filelist) == 0:
return pd.DataFrame(columns=['file_model_id',
'workflow_spec_id',
'md5_hash',
'filename',
'type',
'primary',
'content_type',
'primary_process_id',
'date_created'])
df = pd.DataFrame(filelist).sort_values('date_created').groupby('file_model_id').last()
df['date_created'] = df['date_created'].astype('str')
return df
def get_all_spec_state_dataframe():
"""
Return a list of all workflow specs along with last updated date and a
thumbprint of all of the files that are used for that workflow_spec
Return a dataframe
"""
x = session.query(FileDataModel).join(FileModel)
# there might be a cleaner way of getting a data frome from some of the
# fields in the ORM - but this works OK
filelist = []
for file in x:
filelist.append({'file_model_id':file.file_model_id,
'workflow_spec_id': file.file_model.workflow_spec_id,
'md5_hash':file.md5_hash,
'filename':file.file_model.name,
'date_created':file.date_created})
df = pd.DataFrame(filelist)
# get a distinct list of file_model_id's with the most recent file_data retained
df = df.sort_values('date_created').drop_duplicates(['file_model_id'],keep='last').copy()
# take that list and then group by workflow_spec and retain the most recently touched file
# and make a consolidated hash of the md5_checksums - this acts as a 'thumbprint' for each
# workflow spec
df = df.groupby('workflow_spec_id').agg({'date_created':'max',
'md5_hash':join_uuids}).copy()
# get only the columns we are really interested in returning
df = df[['date_created','md5_hash']].copy()
# convert dates to string
df['date_created'] = df['date_created'].astype('str')
return df

2
crc/models/workflow.py
View File

@ -69,7 +69,7 @@ class WorkflowStatus(enum.Enum):
class WorkflowSpecDependencyFile(db.Model):
"""Connects a workflow to the version of the specification files it depends on to execute"""
"""Connects to a workflow to test the version of the specification files it depends on to execute"""
file_data_id = db.Column(db.Integer, db.ForeignKey(FileDataModel.id), primary_key=True)
workflow_id = db.Column(db.Integer, db.ForeignKey("workflow.id"), primary_key=True)

52
crc/services/workflow_sync.py Normal file
View File

@ -0,0 +1,52 @@
import json
from json import JSONDecodeError
from typing import List, Optional
import requests
from crc import app
from crc.api.common import ApiError
class WorkflowSyncService(object):
@staticmethod
def get_remote_file_by_hash(remote,md5_hash):
url = remote+'/v1.0/file/'+md5_hash+'/hash_data'
return WorkflowSyncService.__make_request(url,return_contents=True)
@staticmethod
def get_remote_workflow_spec_files(remote,workflow_spec_id):
url = remote+'/v1.0/workflow_sync/'+workflow_spec_id+'/files'
return WorkflowSyncService.__make_request(url)
@staticmethod
def get_remote_workflow_spec(remote, workflow_spec_id):
"""
this just gets the details of a workflow spec from the
remote side.
"""
url = remote+'/v1.0/workflow-sync/'+workflow_spec_id+'/spec'
return WorkflowSyncService.__make_request(url)
@staticmethod
def get_all_remote_workflows(remote):
url = remote + '/v1.0/workflow_sync/all'
return WorkflowSyncService.__make_request(url)
@staticmethod
def __make_request(url,return_contents=False):
try:
response = requests.get(url,headers={'X-CR-API-KEY':app.config['API_TOKEN']})
except:
raise ApiError("workflow_sync_error",response.text)
if response.ok and response.text:
if return_contents:
return response.content
else:
return json.loads(response.text)
else:
raise ApiError("workflow_sync_error",
"Received an invalid response from the protocol builder (status %s): %s when calling "
"url '%s'." %
(response.status_code, response.text, url))

95
deploy/requirements.txt
View File

@ -1,75 +1,76 @@
alabaster==0.7.12
alembic==1.4.2
amqp==2.5.2
alembic==1.4.3
aniso8601==8.0.0
attrs==19.3.0
babel==2.8.0
bcrypt==3.1.7
beautifulsoup4==4.9.1
billiard==3.6.3.0
attrs==20.3.0
babel==2.9.0
bcrypt==3.2.0
beautifulsoup4==4.9.3
blinker==1.4
celery==4.4.2
certifi==2020.4.5.1
cffi==1.14.0
certifi==2020.11.8
cffi==1.14.4
chardet==3.0.4
click==7.1.2
clickclick==1.2.2
clickclick==20.10.2
commonmark==0.9.1
configparser==5.0.0
connexion==2.7.0
coverage==5.1
coverage==5.3
deprecated==1.2.10
docutils==0.16
docxtpl==0.9.2
docxtpl==0.11.2
et-xmlfile==1.0.1
flask==1.1.2
flask-admin==1.5.7
flask-bcrypt==0.7.1
flask-cors==3.0.8
flask-marshmallow==0.12.0
flask-cors==3.0.9
flask-mail==0.9.1
flask-marshmallow==0.14.0
flask-migrate==2.5.3
flask-restful==0.3.8
flask-sqlalchemy==2.4.1
flask-sso==0.4.0
future==0.18.2
httpretty==1.0.2
idna==2.9
flask-sqlalchemy==2.4.4
gunicorn==20.0.4
httpretty==1.0.3
idna==2.10
imagesize==1.2.0
importlib-metadata==1.6.0
inflection==0.4.0
inflection==0.5.1
itsdangerous==1.1.0
jdcal==1.4.1
jinja2==2.11.2
jsonschema==3.2.0
kombu==4.6.8
ldap3==2.7
lxml==4.5.1
mako==1.1.2
ldap3==2.8.1
lxml==4.6.2
mako==1.1.3
markdown==3.3.3
markupsafe==1.1.1
marshmallow==3.6.0
marshmallow==3.9.1
marshmallow-enum==1.5.1
marshmallow-sqlalchemy==0.23.0
numpy==1.18.4
openapi-spec-validator==0.2.8
openpyxl==3.0.3
marshmallow-sqlalchemy==0.24.1
numpy==1.19.4
openapi-spec-validator==0.2.9
openpyxl==3.0.5
packaging==20.4
pandas==1.0.3
psycopg2-binary==2.8.5
pandas==1.1.4
psycopg2-binary==2.8.6
pyasn1==0.4.8
pycparser==2.20
pygments==2.6.1
pygithub==1.53
pygments==2.7.2
pyjwt==1.7.1
pyparsing==2.4.7
pyrsistent==0.16.0
pyrsistent==0.17.3
python-box==5.2.0
python-dateutil==2.8.1
python-docx==0.8.10
python-editor==1.0.4
pytz==2020.1
python-levenshtein==0.12.0
pytz==2020.4
pyyaml==5.3.1
recommonmark==0.6.0
requests==2.23.0
six==1.14.0
requests==2.25.0
sentry-sdk==0.14.4
six==1.15.0
snowballstemmer==2.0.0
soupsieve==2.0.1
sphinx==3.0.3
sphinx==3.3.1
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==1.0.3
@ -77,14 +78,14 @@ sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.4
spiffworkflow
sqlalchemy==1.3.17
swagger-ui-bundle==0.0.6
urllib3==1.25.9
vine==1.3.0
waitress==1.4.3
sqlalchemy==1.3.20
swagger-ui-bundle==0.0.8
urllib3==1.26.2
waitress==1.4.4
webob==1.8.6
webtest==2.0.35
werkzeug==1.0.1
wrapt==1.12.1
wtforms==2.3.3
xlrd==1.2.0
xlsxwriter==1.2.8
zipp==3.1.0
xlsxwriter==1.3.7

1
example_data.py
View File

@ -66,6 +66,7 @@ class ExampleDataLoader:
display_order=6
),
]
db.session.execute("select setval('workflow_spec_category_id_seq',7);")
db.session.add_all(categories)
db.session.commit()

8
tests/base_test.py
View File

@ -204,6 +204,14 @@ class BaseTest(unittest.TestCase):
data = myfile.read()
return data
@staticmethod
def workflow_sync_response(file_name):
filepath = os.path.join(app.root_path, '..', 'tests', 'data', 'workflow_sync_responses', file_name)
with open(filepath, 'rb') as myfile:
data = myfile.read()
return data
def assert_success(self, rv, msg=""):
try:
data = json.loads(rv.get_data(as_text=True))

200
tests/data/random_fact/random_fact2.bpmn Normal file
View File

@ -0,0 +1,200 @@
<?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="3.7.0">
<bpmn:process id="Process_SecondFact" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0c7wlth</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:userTask id="Task_User_Select_Type" name="Set Type" camunda:formKey="Get A Random Fun Fact">
<bpmn:documentation># h1 Heading 8-)
## h2 Heading
### h3 Heading
#### h4 Heading
##### h5 Heading
###### h6 Heading
## Horizontal Rules
___
---
***
## Typographic replacements
"double quotes" and 'single quotes'
## Emphasis
**This is bold text**
__This is bold text__
*This is italic text*
_This is italic text_
~~Strikethrough~~
## Blockquotes
&gt; Blockquotes can also be nested...
&gt;&gt; ...by using additional greater-than signs right next to each other...
&gt; &gt; &gt; ...or with spaces between arrows.
## Lists
Unordered
+ Create a list by starting a line with `+`, `-`, or `*`
+ Sub-lists are made by indenting 2 spaces:
- Marker character change forces new list start:
* Ac tristique libero volutpat at
+ Facilisis in pretium nisl aliquet
- Nulla volutpat aliquam velit
+ Very easy!
Ordered
1. Lorem ipsum dolor sit amet
2. Consectetur adipiscing elit
3. Integer molestie lorem at massa
1. You can use sequential numbers...
1. ...or keep all the numbers as `1.`
Start numbering with offset:
57. foo
1. bar
## Tables
| Option | Description |
| ------ | ----------- |
| data | path to data files to supply the data that will be passed into templates. |
| engine | engine to be used for processing templates. Handlebars is the default. |
| ext | extension to be used for dest files. |
Right aligned columns
| Option | Description |
| ------:| -----------:|
| data | path to data files to supply the data that will be passed into templates. |
| engine | engine to be used for processing templates. Handlebars is the default. |
| ext | extension to be used for dest files. |
## Links
[link text](http://dev.nodeca.com)
[link with title](http://nodeca.github.io/pica/demo/ "title text!")
Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
## Images
![Minion](https://octodex.github.com/images/minion.png)
![Stormtroopocat](https://octodex.github.com/images/stormtroopocat.jpg "The Stormtroopocat")</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="type" label="Type" type="enum" defaultValue="cat">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
<camunda:value id="norris" name="Chuck Norris" />
<camunda:value id="cat" name="Cat Fact" />
<camunda:value id="buzzword" name="Business Buzzword" />
</camunda:formField>
</camunda:formData>
<camunda:properties>
<camunda:property name="type" value="string" />
</camunda:properties>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0c7wlth</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0641sh6</bpmn:outgoing>
</bpmn:userTask>
<bpmn:scriptTask id="Task_Get_Fact_From_API" name="Display Fact">
<bpmn:documentation />
<bpmn:extensionElements>
<camunda:inputOutput>
<camunda:inputParameter name="Fact.type" />
</camunda:inputOutput>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0641sh6</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0t29gjo</bpmn:outgoing>
<bpmn:script>FactService = fact_service()</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0u1cgrf">
<bpmn:documentation># Great Job!
You have completed the random fact generator.
You chose to receive a random fact of the type: "{{type}}"
Your random fact is:
{{details}}</bpmn:documentation>
<bpmn:incoming>SequenceFlow_0t29gjo</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_0c7wlth" sourceRef="StartEvent_1" targetRef="Task_User_Select_Type" />
<bpmn:sequenceFlow id="SequenceFlow_0641sh6" sourceRef="Task_User_Select_Type" targetRef="Task_Get_Fact_From_API" />
<bpmn:sequenceFlow id="SequenceFlow_0t29gjo" sourceRef="Task_Get_Fact_From_API" targetRef="EndEvent_0u1cgrf" />
<bpmn:textAnnotation id="TextAnnotation_09fq7kh">
<bpmn:text>User sets the Fact.type to cat, norris, or buzzword</bpmn:text>
</bpmn:textAnnotation>
<bpmn:association id="Association_1cfasjp" sourceRef="Task_User_Select_Type" targetRef="TextAnnotation_09fq7kh" />
<bpmn:textAnnotation id="TextAnnotation_1234e5n">
<bpmn:text>Makes an API  call to get a fact of the required type.</bpmn:text>
</bpmn:textAnnotation>
<bpmn:association id="Association_1qirnyy" sourceRef="Task_Get_Fact_From_API" targetRef="TextAnnotation_1234e5n" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1ds61df">
<bpmndi:BPMNEdge id="SequenceFlow_0t29gjo_di" bpmnElement="SequenceFlow_0t29gjo">
<di:waypoint x="570" y="250" />
<di:waypoint x="692" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0641sh6_di" bpmnElement="SequenceFlow_0641sh6">
<di:waypoint x="370" y="250" />
<di:waypoint x="470" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0c7wlth_di" bpmnElement="SequenceFlow_0c7wlth">
<di:waypoint x="188" y="250" />
<di:waypoint x="270" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="152" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_186s7tw_di" bpmnElement="Task_User_Select_Type">
<dc:Bounds x="270" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0u1cgrf_di" bpmnElement="EndEvent_0u1cgrf">
<dc:Bounds x="692" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="TextAnnotation_09fq7kh_di" bpmnElement="TextAnnotation_09fq7kh">
<dc:Bounds x="330" y="116" width="99.99202297383536" height="68.28334396936822" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="TextAnnotation_1234e5n_di" bpmnElement="TextAnnotation_1234e5n">
<dc:Bounds x="570" y="120" width="100" height="68" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
<dc:Bounds x="470" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Association_1cfasjp_di" bpmnElement="Association_1cfasjp">
<di:waypoint x="344" y="210" />
<di:waypoint x="359" y="184" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Association_1qirnyy_di" bpmnElement="Association_1qirnyy">
<di:waypoint x="561" y="210" />
<di:waypoint x="584" y="188" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

104
tests/data/workflow_sync_responses/random_fact2.bpmn Normal file
View File

@ -0,0 +1,104 @@
<?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="3.7.0">
<bpmn:process id="Process_SecondFact" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0c7wlth</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:userTask id="Task_User_Select_Type" name="Set Type" camunda:formKey="Get A Random Fun Fact">
<bpmn:documentation># h1 Heading 8-)
NEW_FILE_ADDED
![Stormtroopocat](https://octodex.github.com/images/stormtroopocat.jpg "The Stormtroopocat")</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="type" label="Type" type="enum" defaultValue="cat">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
<camunda:value id="norris" name="Chuck Norris" />
<camunda:value id="cat" name="Cat Fact" />
<camunda:value id="buzzword" name="Business Buzzword" />
</camunda:formField>
</camunda:formData>
<camunda:properties>
<camunda:property name="type" value="string" />
</camunda:properties>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0c7wlth</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0641sh6</bpmn:outgoing>
</bpmn:userTask>
<bpmn:scriptTask id="Task_Get_Fact_From_API" name="Display Fact">
<bpmn:documentation />
<bpmn:extensionElements>
<camunda:inputOutput>
<camunda:inputParameter name="Fact.type" />
</camunda:inputOutput>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0641sh6</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0t29gjo</bpmn:outgoing>
<bpmn:script>FactService = fact_service()</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0u1cgrf">
<bpmn:documentation># Great Job!
You have completed the random fact generator.
You chose to receive a random fact of the type: "{{type}}"
Your random fact is:
{{details}}</bpmn:documentation>
<bpmn:incoming>SequenceFlow_0t29gjo</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_0c7wlth" sourceRef="StartEvent_1" targetRef="Task_User_Select_Type" />
<bpmn:sequenceFlow id="SequenceFlow_0641sh6" sourceRef="Task_User_Select_Type" targetRef="Task_Get_Fact_From_API" />
<bpmn:sequenceFlow id="SequenceFlow_0t29gjo" sourceRef="Task_Get_Fact_From_API" targetRef="EndEvent_0u1cgrf" />
<bpmn:textAnnotation id="TextAnnotation_09fq7kh">
<bpmn:text>User sets the Fact.type to cat, norris, or buzzword</bpmn:text>
</bpmn:textAnnotation>
<bpmn:association id="Association_1cfasjp" sourceRef="Task_User_Select_Type" targetRef="TextAnnotation_09fq7kh" />
<bpmn:textAnnotation id="TextAnnotation_1234e5n">
<bpmn:text>Makes an API  call to get a fact of the required type.</bpmn:text>
</bpmn:textAnnotation>
<bpmn:association id="Association_1qirnyy" sourceRef="Task_Get_Fact_From_API" targetRef="TextAnnotation_1234e5n" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1ds61df">
<bpmndi:BPMNEdge id="SequenceFlow_0t29gjo_di" bpmnElement="SequenceFlow_0t29gjo">
<di:waypoint x="570" y="250" />
<di:waypoint x="692" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0641sh6_di" bpmnElement="SequenceFlow_0641sh6">
<di:waypoint x="370" y="250" />
<di:waypoint x="470" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0c7wlth_di" bpmnElement="SequenceFlow_0c7wlth">
<di:waypoint x="188" y="250" />
<di:waypoint x="270" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="152" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_186s7tw_di" bpmnElement="Task_User_Select_Type">
<dc:Bounds x="270" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0u1cgrf_di" bpmnElement="EndEvent_0u1cgrf">
<dc:Bounds x="692" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="TextAnnotation_09fq7kh_di" bpmnElement="TextAnnotation_09fq7kh">
<dc:Bounds x="330" y="116" width="99.99202297383536" height="68.28334396936822" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="TextAnnotation_1234e5n_di" bpmnElement="TextAnnotation_1234e5n">
<dc:Bounds x="570" y="120" width="100" height="68" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
<dc:Bounds x="470" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Association_1cfasjp_di" bpmnElement="Association_1cfasjp">
<di:waypoint x="344" y="210" />
<di:waypoint x="359" y="184" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Association_1qirnyy_di" bpmnElement="Association_1qirnyy">
<di:waypoint x="561" y="210" />
<di:waypoint x="584" y="188" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

2
tests/files/test_files_api.py
View File

@ -46,7 +46,7 @@ class TestFilesApi(BaseTest):
content_type="application/json", headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(2, len(json_data))
self.assertEqual(3, len(json_data))
def test_create_file(self):

2
tests/study/test_study_api.py
View File

@ -165,7 +165,7 @@ class TestStudyApi(BaseTest):
self.assertEqual(study_event.comment, update_comment)
self.assertEqual(study_event.user_uid, self.test_uid)
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_investigators
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies

156
tests/test_workflow_sync.py Normal file
View File

@ -0,0 +1,156 @@
from unittest.mock import patch
from crc import db
from tests.base_test import BaseTest
from crc.api.workflow_sync import get_all_spec_state, \
get_changed_workflows, \
get_workflow_spec_files, \
get_changed_files, \
get_workflow_specification, \
sync_changed_files
from crc.models.workflow import WorkflowSpecModel
from datetime import datetime
from crc.services.file_service import FileService
class TestWorkflowSync(BaseTest):
@patch('crc.services.workflow_sync.WorkflowSyncService.get_all_remote_workflows')
def test_get_no_changes(self, mock_get):
self.load_example_data()
othersys = get_all_spec_state()
mock_get.return_value = othersys
response = get_changed_workflows('localhost:0000') # not actually used due to mock
self.assertIsNotNone(response)
self.assertEqual(response,[])
@patch('crc.services.workflow_sync.WorkflowSyncService.get_all_remote_workflows')
def test_remote_workflow_change(self, mock_get):
self.load_example_data()
othersys = get_all_spec_state()
othersys[1]['date_created'] = str(datetime.now())
othersys[1]['md5_hash'] = '12345'
mock_get.return_value = othersys
response = get_changed_workflows('localhost:0000') #endpoint is not used due to mock
self.assertIsNotNone(response)
self.assertEqual(len(response),1)
self.assertEqual(response[0]['workflow_spec_id'], 'random_fact')
self.assertEqual(response[0]['location'], 'remote')
self.assertEqual(response[0]['new'], False)
@patch('crc.services.workflow_sync.WorkflowSyncService.get_all_remote_workflows')
def test_remote_workflow_has_new(self, mock_get):
self.load_example_data()
othersys = get_all_spec_state()
othersys.append({'workflow_spec_id':'my_new_workflow',
'date_created':str(datetime.now()),
'md5_hash': '12345'})
mock_get.return_value = othersys
response = get_changed_workflows('localhost:0000') #endpoint is not used due to mock
self.assertIsNotNone(response)
self.assertEqual(len(response),1)
self.assertEqual(response[0]['workflow_spec_id'],'my_new_workflow')
self.assertEqual(response[0]['location'], 'remote')
self.assertEqual(response[0]['new'], True)
@patch('crc.services.workflow_sync.WorkflowSyncService.get_all_remote_workflows')
def test_local_workflow_has_new(self, mock_get):
self.load_example_data()
othersys = get_all_spec_state()
mock_get.return_value = othersys
wf_spec = WorkflowSpecModel()
wf_spec.id = 'abcdefg'
wf_spec.display_name = 'New Workflow - Yum!!'
wf_spec.name = 'my_new_workflow'
wf_spec.description = 'yep - its a new workflow'
wf_spec.category_id = 0
wf_spec.display_order = 0
db.session.add(wf_spec)
db.session.commit()
FileService.add_workflow_spec_file(wf_spec,'dummyfile.txt','text',b'this is a test')
# after setting up the test - I realized that this doesn't return anything for
# a workflow that is new locally - it just returns nothing
response = get_changed_workflows('localhost:0000') #endpoint is not used due to mock
self.assertIsNotNone(response)
self.assertEqual(response,[])
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_workflow_spec_files')
def test_file_differences(self, mock_get):
self.load_example_data()
othersys = get_workflow_spec_files('random_fact')
othersys[1]['date_created'] = str(datetime.now())
othersys[1]['md5_hash'] = '12345'
mock_get.return_value = othersys
response = get_changed_files('localhost:0000','random_fact',as_df=False) #endpoint is not used due to mock
self.assertIsNotNone(response)
self.assertEqual(len(response),1)
self.assertEqual(response[0]['filename'], 'random_fact2.bpmn')
self.assertEqual(response[0]['location'], 'remote')
self.assertEqual(response[0]['new'], False)
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_workflow_spec_files')
def test_file_differences(self, mock_get):
self.load_example_data()
othersys = get_workflow_spec_files('random_fact')
othersys[1]['date_created'] = str(datetime.now())
othersys[1]['md5_hash'] = '12345'
mock_get.return_value = othersys
response = get_changed_files('localhost:0000','random_fact',as_df=False) #endpoint is not used due to mock
self.assertIsNotNone(response)
self.assertEqual(len(response),1)
self.assertEqual(response[0]['filename'], 'random_fact2.bpmn')
self.assertEqual(response[0]['location'], 'remote')
self.assertEqual(response[0]['new'], False)
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_file_by_hash')
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_workflow_spec_files')
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_workflow_spec')
def test_file_differences(self, workflow_mock, spec_files_mock, file_data_mock):
self.load_example_data()
remote_workflow = get_workflow_specification('random_fact')
self.assertEqual(remote_workflow['display_name'],'Random Fact')
remote_workflow['description'] = 'This Workflow came from Remote'
remote_workflow['display_name'] = 'Remote Workflow'
workflow_mock.return_value = remote_workflow
othersys = get_workflow_spec_files('random_fact')
othersys[1]['date_created'] = str(datetime.now())
othersys[1]['md5_hash'] = '12345'
spec_files_mock.return_value = othersys
file_data_mock.return_value = self.workflow_sync_response('random_fact2.bpmn')
response = sync_changed_files('localhost:0000','random_fact') # endpoint not used due to mock
self.assertIsNotNone(response)
self.assertEqual(len(response),1)
self.assertEqual(response[0], 'random_fact2.bpmn')
files = FileService.get_spec_data_files('random_fact')
md5sums = [str(f.md5_hash) for f in files]
self.assertEqual('21bb6f9e-0af7-0ab2-0fc7-ec0f94787e58' in md5sums, True)
new_local_workflow = get_workflow_specification('random_fact')
self.assertEqual(new_local_workflow['display_name'],'Remote Workflow')
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_workflow_spec_files')
@patch('crc.services.workflow_sync.WorkflowSyncService.get_remote_workflow_spec')
def test_file_deleted(self, workflow_mock, spec_files_mock):
self.load_example_data()
remote_workflow = get_workflow_specification('random_fact')
workflow_mock.return_value = remote_workflow
othersys = get_workflow_spec_files('random_fact')
del(othersys[1])
spec_files_mock.return_value = othersys
response = sync_changed_files('localhost:0000','random_fact') # endpoint not used due to mock
self.assertIsNotNone(response)
# when we delete a local file, we do not return that it was deleted - just
# a list of updated files. We may want to change this in the future.
self.assertEqual(len(response),0)
files = FileService.get_spec_data_files('random_fact')
self.assertEqual(len(files),1)