def workflow(id=None, dn=None):
"""
Implementation of the /workflow route
Enforces ontological constraints on workflows types retrieved from ontology_terms.
/workflow?do_uri=:uri - GET workflows having dataobject member giving by :uid
"""
#Desperately need to add field error checking. Note, we have access to db.query_map
api_version, root_url, root = get_api_version(request.url)
if apidebug:
print('APIDEBUG: You are: %s' % str(dn))
print('APIDEBUG: workflow url request is %s' % request.url)
if request.method == 'POST':
#check for valid workflow type
wtype = json.loads(request.data).get('type')
ont_entry = rdb.getRecord('ontology_terms', {'path': '/Workflow/Type'},
dn)[0]
vocab = rdb.getRecord('ontology_terms',
{'parent_uid': ont_entry['uid']}, dn)
valid = tuple(x['name'] for x in vocab)
if (wtype in valid):
##Add logic to check for fields or exceptions from query
type_uid = ont_entry.get('uid')
p = json.loads(request.data)
payload = {
"name": p['name'],
"description": p['description'],
"type_uid": type_uid,
"value": wtype
}
r = rdb.addWorkflow(payload, dn=dn)
#should return ENTIRE record created. use rdb.getworkflow internally
else:
payload = {
"url": request.url,
"body": request.data,
"hint": valid,
"uid": -1
}
raise InvalidAPIUsage(message='Invalid workflow type specified',
status_code=400,
payload=payload)
elif request.method == 'GET':
if id:
darg = dict(request.args.items(multi=True) + [('uid', id)])
if apidebug:
print('APIDEBUG: darg is %s' % darg)
r = rdb.getWorkflow({'uid': id}, dn=dn)
else:
if 'do_uri' in request.args:
#find data object by uri
r = rdb.getRecord('dataobject',
{'uri': request.args['do_uri']},
dn=dn)
if len(r) == 1:
do_uid = r[0].get('uid')
#find dataobject instances based on do_uid
doi_list = rdb.getRecord('dataobject_instance',
{'do_uid': do_uid},
dn=dn)
result = []
for doi in doi_list:
result.append(
rdb.getWorkflow({'uid': doi['work_uid']},
dn=dn)[0])
r = {
'result': result,
'count': len(result),
'link-requested': request.url,
'status': 'ok'
}
else:
r = {'uid': '0', 'msg': 'not found'}
#general searches
else:
r = rdb.getWorkflow(request.args, dn=dn)
#add workflow type here in return. Use complete path?
if apidebug:
print('APIDEBUG: workflow returning "%s" len %d' % (
r,
len(r),
))
if apidebug:
print('APIDEBUG: workflow %s' % (r, ))
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=200)
def workflow(id=None, dn=None):
"""
Implementation of the /workflow route
Enforces ontological constraints on workflows types retrieved from ontology_terms.
/workflow?do_uri=:uri - GET workflows having dataobject member giving by :uid
"""
#Desperately need to add field error checking. Note, we have access to db.query_map
api_version,root_url,root=get_api_version(request.url)
if apidebug:
print ('APIDEBUG: You are: %s'% str(dn) )
print ('APIDEBUG: workflow url request is %s' %request.url)
if request.method == 'POST':
#check for valid workflow type
wtype = json.loads(request.data).get('type')
ont_entry = rdb.getRecord('ontology_terms', {'path':'/Workflow/Type'}, dn )[0]
vocab=rdb.getRecord('ontology_terms', {'parent_uid':ont_entry['uid']}, dn )
valid= tuple(x['name'] for x in vocab)
if (wtype in valid):
##Add logic to check for fields or exceptions from query
type_uid = ont_entry.get('uid')
p=json.loads(request.data)
payload={"name":p['name'],"description":p['description'],"type_uid":type_uid,"value":wtype}
r = rdb.addWorkflow(payload,dn=dn)
#should return ENTIRE record created. use rdb.getworkflow internally
else:
payload={"url":request.url, "body":request.data, "hint":valid, "uid":-1}
raise InvalidAPIUsage(message='Invalid workflow type specified',status_code=400,
payload=payload)
elif request.method == 'GET':
if id:
darg=dict(request.args.items(multi=True)+[('uid',id)])
if apidebug:
print('APIDEBUG: darg is %s' %darg)
r = rdb.getWorkflow({'uid':id},dn=dn)
else:
if 'do_uri' in request.args:
#find data object by uri
r = rdb.getRecord('dataobject',{'uri':request.args['do_uri']}, dn=dn)
if len(r)==1:
do_uid=r[0].get('uid')
#find dataobject instances based on do_uid
doi_list = rdb.getRecord('dataobject_instance',{'do_uid':do_uid}, dn=dn )
result=[]
for doi in doi_list:
result.append(rdb.getWorkflow({'uid':doi['work_uid']},dn=dn)[0])
r={'result':result,'count':len(result),'link-requested':request.url, 'status':'ok'}
else:
r={'uid':'0','msg':'not found'}
#general searches
else:
r = rdb.getWorkflow(request.args,dn=dn)
#add workflow type here in return. Use complete path?
if apidebug:
print ('APIDEBUG: workflow returning "%s" len %d'% (r,len(r),))
if apidebug:
print ('APIDEBUG: workflow %s'% (r,) )
return Response(json.dumps(r,cls=MPOSetEncoder),mimetype='application/json',status=200)
def collectionElement(id=None, oid=None, dn=None):
"""
/collection/:id/element - GET a list of objects in a collection
- POST to add to the collection
/collection/:id/element/:oid - GET details of a single object in a collection.
Should resolve oid to full record from relevant table.
/collection/:id/element?detail=full[sparse] - GET collection information with full
details [or default sparse as /collection/<id>]
"""
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
payload = json.loads(request.data)
#make sure the element hasn't been added to the collection already
#elems must be a list of uids that are not already in this collection, if it exists.
elems = payload.get('elements')
if elems:
if not isinstance(elems, list):
elements = [elems]
else:
elements = elems
else:
elements = []
#remove elements already in the collection
for e in elements[:]:
r = rdb.getRecord('collection_elements', {
'uid': e,
'parent_uid': id
},
dn=dn)
if len(r) != 0:
elements.remove(
e) #maybe add to response message this was done
payload['elements'] = elements
#add elements one and a time and create list of returned records
r = []
for e in elements:
rr = rdb.addRecord('collection_elements',
json.dumps({
'uid': e,
'parent_uid': id
}),
dn=dn)
r.append(rr)
morer = rdb.getRecord('collection_elements', {'uid': rr['uid']},
dn=dn)
publishEvent('mpo_collection_elements', onlyone(morer))
elif request.method == 'DELETE':
if oid:
r = rdb.deleteCollectionElement({
'parent_uid': id,
'uid': oid
},
dn=None)
else:
r = []
elif request.method == 'GET':
if oid:
r = rdb.getRecord('collection_elements', {
'parent_uid': id,
'uid': oid
},
dn=dn)
else:
r = rdb.getRecord('collection_elements', {'parent_uid': id}, dn=dn)
#Find original item and add it to record.
for record in r:
print('collection element r', record)
r_uid = record['uid']
#getRecordTable returns a python dict
record['type'] = rdb.getRecordTable(r_uid, dn=dn)
#set default field values
detail = {
'related': 'not sure',
'link-related': root_url,
'related': 'cousins',
'name': 'what is this?',
'description': 'empty',
'time': 'nowhen'
}
#Translation for specific types
if record['type'] == 'workflow':
detail = rdb.getWorkflow({'uid': r_uid}, dn=dn)[0]
print('element workflow', detail)
detail['related'] = rdb.getWorkflowCompositeID(
r_uid, dn=dn).get('alias')
links = {}
links['link1'] = root_url + '/workflow/' + r_uid
links['link2'] = root_url + '/workflow?alias=' + detail[
'related']
detail['link-related'] = links
elif record['type'] == 'dataobject':
detail = rdb.getRecord('dataobject', {'uid': r_uid}, dn=dn)[0]
detail['related'] = detail.get('uri')
detail['link-related'] = root_url + '/dataobject/' + r_uid
elif record['type'] == 'dataobject_instance':
do_uid = (rdb.getRecord('dataobject_instance',
{'uid': record['uid']},
dn=dn)[0]).get('do_uid')
detail = rdb.getRecord('dataobject', {'uid': do_uid}, dn=dn)[0]
detail['related'] = detail.get('uri')
detail['link-related'] = root_url + '/dataobject/' + do_uid
elif record['type'] == 'collection':
thisdetail = rdb.getRecord('collection', {'uid': r_uid},
dn=dn)[0]
detail['related'] = None
detail[
'link-related'] = root_url + '/collection/' + r_uid + '/element'
detail['description'] = thisdetail.get('description')
detail['name'] = thisdetail.get('name')
detail['time'] = thisdetail.get('time')
record['name'] = detail['name']
record['description'] = detail['description']
record['time'] = detail['time']
record['related'] = detail['related']
record['link-related'] = detail['link-related']
istatus = 200
# if len(r) == 0:
# #istatus = 404
# r=[{'mesg':'No records found', 'number_of_records':0, 'status':404}]
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=istatus)
def collectionElement(id=None, oid=None, dn=None):
"""
/collection/:id/element - GET a list of objects in a collection
- POST to add to the collection
/collection/:id/element/:oid - GET details of a single object in a collection.
Should resolve oid to full record from relevant table.
/collection/:id/element?detail=full[sparse] - GET collection information with full
details [or default sparse as /collection/<id>]
"""
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
payload = json.loads(request.data)
#make sure the element hasn't been added to the collection already
#elems must be a list of uids that are not already in this collection, if it exists.
elems = payload.get('elements')
if elems:
if not isinstance(elems,list):
elements=[elems]
else:
elements=elems
else:
elements=[]
#remove elements already in the collection
for e in elements[:]:
r = rdb.getRecord('collection_elements',{'uid':e,'parent_uid':id}, dn=dn)
if len(r)!=0: elements.remove(e) #maybe add to response message this was done
payload['elements'] = elements
#add elements one and a time and create list of returned records
r=[]
for e in elements:
rr=rdb.addRecord('collection_elements',json.dumps({'uid':e,'parent_uid':id}),dn=dn)
r.append(rr)
morer = rdb.getRecord('collection_elements',{'uid':rr['uid']},dn=dn)
publishEvent('mpo_collection_elements',onlyone(morer))
elif request.method == 'DELETE':
if oid:
r = rdb.deleteCollectionElement({'parent_uid':id,'uid':oid}, dn=None)
else:
r = []
elif request.method == 'GET':
if oid:
r = rdb.getRecord('collection_elements',{'parent_uid':id,'uid':oid}, dn=dn)
else:
r = rdb.getRecord('collection_elements',{'parent_uid':id}, dn=dn)
#Find original item and add it to record.
for record in r:
print ('collection element r',record)
r_uid=record['uid']
#getRecordTable returns a python dict
record['type']=rdb.getRecordTable( r_uid, dn=dn )
#set default field values
detail={'related':'not sure','link-related':root_url,'related':'cousins',
'name':'what is this?','description':'empty','time':'nowhen'}
#Translation for specific types
if record['type']=='workflow':
detail=rdb.getWorkflow({'uid':r_uid},dn=dn)[0]
print('element workflow',detail)
detail['related']=rdb.getWorkflowCompositeID(r_uid,dn=dn).get('alias')
links={}
links['link1']=root_url+'/workflow/'+r_uid
links['link2']=root_url+'/workflow?alias='+detail['related']
detail['link-related']=links
elif record['type']=='dataobject':
detail=rdb.getRecord('dataobject',{'uid':r_uid},dn=dn)[0]
detail['related']=detail.get('uri')
detail['link-related']=root_url+'/dataobject/'+r_uid
elif record['type']=='dataobject_instance':
do_uid=(rdb.getRecord('dataobject_instance',{'uid':record['uid']},dn=dn)[0]).get('do_uid')
detail=rdb.getRecord('dataobject',{'uid':do_uid},dn=dn)[0]
detail['related']=detail.get('uri')
detail['link-related']=root_url+'/dataobject/'+do_uid
elif record['type']=='collection':
thisdetail=rdb.getRecord('collection',{'uid':r_uid},dn=dn)[0]
detail['related']=None
detail['link-related']=root_url+'/collection/'+r_uid+'/element'
detail['description']=thisdetail.get('description')
detail['name']=thisdetail.get('name')
detail['time']=thisdetail.get('time')
record['name']=detail['name']
record['description']=detail['description']
record['time']=detail['time']
record['related']=detail['related']
record['link-related']=detail['link-related']
istatus=200
# if len(r) == 0:
# #istatus = 404
# r=[{'mesg':'No records found', 'number_of_records':0, 'status':404}]
return Response(json.dumps(r,cls=MPOSetEncoder),mimetype='application/json',status=istatus)