def _do_get_provider_count_and_objs(self, name=None, **kw):
userid = request.identity['repoze.who.userid']
scompound = ()
dsc = True
order = 'id'
if kw:
try:
smiles = kw['smi']
method = kw['method']
except Exception:
smiles = None
method = None
pass
try:
ogranicz_tekst = kw['ogranicz_tekst']
except Exception:
ogranicz_tekst = None
pass
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
query_bfp = functions.morgan_b(TxtMoleculeElement(smiles), 2)
constraint = SCompound.morgan.dice_similar(query_bfp)
dice_sml = SCompound.morgan.dice_similarity(query_bfp).label('dice')
# scompound = DBSession.query(SCompound, dice_sml).filter(constraint).filter(SCompound.owner.contains(userid))
scompound = DBSession.query(SCompound).filter(constraint).filter(SCompound.owner.contains(userid))
elif method == 'substructure':
constraint = SCompound.structure.contains(smiles)
scompound = DBSession.query(SCompound).filter(constraint).filter(SCompound.owner.contains(userid))
elif method == 'identity':
scompound = DBSession.query(SCompound).filter(SCompound.structure.equals(smiles)).filter(SCompound.owner.contains(userid))
# if ogranicz_tekst:
# scompound = scompound.filter(SCompound.__getattribute__(SCompound, kw['ogranicz']).like(ogranicz_tekst))
else:
flash('SMILES error', 'warning')
scompound = ()
else:
scompound = DBSession.query(SCompound).filter(SCompound.owner.contains(userid))
if ogranicz_tekst:
if kw['ogranicz'] == 'p_id':
try:
p_id = int(ogranicz_tekst)
scompound = scompound.filter_by(p_id = p_id )
except Exception as msg:
flash('P_id should be a number: %s' % msg, 'error')
else:
scompound = scompound.filter(SCompound.__getattribute__(SCompound, kw['ogranicz']).like(ogranicz_tekst))
try:
tagi = kw['tags']
except Exception:
tagi = None
pass
if isinstance(tagi, basestring):
tagi_id = [int(tagi)]
else:
tagi_id = [int(id) for id in tagi]
if tagi_id:
import sqlalchemy
scompound = scompound.filter(SCompound.tags.any(Tags.tags_id.in_(tagi_id)))
# scompound = scompound.filter(SCompound.tags.contain(tagi_id))
# scompound = scompound.join(SCompound.tags).filter_by(not_(tags_id = tagi_id[0]))
if int(kw['status']) > 0:
scompound = scompound.filter(SCompound.status_id == int(kw['status']))
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
order = v
if scompound:
if dsc:
scompound = scompound.order_by(desc(order))
else:
scompound = scompound.order_by((order))
scompound = scompound.all()
# scompound = scompound.all()
return len(scompound), scompound
def index(self, page=1, *args, **kw):
pname = request.environ['PATH_INFO'].split('/')[1]
project = DBSession.query(Projects).filter_by(name=pname).first()
page_url = paginate.PageURL_WebOb(request)
import pickle
try:
cells = pickle.loads([test.cell_line for test in project.tests if test.name == 'CT'][0])
except:
cells = None
lcompound = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).filter(LCompound.showme==True)
dsc = True
order = LCompound.id
tmpl = ''
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
selection = None
similarity = None
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
ulist = None
ulists = set([l for l in user.lists if l.table == 'Results'] + [l for l in user.tg_user_lists if l.table == 'Results'])
items = user.items_per_page
try:
if kw['search'] != u'':
search_clicked = kw['search']
else:
search_clicked = None
except Exception:
search_clicked = None
if kw:
if kw.has_key('mylist'):
try:
ulist_id = int(kw['mylist'])
ulist = DBSession.query(UserLists).get(ulist_id)
except Exception:
flash(l_(u'List error'), 'error')
redirect(request.headers['Referer'])
if (ulist in user.lists) or (user in ulist.permitusers):
if ulist.elements:
import pickle
elements = [int(el) for el in pickle.loads(ulist.elements)]
if ulist.table == 'Results':
lcompound = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).filter(LCompound.id.in_(elements))
else:
flash(l_(u'Table error'), 'error')
redirect(request.headers['Referer'])
else:
flash(l_(u'Permission denied'), 'error')
redirect(request.headers['Referer'])
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
if v in ('gid', 'create_date', 'box', 'form', 'state', 'entry', 'source', 'MDM2', 'MDM4', 'lcode'):
if v=='lcode':
order = LCompound.lcode
else:
order = LCompound.__getattribute__(LCompound, v)
else:
if v=='last_point':
lcompound=lcompound.join(LCompound.solubility)
order = v
elif hasattr(LCompound, v):
order = LCompound.__getattribute__(LCompound, v)
elif 'CTOX_' in v:
v = v.replace('CTOX_', '')
all_lcompounds = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).all()
for l in all_lcompounds:
l.avg_ct = v.replace('pp', '+')
order = '_avg_ct'
else:
order = v
if str(k) != 'select' and str(k) != 'remove' and str(v) != u'':
tmpl += str(k) + '=' + str(v) + '&'
elif str(k) == 'select':
try:
if isinstance(kw['select'], basestring):
selection = [kw['select']]
else:
selection = [id for id in kw['select']]
except Exception:
selection = None
if search_clicked:
try:
smiles = str(kw['smiles'])
if 'pp' in smiles:
smiles = smiles.replace('pp', '+')
method = str(kw['method'])
except Exception:
smiles = None
method = None
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
# from razi.postgresql_rdkit import tanimoto_threshold
query_bfp = functions.morgan_b(TxtMoleculeElement(smiles), 2)
constraint = Compound.morgan.tanimoto_similar(query_bfp)
tanimoto_sml = Compound.morgan.tanimoto_similarity(query_bfp).label('tanimoto')
search = DBSession.query(LCompound, tanimoto_sml).join(LCompound.mol).join(LCompound.purity).filter(Compound.project.any(Projects.name==pname)).filter(constraint)
if order != LCompound.id:
if order == 'purity':
order = LPurity.value
if dsc:
search = search.order_by(desc(order).nullslast())
else:
search = search.order_by(order)
else:
search = search.order_by(desc(tanimoto_sml)).all()
lcompound = ()
similarity = ()
for row in search:
lcompound += (row[0], )
similarity += (row[1], )
currentPage = paginate.Page(lcompound, page, url=page_url, items_per_page=items)
return dict(currentPage=currentPage,tmpl=tmpl, page='results', pname=pname, alltags=alltags, similarity=similarity,htmlRgb=htmlRgb, htmlRgb100=htmlRgb100, Num2Rgb=Num2Rgb, cells=cells, ulists=ulists, ulist=ulist)
elif method == 'substructure':
constraint = Compound.structure.contains(smiles)
lcompound = DBSession.query(LCompound).join(LCompound.mol).filter(Compound.project.any(Projects.name==pname)).filter(constraint)
elif method == 'identity':
lcompound = DBSession.query(LCompound).filter(Compound.project.any(Projects.name==pname)).join(LCompound.mol).filter(Compound.structure.equals(smiles))
else:
if method == 'smarts':
if dsc:
lcompound = lcompound.order_by(desc(order).nullslast())
else:
lcompound = lcompound.order_by(order)
search = lcompound.all()
sub_lcompounds = ()
patt = Chem.MolFromSmarts(smiles)
if not patt:
flash(l_(u'SMARTS error'), 'warning')
redirect(request.headers['Referer'])
for row in search:
m = Chem.MolFromSmiles(str(row.mol.structure))
mol = Chem.AddHs(m)
if mol.HasSubstructMatch(patt):
sub_lcompounds += (row, )
currentPage = paginate.Page(sub_lcompounds, page, url=page_url, items_per_page=items)
return dict(currentPage=currentPage,tmpl=tmpl, page='results', pname=pname, alltags=alltags, similarity=similarity,htmlRgb=htmlRgb, htmlRgb100=htmlRgb100, Num2Rgb=Num2Rgb, cells=cells, ulists=ulists, ulist=ulist)
else:
flash(l_(u'SMILES error'), 'warning')
redirect(request.headers['Referer'])
if kw.has_key('text_GID') and kw['text_GID'] !=u'':
try:
gid = int(kw['text_GID'])
lcompound = lcompound.filter(LCompound.gid == gid)
except Exception as msg:
flash(l_(u'GID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_ID') and kw['text_ID'] !=u'':
try:
id = int(kw['text_ID'])
lcompound = lcompound.filter(LCompound.id == id)
except Exception as msg:
flash(l_(u'ID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_name') and kw['text_name'] !=u'':
lcompound = lcompound.filter(Compound.names.any(Names.name.like(kw['text_name'].strip().replace('*', '%'))))
if kw.has_key('text_notes') and kw['text_notes'] !=u'':
lcompound = lcompound.filter(LCompound.notes.like(kw['text_notes'].replace('*', '%')))
if kw.has_key('text_lso') and kw['text_lso'] !=u'':
lcompound = lcompound.filter(LCompound.lso.like(kw['text_lso'].replace('*', '%')))
if kw.has_key('text_entry') and kw['text_entry'] !=u'':
lcompound = lcompound.filter(LCompound.entry.like(kw['text_entry'].replace('*', '%')))
if kw.has_key('text_box') and kw['text_box'] !=u'':
lcompound = lcompound.filter(LCompound.box.like(kw['text_box'].replace('*', '%')))
if kw.has_key('date_from') and kw['date_from'] !=u'':
date_from = datetime.strptime(str(kw['date_from']), '%Y-%m-%d')
lcompound = lcompound.filter(LCompound.create_date > date_from)
else:
date_from = None
if kw.has_key('date_to') and kw['date_to'] !=u'':
date_to = datetime.strptime(str(kw['date_to']), '%Y-%m-%d')
if date_from:
if date_to>date_from:
lcompound = lcompound.filter(LCompound.create_date < date_to)
else:
flash(l_(u'The End date must be later than the initial'), 'error')
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.create_date < date_to)
if kw.has_key('text_mdm2_hill_from') and kw['text_mdm2_hill_from'] !=u'':
text_mdm2_hill_from = float(kw['text_mdm2_hill_from'])
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm2 >= text_mdm2_hill_from)
else:
text_mdm2_hill_from = None
if kw.has_key('text_mdm2_hill_to') and kw['text_mdm2_hill_to'] !=u'':
text_mdm2_hill_to = float(kw['text_mdm2_hill_to'])
if text_mdm2_hill_from:
if text_mdm2_hill_to>=text_mdm2_hill_from:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm2 <= text_mdm2_hill_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm2 <= text_mdm2_hill_to)
if kw.has_key('text_mdm2_fluor_from') and kw['text_mdm2_fluor_from'] !=u'':
text_mdm2_fluor_from = float(kw['text_mdm2_fluor_from'])
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm2 >= text_mdm2_fluor_from)
else:
text_mdm2_fluor_from = None
if kw.has_key('text_mdm2_fluor_to') and kw['text_mdm2_fluor_to'] !=u'':
text_mdm2_fluor_to = float(kw['text_mdm2_fluor_to'])
if text_mdm2_fluor_from:
if text_mdm2_fluor_to>=text_mdm2_fluor_from:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm2 <= text_mdm2_fluor_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm2 <= text_mdm2_fluor_to)
if kw.has_key('text_mdm2_ki_from') and kw['text_mdm2_ki_from'] !=u'':
text_mdm2_ki_from = float(kw['text_mdm2_ki_from'])
lcompound = lcompound.filter(LCompound.avg_ki_mdm2 >= text_mdm2_ki_from)
else:
text_mdm2_ki_from = None
if kw.has_key('text_mdm2_ki_to') and kw['text_mdm2_ki_to'] !=u'':
text_mdm2_ki_to = float(kw['text_mdm2_ki_to'])
if text_mdm2_ki_from:
if text_mdm2_ki_to>=text_mdm2_ki_from:
lcompound = lcompound.filter(LCompound.avg_ki_mdm2 <= text_mdm2_ki_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_ki_mdm2 <= text_mdm2_ki_to)
if kw.has_key('text_mdm4_hill_from') and kw['text_mdm4_hill_from'] !=u'':
text_mdm4_hill_from = float(kw['text_mdm4_hill_from'])
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm4 >= text_mdm4_hill_from)
else:
text_mdm4_hill_from = None
if kw.has_key('text_mdm4_hill_to') and kw['text_mdm4_hill_to'] !=u'':
text_mdm4_hill_to = float(kw['text_mdm4_hill_to'])
if text_mdm4_hill_from:
if text_mdm4_hill_to>=text_mdm4_hill_from:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm4 <= text_mdm4_hill_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_hillslope_mdm4 <= text_mdm4_hill_to)
if kw.has_key('text_mdm4_fluor_from') and kw['text_mdm4_fluor_from'] !=u'':
text_mdm4_fluor_from = float(kw['text_mdm4_fluor_from'])
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm4 >= text_mdm4_fluor_from)
else:
text_mdm4_fluor_from = None
if kw.has_key('text_mdm4_fluor_to') and kw['text_mdm4_fluor_to'] !=u'':
text_mdm4_fluor_to = float(kw['text_mdm4_fluor_to'])
if text_mdm4_fluor_from:
if text_mdm4_fluor_to>=text_mdm4_fluor_from:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm4 <= text_mdm4_fluor_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_fluorescence_mdm4 <= text_mdm4_fluor_to)
if kw.has_key('text_mdm4_ki_from') and kw['text_mdm4_ki_from'] !=u'':
text_mdm4_ki_from = float(kw['text_mdm4_ki_from'])
lcompound = lcompound.filter(LCompound.avg_ki_mdm4 >= text_mdm4_ki_from)
else:
text_mdm4_ki_from = None
if kw.has_key('text_mdm4_ki_to') and kw['text_mdm4_ki_to'] !=u'':
text_mdm4_ki_to = float(kw['text_mdm4_ki_to'])
if text_mdm4_ki_from:
if text_mdm4_ki_to>=text_mdm4_ki_from:
lcompound = lcompound.filter(LCompound.avg_ki_mdm4 <= text_mdm4_ki_to)
else:
flash(l_(u'The final value must be greater than the initial'))
redirect(request.headers['Referer'])
else:
lcompound = lcompound.filter(LCompound.avg_ki_mdm4 <= text_mdm4_ki_to)
try:
tags = kw['text_tags']
except Exception:
tags = None
pass
if tags:
if isinstance(tags, basestring):
tagi = eval(tags)
if type(tagi) != type([]):
tagi = [int(tags)]
else:
tagi = [int(tid) for tid in tags]
lcompound = lcompound.filter(Compound.tags.any(Tags.id.in_(tagi)))
if dsc:
lcompound = lcompound.order_by(desc(order).nullslast())
else:
lcompound = lcompound.order_by(order)
if search_clicked and kw['search'] == "Download":
if kw['file_type'] and kw['file_type'] != u'' and kw['sell_type'] and kw['sell_type'] != u'':
if kw['sell_type'] == u'all':
lcompounds = lcompound.all()
elif kw['sell_type'] == u'selected':
if selection:
lcompounds = ()
for el in selection:
lcompounds += (DBSession.query(LCompound).get(el), )
else:
flash(l_(u'Lack of selected structures for download'), 'error')
redirect(request.headers['Referer'])
elif kw['sell_type'] == u'range':
lcompounds = lcompound.all()
if kw.has_key('select_from') and kw['select_from'] != u'':
try:
select_from = int(kw['select_from']) -1
if select_from<1 or select_from>len(lcompounds):
select_from = 0
except Exception:
select_from = 0
else:
select_from = 0
if kw.has_key('select_to') and kw['select_to'] != u'':
try:
select_to = int(kw['select_to'])
if select_to<2 or select_to>len(lcompounds):
select_to = len(lcompounds)
except Exception:
select_to = len(lcompounds)
else:
select_to = len(lcompounds)
lcompounds_new = ()
for el in range(select_from, select_to):
lcompounds_new += (lcompounds[el], )
lcompounds = lcompounds_new
else:
flash(l_(u'Lack of items to download'), 'error')
redirect(request.headers['Referer'])
try:
if isinstance(kw['options'], basestring):
options = [kw['options']]
else:
options = kw['options']
except Exception:
flash(l_('Choose download options'), 'error')
redirect(request.headers['Referer'])
if 'getsize' in kw:
size = int(kw['getsize']), int(kw['getsize'])
else:
size = 100, 100
if kw['file_type'] == 'pdf':
filename = userid + '_selected.pdf'
from xhtml2pdf.pisa import CreatePDF
from tg.render import render as render_template
import cStringIO
html = render_template({"length":len(lcompounds), "lcompound":lcompounds, "cells":cells, "options":options, "size":size}, "genshi", "molgears.templates.users.results.print2", doctype=None)
dest = './molgears/files/pdf/' + filename
result = file(dest, "wb")
CreatePDF(cStringIO.StringIO(html.encode("UTF-8")), result, encoding="utf-8")
result.close()
import paste.fileapp
f = paste.fileapp.FileApp('./molgears/files/pdf/'+ filename)
from tg import use_wsgi_app
return use_wsgi_app(f)
elif kw['file_type'] == 'xls':
filename = userid + '_selected.xls'
filepath = os.path.join('./molgears/files/download/', filename)
from PIL import Image
import xlwt
wbk = xlwt.Workbook()
sheet = wbk.add_sheet('sheet1')
j=0
if 'nr' in options:
sheet.write(0,j,u'Nr.')
j+=1
if 'gid' in options:
sheet.write(0,j,u'GID')
j+=1
if 'id' in options:
sheet.write(0,j,u'ID')
j+=1
if 'name' in options:
sheet.write(0,j,u'Name')
j+=1
if 'names' in options:
sheet.write(0,j,u'Names')
j+=1
if 'image' in options:
sheet.write(0,j,u'Image')
j+=1
if 'smiles' in options:
sheet.write(0,j,u'SMILES')
j+=1
if 'inchi' in options:
sheet.write(0,j,u'InChi')
j+=1
if 'lso' in options:
sheet.write(0,j,u'LSO')
j+=1
if 'num_atoms' in options:
sheet.write(0,j,u'Atoms')
j+=1
if 'mw' in options:
sheet.write(0,j,u'MW')
j+=1
if 'hba' in options:
sheet.write(0,j,u'hba')
j+=1
if 'hbd' in options:
sheet.write(0,j,u'hbd')
j+=1
if 'tpsa' in options:
sheet.write(0,j,u'tpsa')
j+=1
if 'logp' in options:
sheet.write(0,j,u'logP')
j+=1
if 'purity' in options:
sheet.write(0,j, u'Purity')
j+=1
if 'create_date' in options:
sheet.write(0,j,u'Date')
j+=1
if 'box' in options:
sheet.write(0,j,u'Box')
j+=1
if 'entry' in options:
sheet.write(0,j,u'Entry')
j+=1
if 'source' in options:
sheet.write(0,j,u'Source')
j+=1
if 'content' in options:
sheet.write(0,j,u'Content')
j+=1
if 'tags' in options:
sheet.write(0,j,u'Tags')
j+=1
if 'notes' in options:
sheet.write(0,j,u'Notes')
j+=1
for cell_line in cells:
if '_CT_%s' % cell_line in options:
sheet.write(0,j,u'CT %s' % cell_line)
j+=1
i = 1
for row in lcompounds:
j=0
if 'nr' in options:
sheet.write(i,j, str(i))
j+=1
if 'gid' in options:
sheet.write(i,j, row.gid)
j+=1
if 'id' in options:
sheet.write(i,j, row.id)
j+=1
if 'name' in options:
sheet.write(i,j, row.mol.name)
j+=1
if 'names' in options:
names = u''
for n in row.mol.names:
names += n.name + u', '
sheet.write(i,j, names)
j+=1
if 'image' in options:
file_in = './molgears/public/img/%s.png' % row.gid
img = Image.open(file_in)
file_out = './molgears/public/img/bitmap/thumb%s.bmp' %row.gid
img.thumbnail(size, Image.ANTIALIAS)
img.save(file_out)
sheet.insert_bitmap(file_out , i,j, 5, 5)
j+=1
if 'smiles' in options:
sheet.write(i,j, str(row.mol.structure))
j+=1
if 'inchi' in options:
sheet.write(i,j, str(row.mol.inchi))
j+=1
if 'lso' in options:
sheet.write(i,j, row.lso)
j+=1
if 'num_atoms' in options:
sheet.write(i,j,str(row.mol.num_hvy_atoms)+'/'+str(row.mol.num_atoms))
j+=1
if 'mw' in options:
sheet.write(i,j, str(row.mol.mw))
j+=1
if 'hba' in options:
sheet.write(i,j, str(row.mol.hba))
j+=1
if 'hbd' in options:
sheet.write(i,j, str(row.mol.hbd))
j+=1
if 'tpsa' in options:
sheet.write(i,j, str(row.mol.tpsa))
j+=1
if 'logp' in options:
sheet.write(i,j, str(row.mol.logp))
j+=1
if 'state' in options:
sheet.write(i,j, str(row.state))
j+=1
if 'purity' in options:
pur = u''
for p in sorted(row.purity, key=lambda p: p.value, reverse=True):
pur += u'%s : %s\n' % (p.value, p.type)
sheet.write(i,j, pur)
j+=1
if 'create_date' in options:
sheet.write(i,j, str(row.create_date))
j+=1
if 'owner' in options:
sheet.write(i,j, row.owner)
j+=1
if 'box' in options:
sheet.write(i,j, row.box)
j+=1
if 'entry' in options:
sheet.write(i,j, row.entry)
j+=1
if 'source' in options:
sheet.write(i,j, row.source)
j+=1
if 'content' in options:
if row.content:
sheet.write(i,j, str(row.content.value))
else:
sheet.write(i,j, 'None')
j+=1
if 'tags' in options:
tagsy=u''
for tag in row.mol.tags:
tagsy += tag.name + u', '
sheet.write(i,j,tagsy)
j+=1
if 'notes' in options:
sheet.write(i,j, row.notes)
j+=1
for cell_line in cells:
if '_CT_%s' % cell_line in options:
res = []
if row.ctoxicity:
for ct in sorted(row.ctoxicity, key=lambda ct: ct.id):
if ct.cell_line==cell_line:
res.append(ct.ic50)
if len(res)>0:
sheet.write(i,j, str(round(sum(res)/len(res), 3)))
else:
sheet.write(i,j, '')
j+=1
i += 1
wbk.save(filepath)
import paste.fileapp
f = paste.fileapp.FileApp(filepath)
from tg import use_wsgi_app
return use_wsgi_app(f)
elif kw['file_type'] == 'sdf':
filepath = './molgears/files/download/out.sdf'
ww = Chem.SDWriter(filepath)
from rdkit.Chem import AllChem
for row in lcompounds:
m2 = Chem.MolFromSmiles(str(row.mol.structure))
AllChem.Compute2DCoords(m2)
AllChem.EmbedMolecule(m2)
AllChem.UFFOptimizeMolecule(m2)
if 'smiles' in options:
m2.SetProp("smiles", str(row.mol.structure))
if 'name' in options:
m2.SetProp("_Name", str(row.mol.name.encode('ascii', 'ignore')))
if 'nr' in options:
m2.SetProp("Nr", str(lcompounds.index(row)+1))
if 'gid' in options:
m2.SetProp("GID", str(row.gid))
if 'names' in options:
names = u''
for n in row.mol.names:
names += n.name + ', '
m2.SetProp("names", str(names.encode('ascii', 'ignore')))
if 'inchi' in options:
m2.SetProp("InChi", str(row.mol.inchi))
if 'lso' in options:
m2.SetProp("LSO", str(row.lso))
if 'num_atoms' in options:
m2.SetProp("atoms", str(row.mol.num_hvy_atoms)+'/'+str(row.mol.num_atoms))
if 'mw' in options:
m2.SetProp("mw", str(row.mol.mw))
if 'hba' in options:
m2.SetProp("hba", str(row.mol.hba))
if 'hbd' in options:
m2.SetProp("hbd", str(row.mol.hbd))
if 'tpsa' in options:
m2.SetProp("TPSA", str(row.mol.tpsa))
if 'logp' in options:
m2.SetProp("logP", str(row.mol.tpsa))
if 'create_date' in options:
m2.SetProp("create_date", str(row.create_date))
if 'owner' in options:
m2.SetProp("owner", str(row.owner))
if 'tags' in options:
tagsy=u''
for tag in row.mol.tags:
tagsy += tag.name + u', '
m2.SetProp("tagi", str(tagsy.encode('ascii', 'ignore')))
if 'purity' in options:
pur = u''
for p in sorted(row.purity, key=lambda p: p.value, reverse=True):
pur += u'%s : %s \n' % (p.value, p.type)
m2.SetProp("purity", str(pur.encode('ascii', 'ignore')))
if 'content' in options:
if row.content:
m2.SetProp("content", str(row.content.value))
else:
m2.SetProp("content", "None")
j+=1
if 'box' in options:
m2.SetProp("box", str(row.box))
if 'entry' in options:
m2.SetProp("entry", str(row.entry))
if 'notes' in options:
if row.notes:
m2.SetProp("notes", str(row.notes.encode('ascii', 'ignore')))
else:
m2.SetProp("notes", " ")
for cell_line in cells:
if '_CT_%s' % cell_line in options:
res = []
if row.ctoxicity:
for ct in sorted(row.ctoxicity, key=lambda ct: ct.id):
if ct.cell_line==cell_line:
res.append(ct.ic50)
if len(res)>0:
m2.SetProp('CT_%s' % cell_line, str(round(sum(res)/len(res), 3)))
else:
m2.SetProp('CT_%s' % cell_line, ' ')
ww.write(m2)
ww.close()
import paste.fileapp
f = paste.fileapp.FileApp(filepath)
from tg import use_wsgi_app
return use_wsgi_app(f)
elif kw['file_type'] == 'csv' or 'txt':
filename = userid + '_selected.' + kw['file_type']
filepath = os.path.join('./molgears/files/download/', filename)
from molgears.widgets.unicodeCSV import UnicodeWriter
import csv
if kw['file_type'] == u'csv':
delimiter = ';'
else:
delimiter = ' '
with open(filepath, 'wb') as csvfile:
spamwriter = UnicodeWriter(csvfile, delimiter=delimiter,
quotechar='|', quoting=csv.QUOTE_MINIMAL)
for row in lcompounds:
line =[]
if 'smiles' in options:
line.append(str(row.mol.structure))
if 'name' in options:
line.append(row.mol.name)
if 'nr' in options:
line.append(unicode(lcompounds.index(row)+1))
if 'gid' in options:
line.append(unicode(row.gid))
if 'names' in options:
names = u''
for n in row.mol.names:
names += n.name + u', '
line.append(names)
if 'inchi' in options:
line.append(row.mol.inchi)
if 'lso' in options:
line.append(row.lso)
if 'num_atoms' in options:
line.append(unicode(row.mol.num_hvy_atoms)+'/'+unicode(row.mol.num_atoms))
if 'mw' in options:
line.append(unicode(row.mol.mw))
if 'hba' in options:
line.append(unicode(row.mol.hba))
if 'hbd' in options:
line.append(unicode(row.mol.hbd))
if 'tpsa' in options:
line.append(unicode(row.mol.tpsa))
if 'logp' in options:
line.append(unicode(row.mol.logp))
if 'purity' in options:
pur = u''
for p in sorted(row.purity, key=lambda p: p.value, reverse=True):
pur += u'%s : %s\n' % (p.value, p.type)
line.append(pur)
if 'create_date' in options:
line.append(unicode(row.create_date))
if 'owner' in options:
line.append(row.owner)
if 'box' in options:
line.append(row.box)
if 'entry' in options:
line.append(row.entry)
if 'source' in options:
line.append(row.source)
if 'content' in options:
if row.content:
line.append(unicode(row.content.value))
else:
line.append(u'None')
if 'tags' in options:
tagsy= ''
for tag in row.mol.tags:
tagsy += tag.name + ', '
line.append(tagsy)
if 'notes' in options:
line.append(row.notes)
spamwriter.writerow(line)
import paste.fileapp
f = paste.fileapp.FileApp(filepath)
from tg import use_wsgi_app
return use_wsgi_app(f)
if selection and not search_clicked:
argv =''
gids = ''
for arg in selection:
argv += '/' + arg
tmp_result = DBSession.query(LCompound).get(arg)
gids += '/' + str(tmp_result.gid)
if kw['akcja'] == u'edit':
redirect('/%s/molecules/multiedit/index%s' % (pname, gids))
elif kw['akcja'] == u'results':
if len(selection) == 1:
redirect('/%s/results/new_result%s' % (pname, argv))
else:
redirect('/%s/results/multiresults/index%s' % (pname, argv))
elif kw['akcja'] == u'htrf':
if len(selection) == 1:
redirect('/%s/results/htrf/add_result2%s' % (pname, argv))
currentPage = paginate.Page(lcompound, page, url=page_url, items_per_page=items)
return dict(currentPage=currentPage,tmpl=tmpl, page='results', htmlRgb=htmlRgb, htmlRgb100=htmlRgb100, Num2Rgb=Num2Rgb, pname=pname, alltags=alltags, similarity=similarity, cells=cells, ulists=ulists, ulist=ulist)
def index(self, page=1, *args, **kw):
"""
Index controller for molecules
"""
pname = request.environ['PATH_INFO'].split('/')[1]
project = DBSession.query(Projects).filter(Projects.name==pname).first()
alltags =[tag for tag in DBSession.query(Tags).order_by('name').all() ]
from sqlalchemy import or_
compound = DBSession.query(Compound).filter(Compound.project.any(Projects.name==pname)).filter(or_(Compound.pcompounds != None, Compound.lcompounds != None))
dsc = True
tmpl = ''
selection = None
similarity = None
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
threshold = float(user.threshold)/100.0
items = user.items_per_page
order = "gid"
try:
if kw['search'] != u'':
search_clicked = kw['search']
else:
search_clicked = None
except Exception:
search_clicked = None
if kw:
delkw = []
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
order = v
if str(k) != 'select' and str(k) != 'remove' and str(v) != u'':
tmpl += str(k) + '=' + str(v) + '&'
elif str(k) == 'select':
try:
if isinstance(kw['select'], basestring):
selection = [kw['select']]
else:
selection = [id for id in kw['select']]
except Exception:
selection = None
elif str(v) == u'':
delkw.append(k)
for k in delkw:
del kw[k]
if search_clicked:
try:
smiles = str(kw['smiles'])
except Exception:
smiles = None
pass
try:
method = str(kw['method'])
except Exception:
method = None
pass
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
from razi.postgresql_rdkit import tanimoto_threshold
DBSession.execute(tanimoto_threshold.set(threshold))
query_bfp = functions.morgan_b(TxtMoleculeElement(smiles), 2)
constraint = Compound.morgan.tanimoto_similar(query_bfp)
tanimoto_sml = Compound.morgan.tanimoto_similarity(query_bfp).label('tanimoto')
limit = user.limit_sim
search = DBSession.query(Compound, tanimoto_sml).filter(constraint).filter(Compound.project.any(Projects.name==pname)).order_by(desc(tanimoto_sml)).limit(limit).all()
compound = ()
similarity = ()
for row in search:
compound += (row[0], )
similarity += (row[1], )
page_url = paginate.PageURL_WebOb(request)
currentPage = paginate.Page(compound, page, url=page_url, items_per_page=items)
return dict(length=len(compound), compound=currentPage.items, currentPage=currentPage, tmpl=tmpl, page='samples', pname=pname, alltags=alltags, similarity=similarity)
elif method == 'substructure':
constraint = Compound.structure.contains(smiles)
compound = DBSession.query(Compound).filter(constraint).filter(Compound.project.any(Projects.name==pname))
elif method == 'identity':
compound = DBSession.query(Compound).filter(Compound.structure.equals(smiles)).filter(Compound.project.any(Projects.name==pname))
else:
flash(l_(u'Smiles error'), 'warning')
redirect(request.headers['Referer'])
if kw.has_key('text_GID') and kw['text_GID'] !=u'':
try:
gid = int(kw['text_GID'])
compound = compound.filter_by(gid = gid )
except Exception as msg:
flash(l_(u'GID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_name') and kw['text_name'] !=u'':
compound = compound.filter(Compound.names.any(Names.name.like(kw['text_name'].strip().replace('*', '%'))))
if kw.has_key('text_creator') and kw['text_creator'] !=u'':
compound = compound.filter(Compound.creator.like(kw['text_creator'].replace('*', '%')))
if kw.has_key('text_notes') and kw['text_notes'] !=u'':
compound = compound.filter(Compound.notes.like(kw['text_notes'].replace('*', '%')))
if kw.has_key('date_from') and kw['date_from'] !=u'':
date_from = datetime.strptime(str(kw['date_from']), '%Y-%m-%d')
compound = compound.filter(Compound.create_date > date_from)
else:
date_from = None
if kw.has_key('date_to') and kw['date_to'] !=u'':
date_to = datetime.strptime(str(kw['date_to']), '%Y-%m-%d')
if date_from:
if date_to>date_from:
compound = compound.filter(Compound.create_date < date_to)
else:
flash(l_(u'The End date must be later than the initial'), 'error')
redirect(request.headers['Referer'])
else:
compound = compound.filter(Compound.create_date < date_to)
try:
tags = kw['text_tags']
except Exception:
tags = None
pass
if tags:
if isinstance(tags, basestring):
tagi = eval(tags)
if type(tagi) != type([]):
tagi = [int(tags)]
else:
tagi = [int(id) for id in tags]
# import sqlalchemy
compound = compound.filter(Compound.tags.any(Tags.id.in_(tagi)))
if selection and not search_clicked:
argv =''
for arg in selection:
argv += '/' + arg
if kw['akcja'] == u'edit':
if len(selection) == 1:
redirect('/%s/samples/edit%s' % (pname, argv))
else:
redirect('/%s/samples/multiedit/index%s' % (pname, argv))
elif kw['akcja'] == u'accept':
if len(selection) == 1:
redirect('/%s/samples/accept%s' % (pname, argv))
else:
redirect('/%s/samples/multiaccept/index%s' % (pname, argv))
elif kw['akcja'] == u'library':
if len(selection) == 1:
redirect('/%s/samples/library%s' % (pname, argv))
else:
redirect('/%s/samples/multilibrary/index%s' % (pname, argv))
elif kw['akcja'] == u'pdf':
redirect('/%s/samples/index/download%s/pdf/samples_selected.pdf' % (pname, argv))
elif kw['akcja'] == u'xls':
redirect('/%s/samples/download%s/xls/samples_selected.xls' % (pname, argv))
elif kw['akcja'] == u'txt':
redirect('/%s/samples/download%s/txt/samples_selected.txt' % (pname, argv))
elif kw['akcja'] == u'delete':
redirect('/%s/samples/remove%s' % (pname, argv))
else:
flash(l_(u'Action error'), 'error')
redirect(request.headers['Referer'])
else:
try:
akcja = kw['akcja']
except Exception:
akcja = None
if akcja:
if akcja == u'pdf':
redirect('/%s/samples/index/download/pdf/samples_all.pdf' % pname)
elif akcja == u'xls':
redirect('/%s/samples/download/xls/samples_all.xls' % pname)
elif akcja == u'txt':
redirect('/%s/samples/download/txt/samples_all.txt' % pname)
if dsc:
compound = compound.order_by(desc(order).nullslast())
else:
compound = compound.order_by((order))
page_url = paginate.PageURL_WebOb(request)
currentPage = paginate.Page(compound, page, url=page_url, items_per_page=items)
return dict(compound=currentPage.items, currentPage=currentPage, tmpl=tmpl, page='samples', pname=pname, alltags=alltags, similarity=similarity)
def index(self, page=1, *args, **kw):
"""
Index controller for molecules
"""
pname = request.environ['PATH_INFO'].split('/')[1]
project = DBSession.query(Projects).filter(
Projects.name == pname).first()
alltags = [tag for tag in DBSession.query(Tags).order_by('name').all()]
from sqlalchemy import or_
compound = DBSession.query(Compound).filter(
Compound.project.any(Projects.name == pname)).filter(
or_(Compound.pcompounds != None, Compound.lcompounds != None))
dsc = True
tmpl = ''
selection = None
similarity = None
userid = request.identity['repoze.who.userid']
user = DBSession.query(User).filter_by(user_name=userid).first()
threshold = float(user.threshold) / 100.0
items = user.items_per_page
order = "gid"
try:
if kw['search'] != u'':
search_clicked = kw['search']
else:
search_clicked = None
except Exception:
search_clicked = None
if kw:
delkw = []
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
order = v
if str(k) != 'select' and str(k) != 'remove' and str(v) != u'':
tmpl += str(k) + '=' + str(v) + '&'
elif str(k) == 'select':
try:
if isinstance(kw['select'], basestring):
selection = [kw['select']]
else:
selection = [id for id in kw['select']]
except Exception:
selection = None
elif str(v) == u'':
delkw.append(k)
for k in delkw:
del kw[k]
if search_clicked:
try:
smiles = str(kw['smiles'])
except Exception:
smiles = None
pass
try:
method = str(kw['method'])
except Exception:
method = None
pass
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
from razi.postgresql_rdkit import tanimoto_threshold
DBSession.execute(
tanimoto_threshold.set(threshold))
query_bfp = functions.morgan_b(
TxtMoleculeElement(smiles), 2)
constraint = Compound.morgan.tanimoto_similar(
query_bfp)
tanimoto_sml = Compound.morgan.tanimoto_similarity(
query_bfp).label('tanimoto')
limit = user.limit_sim
search = DBSession.query(
Compound,
tanimoto_sml).filter(constraint).filter(
Compound.project.
any(Projects.name == pname)).order_by(
desc(tanimoto_sml)).limit(limit).all()
compound = ()
similarity = ()
for row in search:
compound += (row[0], )
similarity += (row[1], )
page_url = paginate.PageURL_WebOb(request)
currentPage = paginate.Page(compound,
page,
url=page_url,
items_per_page=items)
return dict(length=len(compound),
compound=currentPage.items,
currentPage=currentPage,
tmpl=tmpl,
page='samples',
pname=pname,
alltags=alltags,
similarity=similarity)
elif method == 'substructure':
constraint = Compound.structure.contains(smiles)
compound = DBSession.query(Compound).filter(
constraint).filter(
Compound.project.any(
Projects.name == pname))
elif method == 'identity':
compound = DBSession.query(Compound).filter(
Compound.structure.equals(smiles)).filter(
Compound.project.any(
Projects.name == pname))
else:
flash(l_(u'Smiles error'), 'warning')
redirect(request.headers['Referer'])
if kw.has_key('text_GID') and kw['text_GID'] != u'':
try:
gid = int(kw['text_GID'])
compound = compound.filter_by(gid=gid)
except Exception as msg:
flash(l_(u'GID should be a number: %s' % msg), 'error')
redirect(request.headers['Referer'])
if kw.has_key('text_name') and kw['text_name'] != u'':
compound = compound.filter(
Compound.names.any(
Names.name.like(kw['text_name'].strip().replace(
'*', '%'))))
if kw.has_key('text_creator') and kw['text_creator'] != u'':
compound = compound.filter(
Compound.creator.like(kw['text_creator'].replace(
'*', '%')))
if kw.has_key('text_notes') and kw['text_notes'] != u'':
compound = compound.filter(
Compound.notes.like(kw['text_notes'].replace('*',
'%')))
if kw.has_key('date_from') and kw['date_from'] != u'':
date_from = datetime.strptime(str(kw['date_from']),
'%Y-%m-%d')
compound = compound.filter(
Compound.create_date > date_from)
else:
date_from = None
if kw.has_key('date_to') and kw['date_to'] != u'':
date_to = datetime.strptime(str(kw['date_to']), '%Y-%m-%d')
if date_from:
if date_to > date_from:
compound = compound.filter(
Compound.create_date < date_to)
else:
flash(
l_(u'The End date must be later than the initial'
), 'error')
redirect(request.headers['Referer'])
else:
compound = compound.filter(
Compound.create_date < date_to)
try:
tags = kw['text_tags']
except Exception:
tags = None
pass
if tags:
if isinstance(tags, basestring):
tagi = eval(tags)
if type(tagi) != type([]):
tagi = [int(tags)]
else:
tagi = [int(id) for id in tags]
# import sqlalchemy
compound = compound.filter(
Compound.tags.any(Tags.id.in_(tagi)))
if selection and not search_clicked:
argv = ''
for arg in selection:
argv += '/' + arg
if kw['akcja'] == u'edit':
if len(selection) == 1:
redirect('/%s/samples/edit%s' % (pname, argv))
else:
redirect('/%s/samples/multiedit/index%s' % (pname, argv))
elif kw['akcja'] == u'accept':
if len(selection) == 1:
redirect('/%s/samples/accept%s' % (pname, argv))
else:
redirect('/%s/samples/multiaccept/index%s' % (pname, argv))
elif kw['akcja'] == u'library':
if len(selection) == 1:
redirect('/%s/samples/library%s' % (pname, argv))
else:
redirect('/%s/samples/multilibrary/index%s' %
(pname, argv))
elif kw['akcja'] == u'pdf':
redirect(
'/%s/samples/index/download%s/pdf/samples_selected.pdf' %
(pname, argv))
elif kw['akcja'] == u'xls':
redirect('/%s/samples/download%s/xls/samples_selected.xls' %
(pname, argv))
elif kw['akcja'] == u'txt':
redirect('/%s/samples/download%s/txt/samples_selected.txt' %
(pname, argv))
elif kw['akcja'] == u'delete':
redirect('/%s/samples/remove%s' % (pname, argv))
else:
flash(l_(u'Action error'), 'error')
redirect(request.headers['Referer'])
else:
try:
akcja = kw['akcja']
except Exception:
akcja = None
if akcja:
if akcja == u'pdf':
redirect('/%s/samples/index/download/pdf/samples_all.pdf' %
pname)
elif akcja == u'xls':
redirect('/%s/samples/download/xls/samples_all.xls' %
pname)
elif akcja == u'txt':
redirect('/%s/samples/download/txt/samples_all.txt' %
pname)
if dsc:
compound = compound.order_by(desc(order).nullslast())
else:
compound = compound.order_by((order))
page_url = paginate.PageURL_WebOb(request)
currentPage = paginate.Page(compound,
page,
url=page_url,
items_per_page=items)
return dict(compound=currentPage.items,
currentPage=currentPage,
tmpl=tmpl,
page='samples',
pname=pname,
alltags=alltags,
similarity=similarity)
def _do_get_provider_count_and_objs(self, name=None, **kw):
userid = request.identity['repoze.who.userid']
scompound = ()
dsc = True
order = 'id'
if kw:
try:
smiles = kw['smi']
method = kw['method']
except Exception:
smiles = None
method = None
pass
try:
ogranicz_tekst = kw['ogranicz_tekst']
except Exception:
ogranicz_tekst = None
pass
if smiles:
if checksmi(smiles):
from razi.functions import functions
from razi.expression import TxtMoleculeElement
if method == 'similarity':
query_bfp = functions.morgan_b(
TxtMoleculeElement(smiles), 2)
constraint = SCompound.morgan.dice_similar(query_bfp)
dice_sml = SCompound.morgan.dice_similarity(
query_bfp).label('dice')
# scompound = DBSession.query(SCompound, dice_sml).filter(constraint).filter(SCompound.owner.contains(userid))
scompound = DBSession.query(
SCompound).filter(constraint).filter(
SCompound.owner.contains(userid))
elif method == 'substructure':
constraint = SCompound.structure.contains(smiles)
scompound = DBSession.query(
SCompound).filter(constraint).filter(
SCompound.owner.contains(userid))
elif method == 'identity':
scompound = DBSession.query(SCompound).filter(
SCompound.structure.equals(smiles)).filter(
SCompound.owner.contains(userid))
# if ogranicz_tekst:
# scompound = scompound.filter(SCompound.__getattribute__(SCompound, kw['ogranicz']).like(ogranicz_tekst))
else:
flash('SMILES error', 'warning')
scompound = ()
else:
scompound = DBSession.query(SCompound).filter(
SCompound.owner.contains(userid))
if ogranicz_tekst:
if kw['ogranicz'] == 'p_id':
try:
p_id = int(ogranicz_tekst)
scompound = scompound.filter_by(p_id=p_id)
except Exception as msg:
flash('P_id should be a number: %s' % msg, 'error')
else:
scompound = scompound.filter(
SCompound.__getattribute__(
SCompound, kw['ogranicz']).like(ogranicz_tekst))
try:
tagi = kw['tags']
except Exception:
tagi = None
pass
if isinstance(tagi, basestring):
tagi_id = [int(tagi)]
else:
tagi_id = [int(id) for id in tagi]
if tagi_id:
import sqlalchemy
scompound = scompound.filter(
SCompound.tags.any(Tags.tags_id.in_(tagi_id)))
# scompound = scompound.filter(SCompound.tags.contain(tagi_id))
# scompound = scompound.join(SCompound.tags).filter_by(not_(tags_id = tagi_id[0]))
if int(kw['status']) > 0:
scompound = scompound.filter(
SCompound.status_id == int(kw['status']))
for k, v in kw.iteritems():
if str(k) == 'desc' and str(v) != '1':
dsc = None
elif str(k) == 'order_by':
order = v
if scompound:
if dsc:
scompound = scompound.order_by(desc(order))
else:
scompound = scompound.order_by((order))
scompound = scompound.all()
# scompound = scompound.all()
return len(scompound), scompound