def do_save(user, **kwargs):
can_approve = user.role.Type == 'super-admin'
id = kwargs.get("ID", None)
was_approved = None
uid = None
if not id or can_approve:# Only super-admins can edit a molecule for now
if id:
mole = Molecule.query.filter_by(ID=kwargs['ID']).first()
already_approved = mole.Approved
mole.merge_fields(**kwargs)
was_approved = mole.Approved and not already_approved
mole.validate_required_fields()
else:
mole = Molecule()
mole.merge_fields(**kwargs)
mole.UserID = user.UserID
mole.Approved = can_approve and kwargs['Approved']
mole.validate_required_fields()
mole.save()
uid = mole.ID
if was_approved:
message = "%s was approved" % mole.Name
comment = Comment(UserID=user.UserID, Type='Molecules',ParentID=mole.ID, Message=message, RenderType='text')
comment.save()
if uid:
mole = Molecule.query.filter_by(ID=uid).first()
return mole
return None
def autofill(cid):
mole = Molecule(CID=cid)
mole.autofill(get_image=False)
keywords = mole.get_keywords()
keyword_resp = [keyword.to_hash() for keyword in keywords]
resp = {"molecule": mole.to_hash(), "keywords": keyword_resp}
return Response(json.dumps(resp), content_type="application/json")
def create_molecules(user_ids):
molecule_sofie_id = {}
for x in xrange(1, 30):
res = requests.get('http://www.sofienetwork.com/probe/%i/' % x, \
headers={'Accept': 'application/json', 'Authorization': authorization})
try:
molecule_json = res.json()
spn_id = molecule_json["ID"]
del molecule_json['ID']
user_id = molecule_json['UserID']
molecule_json['UserID'] = user_ids[user_id] if user_id in user_ids else None
molecule = Molecule(**molecule_json)
res = requests.get('http://www.sofienetwork.com/probe/%i/image/' % x, headers={'Authorization': authorization})
molecule._Image = res.content
molecule.save()
print molecule.ID
molecule_sofie_id[spn_id] = molecule.ID
res = requests.get('http://www.sofienetwork.com/keyword/Molecules/%i/' % x, headers={'Authorization': authorization})
keywords = res.json()
for keyword in keywords:
del keyword['CreationDate']
del keyword['KeywordID']
key = Keyword(**keyword)
key.ParentID = molecule.ID
key.save()
except Exception as e:
print str(e)
print 'molecule insertion error'
db.session.rollback()
return molecule_sofie_id
def construct_ingredient(json: Dict, type: str) -> Ingredient:
""" Returns an Ingredient object from a given JSON file
"""
ingredient_type = IngredientType(type)
molecules: List[Molecule] = [
Molecule(m["pubchem_id"], m["common_name"],
tuple(m["fooddb_flavor_profile"].split("@")))
for m in json["molecules"]
]
return Ingredient(json["entity_alias_readable"], json["category_readable"],
json["entity_id"], molecules, ingredient_type)
def create():
data = request.json
try:
mole = do_save(g.user, **data)
if request.headers.get("Accept") == "application/json":
return Response(json.dumps(mole.to_hash()), headers={"Content-Type": "application/json"})
return redirect("/")
except Exception as e:
db.session.rollback()
msg = str(e)
if e.__class__ == ValidationException().__class__:
msg = e.errors()
if request.headers.get("Accept") == "application/json":
return Response(json.dumps({"molecule": Molecule.to_hash(), "error_details": msg}), status=400, headers={"Content-Type": "application/json"})
flash(msg)
return render_template("molecule/new.html", molecule=Molecule().to_hash())
"""
def new():
mole = Molecule()
resp = json.dumps(mole.to_hash())
return render_template("molecule/edit.html", molecule=resp, runninguser=json.dumps(g.user.to_hash()))
for my_cids in chunks(objs.keys(), 10):
local_cids = [str(cid) for cid in my_cids]
url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/%s/property/MolecularFormula/JSON" % ",".join(local_cids)
res = requests.get(url)
res = res.json()
for prop in res['PropertyTable']['Properties']:
cid = prop["CID"]
objs[cid]["Formula"] = prop["MolecularFormula"]
time.sleep(1)
for key in objs.keys():
obj = objs[key]
try:
mole = Molecule(**obj)
mole.save()
except:
db.session.rollback()
print 'failed to save'
### Get Molecule Images
moles = Molecule.query.all()
"""
for mole in moles:
mole.save_image_from_pubchem()
print 'saving image'
time.sleep(1)
"""
def seed_data():
molecule = Molecule(CID=3232583, DisplayFormat="<p>[<sup>18</sup>F]-<sub>D</sub>-FEAU</p>", \
Description="FEAU is an nucleoside analog and a highly specific substrate for herpes simplex " \
"virus 1 thymidine kinase (HSV1-tk). FEAU is phosphorylated by HSV1-tk " \
"and subsequently retained intracellularly; hence it can annotate HSV1-tk " \
"expression in vivo. The gene encoding HSV1-tk is a commonly used reporter gene " \
"in cell-based therapy studies.",
Name="<p>[<sup>18</sup>F]-<sub>D</sub>-FEAU</p>")
molecule.save()
molecule1 = Molecule(CID=3232584, DisplayFormat="<p>[<sup>18</sup>F]-<sub>D</sub>-FEAU</p>", \
Description="FEAU is an nucleoside analog and a highly specific substrate for herpes simplex " \
"virus 1 thymidine kinase (HSV1-tk). FEAU is phosphorylated by HSV1-tk " \
"and subsequently retained intracellularly; hence it can annotate HSV1-tk " \
"expression in vivo. The gene encoding HSV1-tk is a commonly used reporter gene " \
"in cell-based therapy studies.",
Name="FEAU")
molecule1.save()
molecule2 = Molecule(CID=3232585, DisplayFormat="<p>[<sup>18</sup>F]-<sub>D</sub>-FEAU</p>", \
Description="FEAU is an nucleoside analog and a highly specific substrate for herpes simplex " \
"virus 1 thymidine kinase (HSV1-tk). FEAU is phosphorylated by HSV1-tk " \
"and subsequently retained intracellularly; hence it can annotate HSV1-tk " \
"expression in vivo. The gene encoding HSV1-tk is a commonly used reporter gene " \
"in cell-based therapy studies.",
Name="FEAU")
molecule2.save()
molecule3 = Molecule(CID=3232586, DisplayFormat="<p>[<sup>18</sup>F]-<sub>D</sub>-FEAU</p>", \
Description="FEAU is an nucleoside analog and a highly specific substrate for herpes simplex " \
"virus 1 thymidine kinase (HSV1-tk). FEAU is phosphorylated by HSV1-tk " \
"and subsequently retained intracellularly; hence it can annotate HSV1-tk " \
"expression in vivo. The gene encoding HSV1-tk is a commonly used reporter gene " \
"in cell-based therapy studies.",
Name="FEAU")
molecule3.save()
molecule.save_synonyms_from_pubchem()
accounts = generate_accounts()
main_account = accounts[0]
generate_forums(main_account.id)
alternative_account = accounts[1]
chemist, admin, super_admin = generate_roles()
main_user = generate_user(main_account.id, "test", super_admin.RoleID)
create_approval_following()
main_account_users = generate_users(main_account.id, 5, chemist.RoleID)
alternative_account_users = generate_users(alternative_account.id, 5, chemist.RoleID)
competitor_user = alternative_account_users[0]
sequence_id = generate_zipped_sequence(main_user, molecule.ID)
data = open(os.path.join("seeds", "molecule.jpeg"), 'r')
data = data.read()
reaction_scheme = SequenceAttachment(SequenceID=sequence_id, FileName='molecules.jpg', Type="ReactionScheme", Attachment=data)
reaction_scheme.save()
competitor_sequence = generate_zipped_sequence(competitor_user, molecule.ID)
follow = Follower(UserID=main_user, Type="Sequences", ParentID=competitor_sequence)
follow.save()
follow = Follower(UserID=main_user, Type="Molecules", ParentID=molecule.ID)
follow.save()
generate_comment(main_user, sequence_id)
generate_comment(competitor_user, sequence_id, "My #sequence produces a better yield")
generate_private_sequence(main_user, molecule.ID)
generate_private_sequence(main_user, molecule.ID, False)
for x in xrange(PAGINATION_SIZE+2):
sequence_id = generate_sequence(main_user, molecule.ID)
sequence = Sequence.query.filter_by(SequenceID=sequence_id).first()
sequence.StartingActivity = 21.33
sequence.Yield = 12.55
sequence.SpecificActivity = 20.3
sequence.NumberOfSteps = 20
sequence.SynthesisTime = 400
sequence.save()
generate_comment(main_user, competitor_sequence, "Testing Pagination size %i" % x)
image_comment = Comment(ParentID=1,Type='Sequences',RenderType='image',Message='',UserID=main_user)
image_comment.save()
data = open(os.path.join("seeds", "molecule.jpeg"), 'r')
data = data.read()
image = SequenceAttachment(ParentID=image_comment.CommentID,Type='comments',Attachment=data)
image.save()
generate_unique_downloads()
generate_issues()
time.sleep(15)
generate_issues()