def post(self, project):
note = self.get_argument('note', '')
category = self.get_argument('category', '')
user = self.get_secure_cookie('user')
email = self.get_secure_cookie('email')
timestamp = datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S')
if not note:
self.set_status(400)
self.finish('<html><body>No project id or note parameters found</body></html>')
else:
newNote = {'user': user, 'email': email, 'note': note, 'category' : category, 'timestamp': timestamp}
p = Project(lims, id=project)
p.get(force=True)
running_notes = json.loads(p.udf['Running Notes']) if 'Running Notes' in p.udf else {}
running_notes[timestamp] = newNote
p.udf['Running Notes'] = json.dumps(running_notes)
p.put()
#saving running notes directly in genstat, because reasons.
v=self.application.projects_db.view("project/project_id")
for row in v[project]:
doc_id=row.value
doc=self.application.projects_db.get(doc_id)
doc['details']['running_notes']=json.dumps(running_notes)
self.application.projects_db.save(doc)
self.set_status(201)
self.write(json.dumps(newNote))
def post(self, project):
user = self.get_secure_cookie('user')
email = self.get_secure_cookie('email')
a_type = self.get_argument('type', '')
title = self.get_argument('title', '')
url = self.get_argument('url', '')
desc = self.get_argument('desc','')
if not a_type or not title:
self.set_status(400)
self.finish('<html><body>Link title and type is required</body></html>')
else:
p = Project(lims, id=project)
p.get(force=True)
links = json.loads(p.udf['Links']) if 'Links' in p.udf else {}
links[str(datetime.datetime.now())] = {'user': user,
'email': email,
'type': a_type,
'title': title,
'url': url,
'desc': desc}
p.udf['Links'] = json.dumps(links)
p.put()
self.set_status(200)
#ajax cries if it does not get anything back
self.set_header("Content-type", "application/json")
self.finish(json.dumps(links))
def post(self, project):
user = self.get_current_user()
a_type = self.get_argument('type', '')
title = self.get_argument('title', '')
url = self.get_argument('url', '')
desc = self.get_argument('desc', '')
if not a_type or not title:
self.set_status(400)
self.finish(
'<html><body>Link title and type is required</body></html>')
else:
p = Project(lims, id=project)
p.get(force=True)
links = json.loads(p.udf['Links']) if 'Links' in p.udf else {}
links[str(datetime.datetime.now())] = {
'user': user.name,
'email': user.email,
'type': a_type,
'title': title,
'url': url,
'desc': desc
}
p.udf['Links'] = json.dumps(links)
p.put()
self.set_status(200)
#ajax cries if it does not get anything back
self.set_header("Content-type", "application/json")
self.finish(json.dumps(links))
def make_project_running_note(application, project, note, category, user, email):
timestamp = datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S')
newNote = {'user': user, 'email': email, 'note': note, 'category' : category, 'timestamp': timestamp}
p = Project(lims, id=project)
p.get(force=True)
running_notes = json.loads(p.udf['Running Notes']) if 'Running Notes' in p.udf else {}
running_notes.update({timestamp: newNote})
# Saving running note in LIMS
p.udf['Running Notes'] = json.dumps(running_notes)
p.put()
p.get(force=True)
#Retry once more
if p.udf['Running Notes'] != json.dumps(running_notes):
p.udf['Running Notes'] = json.dumps(running_notes)
p.put()
p.get(force=True)
#In the rare case saving to LIMS does not work
assert (p.udf['Running Notes'] == json.dumps(running_notes)), "The Running note wasn't saved in LIMS!"
#saving running notes directly in genstat, because reasons.
v=application.projects_db.view("project/project_id")
for row in v[project]:
doc_id=row.value
doc=application.projects_db.get(doc_id)
doc['details']['running_notes']=json.dumps(running_notes)
application.projects_db.save(doc)
#### Check and send mail to tagged users
pattern = re.compile("(@)([a-zA-Z0-9.-]+)")
userTags = pattern.findall(note)
if userTags:
RunningNotesDataHandler.notify_tagged_user(application, userTags, project, note, category, user, timestamp)
####
return newNote
def post(self, project):
note = self.get_argument('note', '')
category = self.get_argument('category', '')
user = self.get_secure_cookie('user')
email = self.get_secure_cookie('email')
timestamp = datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S')
if not note:
self.set_status(400)
self.finish('<html><body>No project id or note parameters found</body></html>')
else:
newNote = {'user': user, 'email': email, 'note': note, 'category' : category, 'timestamp': timestamp}
p = Project(lims, id=project)
p.get(force=True)
running_notes = json.loads(p.udf['Running Notes']) if 'Running Notes' in p.udf else {}
running_notes[timestamp] = newNote
p.udf['Running Notes'] = json.dumps(running_notes)
p.put()
#saving running notes directly in genstat, because reasons.
v=self.application.projects_db.view("project/project_id")
for row in v[project]:
doc_id=row.value
doc=self.application.projects_db.get(doc_id)
doc['details']['running_notes']=json.dumps(running_notes)
self.application.projects_db.save(doc)
self.set_status(201)
self.write(json.dumps(newNote))
def main(lims, args):
p=Process(lims, id=args.pid)
log=[]
datamap={}
wsname=None
username="******".format(p.technician.first_name, p.technician.last_name)
user_email=p.technician.email
for art in p.all_inputs():
if len(art.samples)!=1:
log.append("Warning : artifact {0} has more than one sample".format(art.id))
for sample in art.samples:
#take care of lamda DNA
if sample.project:
if sample.project.id not in datamap:
datamap[sample.project.id]=[sample.name]
else:
datamap[sample.project.id].append(sample.name)
for art in p.all_outputs():
try:
wsname=art.location[0].name
break
except:
pass
now=datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f")
for pid in datamap:
pj=Project(lims, id=pid)
running_notes=json.loads(pj.udf['Running Notes'])
if len(datamap[pid]) > 1:
rnt="{0} samples planned for {1}".format(len(datamap[pid]), wsname)
else:
rnt="{0} sample planned for {1}".format(len(datamap[pid]), wsname)
running_notes[now]={"note": rnt, "user" : username, "email":user_email, "category":"Workset"}
pj.udf['Running Notes']=json.dumps(running_notes)
pj.put()
log.append("Updated project {0} : {1}, {2} samples in this workset".format(pid,pj.name, len(datamap[pid])))
with open("EPP_Notes.log", "w") as flog:
flog.write("\n".join(log))
for out in p.all_outputs():
#attach the log file
if out.name=="RNotes Log":
attach_file(os.path.join(os.getcwd(), "EPP_Notes.log"), out)
sys.stderr.write("Updated {0} projects successfully".format(len(datamap.keys())))
def post(self, project):
note = self.get_argument('note', '')
user = self.get_secure_cookie('user')
email = self.get_secure_cookie('email')
if not note:
self.set_status(400)
self.finish('<html><body>No project id or note parameters found</body></html>')
else:
newNote = {'user': user, 'email': email, 'note': note}
p = Project(lims, id=project)
p.get(force=True)
running_notes = json.loads(p.udf['Running Notes']) if 'Running Notes' in p.udf else {}
running_notes[str(datetime.datetime.now())] = newNote
p.udf['Running Notes'] = json.dumps(running_notes)
p.put()
self.set_status(201)
self.write(json.dumps(newNote))
def make_project_running_note(application, project, note, category, user, email):
timestamp = datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S')
newNote = {'user': user, 'email': email, 'note': note, 'category' : category, 'timestamp': timestamp}
p = Project(lims, id=project)
p.get(force=True)
running_notes = json.loads(p.udf['Running Notes']) if 'Running Notes' in p.udf else {}
running_notes.update({timestamp: newNote})
# Saving running note in LIMS
p.udf['Running Notes'] = json.dumps(running_notes)
p.put()
#saving running notes directly in genstat, because reasons.
v=application.projects_db.view("project/project_id")
for row in v[project]:
doc_id=row.value
doc=application.projects_db.get(doc_id)
doc['details']['running_notes']=json.dumps(running_notes)
application.projects_db.save(doc)
return newNote
def post(self, project_id):
try:
data = json.loads(self.request.body)
text=data.get('text', '')
p=Project(lims, id=project_id)
p.udf['Lab Status']=text
p.put()
view=self.application.projects_db.view("project/project_id")
for row in view[project_id]:
doc=self.application.projects_db.get(row.id)
doc['details']['lab_status']=text
self.application.projects_db.save(doc)
except Exception as e:
self.set_status(400)
self.finish('<html><body><p>could not update Entity {} :</p><pre>{}</pre></body></html>'.format( cl_id, e))
else:
self.set_status(200)
self.set_header("Content-type", "application/json")
self.write(self.request.body)
def post(self, project_id):
try:
data = json.loads(self.request.body)
text = data.get('text', '')
p = Project(lims, id=project_id)
p.udf['Internal Costs'] = text
p.put()
view = self.application.projects_db.view("project/project_id")
for row in view[project_id]:
doc=self.application.projects_db.get(row.id)
doc['details']['internal_costs']=text
self.application.projects_db.save(doc)
except Exception as e:
self.set_status(400)
self.finish('<html><body><p>could not update Entity {} :</p><pre>{}</pre></body></html>'.format( project_id, e))
else:
self.set_status(200)
self.set_header("Content-type", "application/json")
self.write(self.request.body)
def update_project(self, lims_id: str, name: str = None) -> None:
"""Update information about a project."""
lims_project = Project(self, id=lims_id)
if name:
lims_project.name = name
lims_project.put()
def main(lims, args):
p = Process(lims, id=args.pid)
log = []
datamap = {}
wsname = None
username = "******".format(p.technician.first_name,
p.technician.last_name)
user_email = p.technician.email
for art in p.all_inputs():
if len(art.samples) != 1:
log.append(
"Warning : artifact {0} has more than one sample".format(
art.id))
for sample in art.samples:
#take care of lamda DNA
if sample.project:
if sample.project.id not in datamap:
datamap[sample.project.id] = [sample.name]
else:
datamap[sample.project.id].append(sample.name)
for art in p.all_outputs():
try:
wsname = art.location[0].name
break
except:
pass
now = datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f")
for pid in datamap:
pj = Project(lims, id=pid)
running_notes = json.loads(pj.udf['Running Notes'])
if len(datamap[pid]) > 1:
rnt = "{0} samples planned for {1}".format(len(datamap[pid]),
wsname)
else:
rnt = "{0} sample planned for {1}".format(len(datamap[pid]),
wsname)
running_notes[now] = {
"note": rnt,
"user": username,
"email": user_email,
"category": "Workset"
}
pj.udf['Running Notes'] = json.dumps(running_notes)
pj.put()
log.append(
"Updated project {0} : {1}, {2} samples in this workset".format(
pid, pj.name, len(datamap[pid])))
with open("EPP_Notes.log", "w") as flog:
flog.write("\n".join(log))
for out in p.all_outputs():
#attach the log file
if out.name == "RNotes Log":
attach_file(os.path.join(os.getcwd(), "EPP_Notes.log"), out)
sys.stderr.write("Updated {0} projects successfully".format(
len(datamap.keys())))
