def metadata(id=None, dn=None):
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
r = rdb.addMetadata(request.data, dn=dn)
id = r['uid']
morer = rdb.getRecord('metadata', {'uid': id}, dn=dn)
publishEvent('mpo_metadata', onlyone(morer))
elif request.method == 'GET':
#Add logic to parse id if comma separated
if id:
ids = id.strip().split(',')
r = {}
for id in ids:
rs = rdb.getRecord('metadata', {'uid': id}, dn=dn)
if len(rs) == 1:
r[id] = rs[0] #unpack single element list
else:
r[id] = [
] #{'uid':'0','msg':'invalid response','len':len(rs),'resp':rs}
if len(ids) == 1: #return just single record if one uid
r = rs
else:
r = r
else:
r = rdb.getRecord('metadata', request.args, dn=dn)
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json')
def ontologyInstance(id=None, dn=None):
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
r = rdb.addOntologyInstance(request.data,dn=dn)
elif request.method == 'PUT':
r = rdb.modifyOntologyInstance(request.data,dn=dn)
elif request.method == 'GET':
if id:
r = rdb.getRecord('ontology_instances', {'uid':id}, dn=dn )
else:
p_uids=request.args.get('parent_uid')
if p_uids:
p_uids=p_uids.strip().split(',')
r={}
rargs=request.args.to_dict() #multidict conversion to dict
for pid in p_uids:
rargs['parent_uid']=pid
rs = rdb.getRecord('ontology_instances', rargs, dn=dn )
r[pid]=rs #element list, can have multiple instances
if len(p_uids)==1: #return just single record if one uid
r=rs
else:
r = rdb.getRecord('ontology_instances', request.args, dn=dn )
return Response(json.dumps(r,cls=MPOSetEncoder), mimetype='application/json')
def collection(id=None,dn=None):
"""
Create and add to collections.
Supported routes:
/collection - GET a list of all (or filtered) collections
- POST a new collection
/collection/<id> - GET collection information, including list of member UUIDs
- DELETE a collection and the associated elements
/collection/?element_uid=:uid - GET collections having element member giving by :uid
"""
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
print('api post collection',request.data)
r = rdb.addCollection(request.data,dn=dn)
morer = rdb.getRecord('collection',{'uid':r['uid']},dn=dn)
publishEvent('mpo_collection',onlyone(morer))
elif request.method == 'GET':
if id:
r = rdb.getRecord('collection',{'uid':id}, dn=dn)
else:
#particular cases
#?element_uid
if 'element_uid' in request.args:
r = rdb.getRecord('collection_elements',{'uid':request.args['element_uid']}, dn=dn)
#general searches
else:
r = rdb.getRecord('collection',request.args, dn=dn)
elif request.method == 'DELETE':
if id:
r = rdb.deleteCollection({'uid':id}, dn=dn )
else:
r=[]
return Response(json.dumps(r,cls=MPOSetEncoder),mimetype='application/json',status=200)
def ontologyInstance(id=None, dn=None):
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
r = rdb.addOntologyInstance(request.data, dn=dn)
elif request.method == 'PUT':
r = rdb.modifyOntologyInstance(request.data, dn=dn)
elif request.method == 'GET':
if id:
r = rdb.getRecord('ontology_instances', {'uid': id}, dn=dn)
else:
p_uids = request.args.get('parent_uid')
if p_uids:
p_uids = p_uids.strip().split(',')
r = {}
rargs = request.args.to_dict() #multidict conversion to dict
for pid in p_uids:
rargs['parent_uid'] = pid
rs = rdb.getRecord('ontology_instances', rargs, dn=dn)
r[pid] = rs #element list, can have multiple instances
if len(p_uids) == 1: #return just single record if one uid
r = rs
else:
r = rdb.getRecord('ontology_instances', request.args, dn=dn)
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json')
def getWorkflowElement(wid, uid=None, dn=None):
"""
/workflow/:wid/dataobject/:uid - GET dataobjects in workflow specified by :wid
if :uid supplied, get specific dataobject
"""
api_version, root_url, root = get_api_version(request.url)
if uid:
records = rdb.getRecord('dataobject_instance', {
'work_uid': wid,
'uid': uid
},
dn=dn)
else:
records = rdb.getRecord('dataobject_instance', {'work_uid': wid},
dn=dn)
for rr in records:
do_uid = rr['do_uid']
rr['do_info'] = rdb.getRecord('dataobject', {'uid': do_uid}, dn=dn)[0]
r = {
'result': records,
'count': len(records),
'link-requested': request.url,
'status': 'ok'
}
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=200)
def activity(id=None, dn=None):
istatus=200
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
r = rdb.addRecord('activity',request.data,dn=dn)
id = r['uid']
morer = rdb.getRecord('activity',{'uid':id},dn=dn)
publishEvent('mpo_activity',onlyone(morer))
elif request.method == 'GET':
if id:
ids=id.strip().split(',')
r={}
for id in ids:
rs = rdb.getRecord('activity',{'uid':id},dn=dn)
if rs:
r[id]=rs
else:
r[id]=[]#{'uid':'0','msg':'invalid response','len':len(rs),'resp':rs}
if len(ids)==1: #return just single record if one uid
r=rs
else:
r = rdb.getRecord('activity',request.args,dn=dn)
#if r='[]', later set metadata with number of records
if len(r) == 2 :
istatus=404
return Response(json.dumps(r,cls=MPOSetEncoder), mimetype='application/json',status=istatus)
def ontologyTerm(id=None, dn=None):
'''
Retrieves the record of an ontology term from its <id> or path.
valid routes:
ontology/term/<id>
ontology/term?path=term/term2/termN
'''
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
objs = json.loads(request.data)
#allow for ontology terms with null parents
if not objs.has_key('parent_uid'): objs['parent_uid']=None
# make sure the term doesn't exist already
vocab = rdb.getRecord('ontology_terms', {'parent_uid':objs['parent_uid']}, dn=dn )
for x in vocab:
if objs['name'] == x['name']:
return Response(json.dumps({'uid':x['uid']}),mimetype='application/json')
r = rdb.addRecord('ontology_terms',json.dumps(objs),dn=dn)
elif request.method == 'DELETE':
if id:
r = rdb.deleteOntologyTerms({'uid':id}, dn=dn )
else:
r = rdb.deleteOntologyTerms(request.args, dn=dn )
else:
if id:
r = rdb.getRecord('ontology_terms', {'uid':id}, dn=dn )
else:
r = rdb.getRecord('ontology_terms', request.args, dn=dn )
return Response(json.dumps(r,cls=MPOSetEncoder),mimetype='application/json',status=200)
def metadata(id=None, dn=None):
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
r = rdb.addMetadata( request.data, dn=dn)
id = r['uid']
morer = rdb.getRecord('metadata',{'uid':id},dn=dn)
publishEvent('mpo_metadata',onlyone(morer))
elif request.method == 'GET':
#Add logic to parse id if comma separated
if id:
ids=id.strip().split(',')
r={}
for id in ids:
rs = rdb.getRecord('metadata',{'uid':id},dn=dn)
if len(rs)==1:
r[id]=rs[0] #unpack single element list
else:
r[id]=[]#{'uid':'0','msg':'invalid response','len':len(rs),'resp':rs}
if len(ids)==1: #return just single record if one uid
r=rs
else:
r=r
else:
r = rdb.getRecord('metadata',request.args,dn=dn)
return Response(json.dumps(r,cls=MPOSetEncoder), mimetype='application/json')
def activity(id=None, dn=None):
istatus = 200
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
r = rdb.addRecord('activity', request.data, dn=dn)
id = r['uid']
morer = rdb.getRecord('activity', {'uid': id}, dn=dn)
publishEvent('mpo_activity', onlyone(morer))
elif request.method == 'GET':
if id:
ids = id.strip().split(',')
r = {}
for id in ids:
rs = rdb.getRecord('activity', {'uid': id}, dn=dn)
if rs:
r[id] = rs
else:
r[id] = [
] #{'uid':'0','msg':'invalid response','len':len(rs),'resp':rs}
if len(ids) == 1: #return just single record if one uid
r = rs
else:
r = rdb.getRecord('activity', request.args, dn=dn)
#if r='[]', later set metadata with number of records
if len(r) == 2:
istatus = 404
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=istatus)
def getWorkflowElement(wid,uid=None,dn=None):
"""
/workflow/:wid/dataobject/:uid - GET dataobjects in workflow specified by :wid
if :uid supplied, get specific dataobject
"""
api_version,root_url,root=get_api_version(request.url)
if uid:
records = rdb.getRecord('dataobject_instance',{'work_uid':wid,'uid':uid}, dn=dn )
else:
records = rdb.getRecord('dataobject_instance',{'work_uid':wid}, dn=dn )
for rr in records:
do_uid=rr['do_uid']
rr['do_info']=rdb.getRecord('dataobject',{'uid':do_uid}, dn=dn )[0]
r={'result':records,'count':len(records),'link-requested':request.url, 'status':'ok'}
return Response(json.dumps(r,cls=MPOSetEncoder),mimetype='application/json',status=200)
def comment(id=None, dn=None):
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
req = json.loads(request.data)
req['ptype'] = rdb.getRecordTable(req['parent_uid'], dn=dn)
r = rdb.addRecord('comment', json.dumps(req), dn=dn)
id = r['uid']
if apidebug: print('APIDEBUG comment route:: dn = ', dn)
try: #JCW just being careful here on first implementation
morer = rdb.getRecord('comment', {'uid': id}, dn=dn)
except Exception as e:
import sys, os
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print('get comment exception', exc_type, fname, exc_tb.tb_lineno)
publishEvent('mpo_comment', onlyone(morer))
elif request.method == 'GET':
#Add logic to parse id if comma separated
if id:
ids = id.strip().split(',')
r = {}
for id in ids:
rs = rdb.getRecord('comment', {'uid': id}, dn=dn)
if len(rs) == 1:
r[id] = rs[0] #unpack single element list
else:
r[id] = [
] #{'uid':'0','msg':'invalid response','len':len(rs),'resp':rs}
if len(ids) == 1: #return just single record if one uid
r = rs
else:
r = r
else:
r = rdb.getRecord('comment', request.args, dn=dn)
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json')
def ontologyTerm(id=None, dn=None):
'''
Retrieves the record of an ontology term from its <id> or path.
valid routes:
ontology/term/<id>
ontology/term?path=term/term2/termN
'''
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
objs = json.loads(request.data)
#allow for ontology terms with null parents
if not objs.has_key('parent_uid'): objs['parent_uid'] = None
# make sure the term doesn't exist already
vocab = rdb.getRecord('ontology_terms',
{'parent_uid': objs['parent_uid']},
dn=dn)
for x in vocab:
if objs['name'] == x['name']:
return Response(json.dumps({'uid': x['uid']}),
mimetype='application/json')
r = rdb.addRecord('ontology_terms', json.dumps(objs), dn=dn)
elif request.method == 'DELETE':
if id:
r = rdb.deleteOntologyTerms({'uid': id}, dn=dn)
else:
r = rdb.deleteOntologyTerms(request.args, dn=dn)
else:
if id:
r = rdb.getRecord('ontology_terms', {'uid': id}, dn=dn)
else:
r = rdb.getRecord('ontology_terms', request.args, dn=dn)
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=200)
def comment(id=None, dn=None):
api_version,root_url,root=get_api_version(request.url)
if request.method == 'POST':
req = json.loads(request.data)
req['ptype']=rdb.getRecordTable(req['parent_uid'], dn=dn)
r = rdb.addRecord('comment',json.dumps(req),dn=dn)
id = r['uid']
if apidebug: print('APIDEBUG comment route:: dn = ',dn)
try: #JCW just being careful here on first implementation
morer = rdb.getRecord('comment',{'uid':id},dn=dn)
except Exception as e:
import sys,os
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print('get comment exception',exc_type, fname, exc_tb.tb_lineno)
publishEvent('mpo_comment',onlyone(morer))
elif request.method == 'GET':
#Add logic to parse id if comma separated
if id:
ids=id.strip().split(',')
r={}
for id in ids:
rs = rdb.getRecord('comment',{'uid':id},dn=dn)
if len(rs)==1:
r[id]=rs[0] #unpack single element list
else:
r[id]=[]#{'uid':'0','msg':'invalid response','len':len(rs),'resp':rs}
if len(ids)==1: #return just single record if one uid
r=rs
else:
r=r
else:
r = rdb.getRecord('comment',request.args,dn=dn)
return Response(json.dumps(r,cls=MPOSetEncoder), mimetype='application/json')
def collection(id=None, dn=None):
"""
Create and add to collections.
Supported routes:
/collection - GET a list of all (or filtered) collections
- POST a new collection
/collection/<id> - GET collection information, including list of member UUIDs
- DELETE a collection and the associated elements
/collection/?element_uid=:uid - GET collections having element member giving by :uid
"""
api_version, root_url, root = get_api_version(request.url)
if request.method == 'POST':
print('api post collection', request.data)
r = rdb.addCollection(request.data, dn=dn)
morer = rdb.getRecord('collection', {'uid': r['uid']}, dn=dn)
publishEvent('mpo_collection', onlyone(morer))
elif request.method == 'GET':
if id:
r = rdb.getRecord('collection', {'uid': id}, dn=dn)
else:
#particular cases
#?element_uid
if 'element_uid' in request.args:
r = rdb.getRecord('collection_elements',
{'uid': request.args['element_uid']},
dn=dn)
#general searches
else:
r = rdb.getRecord('collection', request.args, dn=dn)
elif request.method == 'DELETE':
if id:
r = rdb.deleteCollection({'uid': id}, dn=dn)
else:
r = []
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=200)
def ontologyTermVocabulary(id=None, dn=None):
'''
Resource: ontology vocabulary
Convenience route, equivalent to ontology/term?parent_uid=<id>
This function returns the vocabulary of an ontology term specified by its <id>=parent_id.
Vocabulary is defined as the next set of terms below it in the
ontology term tree.
It is a convenience route equivalent to GET ontology_term?parent_uid=uid
'''
api_version,root_url,root=get_api_version(request.url)
if not id:
id='None'
r = rdb.getRecord('ontology_terms', {'parent_uid':id}, dn=dn )
r.append( {'link-requested':request.url} )
return Response(json.dumps(r,cls=MPOSetEncoder),mimetype='application/json',status=200)
def ontologyTermVocabulary(id=None, dn=None):
'''
Resource: ontology vocabulary
Convenience route, equivalent to ontology/term?parent_uid=<id>
This function returns the vocabulary of an ontology term specified by its <id>=parent_id.
Vocabulary is defined as the next set of terms below it in the
ontology term tree.
It is a convenience route equivalent to GET ontology_term?parent_uid=uid
'''
api_version, root_url, root = get_api_version(request.url)
if not id:
id = 'None'
r = rdb.getRecord('ontology_terms', {'parent_uid': id}, dn=dn)
r.append({'link-requested': request.url})
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 dataobject(id=None, dn=None):
"""
Route to add data objects and connect their instances to workflows.
Route: GET /dataobject/<id>
Retrieves information on a specific dataobject.
In the case <id> is <id> of an instance, instance inherits properties of the original object.
In the case <id> is <id> of an dataobject, just the properties of the dataobject are returned.
NOT IMPLEMENTED: ?instance filter will optionally return instances of a specified dataobject.
Route: GET /dataobject returns all dataobjects
GET /dataobject?instance returns all dataobject instances
Route: POST /dataobject
databody:
{'name':, 'description':,'work_uid':, 'uri':, 'parent_uid':, 'uid': }
If 'work_uid' is present, create an instance, connect it to the parent in the workflow
and link instance to the dataobject as determined by the 'uri'.
If 'work_uid' is NOT present, 'parent_uid' must also not be present. A new dataobject is created.
Dataobject instances in workflows can be created by
supplying a URI, DO_UID, or DOI_UID. If a doi_uid is
given, it is resolved to the parent do_uid. If both URI and
UID are provided, the URI takes precedence.
"""
api_version,root_url,root=get_api_version(request.url)
istatus=200
messages={}
messages['api_version']=api_version
if request.method == 'POST':
req = json.loads(request.data)
#Make sure name and description are present
if req.get('name')==None:
req['name']="None given"
if req.get('description')==None:
req['description']="None given"
#find the dataobject with the specified uri (assumed to be unique)
#or if no URI given, find it by UID. If not found, we make it.
if req.get('uri'):
do = rdb.getRecord('dataobject',{'uri':req['uri']},dn=dn)
if req.get('uid'): #check if consistent
if do[0].get('uid'):
if not do[0].get('uid') == req.get('uid'):
messages['warning']="\nCaution, dataobject UID does not match record from URI."
elif req.get('uid'): #if we get here, there is no URI only perhaps a UID
do = rdb.getRecord('dataobject',{'uid':req['uid']},dn=dn)
#now remove the uid from the request so it does not get passed to
#the dataobject_instance creation
popuid=req.pop('uid')
else:
do = False
#If the D.O. exists, point to it, if not, make it and point to it
if do:
if not (req.get('work_uid') and req.get('parent_uid')):
messages['info']='dataobject found. provide both work_uid and parent_uid to attach to a workflow.'
do[0]['messages']=messages
return Response(json.dumps(do,cls=MPOSetEncoder), mimetype='application/json',status=istatus)
else:
req['do_uid']=do[0]['uid']
else:
do_add = rdb.addRecord('dataobject',request.data,dn=dn)
do = rdb.getRecord('dataobject',{'uid':do_add['uid']},dn=dn) #retrieve it to get full record
if not (req.get('work_uid') and req.get('parent_uid')):
messages['info']='dataobject created. provide both work_uid and parent_uid to attach to a workflow.'
do[0]['messages']=messages
return Response(json.dumps(do,cls=MPOSetEncoder), mimetype='application/json',status=istatus)
else:
if apidebug: print('do is ',str(do) )
req['do_uid']=do[0]['uid']
#At this point, we have a dataobject record. Now add it to the workflow since should
#also have a work_uid and parent_uid
#First check if we already have an instance attached to this parent_uid
#we only permit one instance per parent of the same object
#We needs something like get dataobject?instance&do_uid=do_uid&work_uid=wid
#to get a list of uses in this workflow and then figure out if they have the same parent.
#perhaps by using rdb.getWorkflowElements. This is really a topological question - we may
#have more of these.
#check = rdb.getRecord('dataobject_instance',{'do_uid':id},dn=dn)
r = rdb.addRecord('dataobject_instance',json.dumps(req),dn=dn)
id = r['uid']
morer = rdb.getRecord('dataobject_instance',{'uid':id},dn=dn)
publishEvent('mpo_dataobject',onlyone(morer))
elif request.method == 'GET':
#handling for comma separated UIDs
if id:
ids=id.strip().split(',')
r={}
for id in ids:
rs = rdb.getRecord('dataobject',{'uid':id},dn=dn)
if len(rs)==1:
rs=rs[0]
rs['link-related']='link to get workflows using dataobject'
r[id]=rs
else: #record was not found, check other route
rs = rdb.getRecord('dataobject_instance',{'uid':id},dn=dn)
if len(rs)==1:
rs=rs[0]
#add dataobject fields
do_info=rdb.getRecord('dataobject',{'uid':rs.get('do_uid')},dn=dn)
rs['do_info']=do_info[0]
r[id]=rs
else:
rs={'uid':'0','msg':'not found'}
r[id]=rs
if len(ids)==1: #return just single record if one uid
r=[rs] #following convention that a list is always returned
#Get all records, possibly with filters, support 'instance' flag
else:
if request.args.has_key('instance'):
records = rdb.getRecord('dataobject_instance',request.args,dn=dn)
for rr in records:
do_uid=rr['do_uid']
rr['do_info']=rdb.getRecord('dataobject',{'uid':do_uid}, dn=dn )[0]
r=records
else:
r = rdb.getRecord('dataobject',request.args,dn=dn)
return Response(json.dumps(r,cls=MPOSetEncoder), mimetype='application/json',status=istatus)
def dataobject(id=None, dn=None):
"""
Route to add data objects and connect their instances to workflows.
Route: GET /dataobject/<id>
Retrieves information on a specific dataobject.
In the case <id> is <id> of an instance, instance inherits properties of the original object.
In the case <id> is <id> of an dataobject, just the properties of the dataobject are returned.
NOT IMPLEMENTED: ?instance filter will optionally return instances of a specified dataobject.
Route: GET /dataobject returns all dataobjects
GET /dataobject?instance returns all dataobject instances
Route: POST /dataobject
databody:
{'name':, 'description':,'work_uid':, 'uri':, 'parent_uid':, 'uid': }
If 'work_uid' is present, create an instance, connect it to the parent in the workflow
and link instance to the dataobject as determined by the 'uri'.
If 'work_uid' is NOT present, 'parent_uid' must also not be present. A new dataobject is created.
Dataobject instances in workflows can be created by
supplying a URI, DO_UID, or DOI_UID. If a doi_uid is
given, it is resolved to the parent do_uid. If both URI and
UID are provided, the URI takes precedence.
"""
api_version, root_url, root = get_api_version(request.url)
istatus = 200
messages = {}
messages['api_version'] = api_version
if request.method == 'POST':
req = json.loads(request.data)
#Make sure name and description are present
if req.get('name') == None:
req['name'] = "None given"
if req.get('description') == None:
req['description'] = "None given"
#find the dataobject with the specified uri (assumed to be unique)
#or if no URI given, find it by UID. If not found, we make it.
if req.get('uri'):
do = rdb.getRecord('dataobject', {'uri': req['uri']}, dn=dn)
if req.get('uid'): #check if consistent
if do[0].get('uid'):
if not do[0].get('uid') == req.get('uid'):
messages[
'warning'] = "\nCaution, dataobject UID does not match record from URI."
elif req.get(
'uid'): #if we get here, there is no URI only perhaps a UID
do = rdb.getRecord('dataobject', {'uid': req['uid']}, dn=dn)
#now remove the uid from the request so it does not get passed to
#the dataobject_instance creation
popuid = req.pop('uid')
else:
do = False
#If the D.O. exists, point to it, if not, make it and point to it
if do:
if not (req.get('work_uid') and req.get('parent_uid')):
messages[
'info'] = 'dataobject found. provide both work_uid and parent_uid to attach to a workflow.'
do[0]['messages'] = messages
return Response(json.dumps(do, cls=MPOSetEncoder),
mimetype='application/json',
status=istatus)
else:
req['do_uid'] = do[0]['uid']
else:
do_add = rdb.addRecord('dataobject', request.data, dn=dn)
do = rdb.getRecord('dataobject', {'uid': do_add['uid']},
dn=dn) #retrieve it to get full record
if not (req.get('work_uid') and req.get('parent_uid')):
messages[
'info'] = 'dataobject created. provide both work_uid and parent_uid to attach to a workflow.'
do[0]['messages'] = messages
return Response(json.dumps(do, cls=MPOSetEncoder),
mimetype='application/json',
status=istatus)
else:
if apidebug: print('do is ', str(do))
req['do_uid'] = do[0]['uid']
#At this point, we have a dataobject record. Now add it to the workflow since should
#also have a work_uid and parent_uid
#First check if we already have an instance attached to this parent_uid
#we only permit one instance per parent of the same object
#We needs something like get dataobject?instance&do_uid=do_uid&work_uid=wid
#to get a list of uses in this workflow and then figure out if they have the same parent.
#perhaps by using rdb.getWorkflowElements. This is really a topological question - we may
#have more of these.
#check = rdb.getRecord('dataobject_instance',{'do_uid':id},dn=dn)
r = rdb.addRecord('dataobject_instance', json.dumps(req), dn=dn)
id = r['uid']
morer = rdb.getRecord('dataobject_instance', {'uid': id}, dn=dn)
publishEvent('mpo_dataobject', onlyone(morer))
elif request.method == 'GET':
#handling for comma separated UIDs
if id:
ids = id.strip().split(',')
r = {}
for id in ids:
rs = rdb.getRecord('dataobject', {'uid': id}, dn=dn)
if len(rs) == 1:
rs = rs[0]
rs['link-related'] = 'link to get workflows using dataobject'
r[id] = rs
else: #record was not found, check other route
rs = rdb.getRecord('dataobject_instance', {'uid': id},
dn=dn)
if len(rs) == 1:
rs = rs[0]
#add dataobject fields
do_info = rdb.getRecord('dataobject',
{'uid': rs.get('do_uid')},
dn=dn)
rs['do_info'] = do_info[0]
r[id] = rs
else:
rs = {'uid': '0', 'msg': 'not found'}
r[id] = rs
if len(ids) == 1: #return just single record if one uid
r = [rs] #following convention that a list is always returned
#Get all records, possibly with filters, support 'instance' flag
else:
if request.args.has_key('instance'):
records = rdb.getRecord('dataobject_instance',
request.args,
dn=dn)
for rr in records:
do_uid = rr['do_uid']
rr['do_info'] = rdb.getRecord('dataobject',
{'uid': do_uid},
dn=dn)[0]
r = records
else:
r = rdb.getRecord('dataobject', request.args, dn=dn)
return Response(json.dumps(r, cls=MPOSetEncoder),
mimetype='application/json',
status=istatus)
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)
