def search_to_json(self, *args, **kw):
#TODO : sort by column on user's click
user_lab = session.get("current_lab", None)
#get parameters from ajax request
search_value = kw.get("search[value]", None)
if search_value == '':
search_value = None
#word lenght > 2 to avoid DDoS in your server....
elif search_value is not None:
list_search_words = [x for x in search_value.split(" ") if len(x) > 2]
draw = int(kw.get("draw", 1))
start_point = int(kw.get("start", 0))
data_by_page = int(kw.get("length", 50))
stop_point = start_point + data_by_page
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
measurements_total = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
measurements = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).distinct()[start_point:stop_point]
if search_value is not None:
final_request = self.search_engine(list_search_words, lab)
#query mixed with results from all the table of interest
paginated_request = final_request[start_point:stop_point]
searching_tosort = [SW(meas).to_json_test() for meas in paginated_request]
searching = sorted(searching_tosort, key=lambda k: (k['User'], k['Type']))
return json.dumps({"draw": draw, "recordsTotal": len(measurements_total), "recordsFiltered": len(final_request), "data": searching})
searching_tosort = [SW(meas).to_json_test() for meas in measurements]
searching = sorted(searching_tosort, key=lambda k: (k['User'], k['Type']))
return json.dumps({"draw": draw, "recordsTotal": len(measurements_total), "recordsFiltered": len(measurements_total), "data": searching})
def change_project_owner(self, p_id, new_owner_id, mail, key):
'''
Allow to change the owner of one given project (include its sample(s) and measurement(s))
'''
try:
p_target = DBSession.query(Projects).filter(Projects.id == p_id).first()
#just one lab by project, so the first is the good one
project_lab = p_target.labs[0]
new_owner = DBSession.query(User).filter(User.id == new_owner_id).first()
if project_lab in new_owner.labs:
list_samples = p_target.samples
for s in list_samples:
list_meas = s.measurements
for m in list_meas:
m.user_id = new_owner.id
DBSession.add(m)
DBSession.flush()
p_target.user_id = new_owner.id
DBSession.add(p_target)
DBSession.flush()
print "Update done."
else:
raise Exception("The new owner is not a member of this lab project. Impossible to continue the operation.")
except:
print_traceback()
def get_dl_url(self, mail, key, meas_id):
'''
provide dl URL from measurements id
'''
list_ids = meas_id.split(',')
user = DBSession.query(User).filter(User._email == mail).first()
if user is None:
return {'ERROR': "User " + mail + " not in BioRepo."}
else:
dico_urls = {}
user_labs = user.labs
for labo in user_labs:
lab = DBSession.query(Labs).filter(Labs.name == labo.name).first()
for m_id in list_ids:
meas = DBSession.query(Measurements).join(Measurements.attributs)\
.filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False))\
.filter(Measurements.id == m_id).first()
if meas is not None:
list_fus = meas.fus
if len(list_fus)>0:
for f in list_fus:
sha1 = f.sha1
if meas.status_type:
dico_urls[m_id] = "/biorepo/public/public_link?m_id=" + str(m_id) + "&sha1=" + str(sha1)
else:
dico_urls["ERROR " + str(m_id)] = "This file is registered as private. BioRepo can't produce a public link."
else:
dico_urls["ERROR " + str(m_id)] = "No file attached with this measurements. The saved description is : " + str(meas.description)
else:
dico_urls["ERROR " + str(m_id)] = "This measurements id does not exist or you can access to it with your current rights."
#TODO test and add to devdoc #API
return dico_urls
def get_samples_from_project(self, mail, key, p_id):
'''
Get a JSON with all samples from a given project
input : mail and biorepo key, p_id (project id)
output : {"project id": [{"sample id": {"name": "my sample name", "type": "4C-seq",
"protocole": "my sample protocole", "dynamic field": "my dynamic field, ..."}}, ...]}
'''
user = DBSession.query(User).filter(User._email == mail).first()
user_lab = user.labs
list_samples = []
dico_final = {}
target = DBSession.query(Projects).filter(Projects.id == p_id).first()
if target is None:
return {'ERROR': "This project ID does not exist."}
lab_target = target.labs[0]
#check if the project is owned by the user or his lab
access_ok = False
for l in user_lab:
if l.id == lab_target.id:
access_ok = True
if access_ok:
samples = target.samples
if len(samples) == 0:
return {'ERROR': 'This project id : ' + str(target.id) + ' is empty.'}
for s in samples:
dico_sample = {}
dico_dynamic = {}
sample_attributs = s.attributs
sample_a_values = s.a_values
for att in sample_attributs:
att_id = att.id
att_key = att.key
for val in sample_a_values:
value = val.value
if val.attribut_id == att_id:
#for the true weird checkbox
if value == "true":
dico_dynamic[att_key] = att_key
else:
dico_dynamic[att_key] = value
#check the weird checkbox widget with "false" value
if len(sample_attributs) != len(dico_dynamic.keys()):
for att in sample_attributs:
att_key = att.key
att_widget = att.widget
if att_key not in dico_dynamic.keys() and att_widget == "checkbox":
dico_dynamic[att_key] = "Not " + str(att_key)
elif att_key not in dico_dynamic.keys() and att_widget != "checkbox":
dico_dynamic[att_key] = "Not specified"
dico_sample = {"name": s.name, "type": s.type, "protocole": s.protocole}
dico_sample.update(dico_dynamic)
list_samples.append({s.id: dico_sample})
dico_final[p_id] = list_samples
return dico_final
else:
return {'ERROR': "This project is not a project from your lab, you cannot access to it."}
def searchlists_to_json(self, *args, **kw):
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
one_meas = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).first()
search_grid, hidden_positions, positions_not_searchable = build_search_grid(one_meas)
searchlists = json.dumps([hidden_positions, positions_not_searchable])
return searchlists
def get_permissions(admin):
'''
Get the right permissions for an user.
@param admin : True if the user is an admin.
@type admin : a boolean.
'''
if admin:
return DBSession.query(Permission).all()
return DBSession.query(Permission).filter(Permission.name != 'admin').all()
def get_my_lab_projects(self, mail, key):
'''
Get a JSON with all user's projects by lab
input : mail an biorepo key
output : {'lab':{'project id':{'name': "my_project_name", 'description': "my project description",
"owner": "project owner name"}}}
'''
dico_lab_projects = {}
dico_by_labs = {}
user = DBSession.query(User).filter(User._email == mail).first()
if user is None:
return {'ERROR': "User " + mail + " not in BioRepo."}
else:
user_labs = user.labs
if len(user_labs) == 1:
for lab in user_labs:
lab_projects = lab.projects
if isinstance(lab_projects, list):
for p in lab_projects:
u = DBSession.query(User).filter(User.id == p.user_id).first()
owner = u.name
dico_lab_projects[p.id] = {'name': p.project_name, 'description': p.description,
'owner': owner}
else:
u = DBSession.query(User).filter(User.id == p.user_id).first()
owner = u.name
dico_lab_projects[lab_projects.id] = {'name': lab_projects.project_name, 'description': lab_projects.description,
'owner': owner}
if len(lab_projects) == 0:
return {'ERROR': "No projects found for " + lab.name}
dico_by_labs[lab.name] = dico_lab_projects
return dico_by_labs
elif len(user.labs) > 1:
for l in user.labs:
lab_projects = l.projects
if isinstance(lab_projects, list):
for p in lab_projects:
u = DBSession.query(User).filter(User.id == p.user_id).first()
owner = u.name
dico_lab_projects[p.id] = {'name': p.project_name, 'description': p.description,
'owner': owner}
else:
u = DBSession.query(User).filter(User.id == p.user_id).first()
owner = u.name
dico_lab_projects[lab_projects.id] = {'name': lab_projects.project_name, 'description': lab_projects.description,
'owner': owner}
dico_by_labs[l.name] = dico_lab_projects
dico_lab_projects = {}
return dico_by_labs
else:
return {'ERROR': "This user " + mail + " has no lab. Contact the administrator please."}
def index(self, *args, **kw):
user_lab = session.get("current_lab", None)
user_projects = []
u_projects = []
u_samples = []
u_meas = []
u_children = []
u_global = []
dico_final = {}
#TODO : admin view - watch for a dl link
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
lab_users = lab.users
for u in lab_users:
projects = DBSession.query(Projects).filter(Projects.user_id == u.id).all()
if len(projects) > 0:
for p in projects:
for lab in p.labs:
if lab.name == user_lab:
user_projects.append(p)
for proj in user_projects:
for sample in proj.samples:
if len(sample.measurements) > 0:
for meas in sample.measurements:
if len(meas.children) == 0:
u_meas.append({"name": str(meas.name) + "(" + str(meas.id) + ")"})
else:
for child in meas.children:
u_children.append({"name": str(child.name) + "(" + str(child.id) + ")"})
u_meas.append({"name": str(meas.name) + "(" + str(meas.id) + ")", "children": u_children})
u_children = []
u_samples.append({"name": str(sample.name) + "(" + str(sample.type) + ")", "children": u_meas})
u_meas = []
else:
u_samples.append({"name": str(sample.name + "(" + str(sample.type) + ")")})
if len(proj.samples) > 0:
u_projects.append({"name": str(proj.project_name), "children": u_samples})
u_samples = []
else:
u_projects.append({"name": str(proj.project_name)})
u_global.append({"name": u.firstname + " " + u.name, "children": u_projects})
u_projects = []
user_projects = []
#uncomment these 4 lines if you want to see every lab users registered in BioRepo
#else:
#u_global.append({"name": u.firstname + " " + u.name})
#u_projects = []
#user_projects = []
dico_final["name"] = user_lab
dico_final["children"] = u_global
return {"data": json.dumps(dico_final)}
def new(self, *args, **kw):
tmpl_context.widget = new_attribut_form
#take the logged user
user = handler.user.get_user_in_session(request)
#take the logged user samples
samples = DBSession.query(Samples).join(Projects).join(User).filter(User.id == user.id).all()
meas = DBSession.query(Measurements).all()
attributs = DBSession.query(Attributs).all()
tmpl_context.samples = samples
tmpl_context.meas = meas
tmpl_context.attributs = attributs
return dict(page='samples', value=kw, title='New Sample', model='Sample')
def Gviz_link(self, sha1, meas_id, *args, **kw):
'''
redirect to Gviz BAM viewer hosted on HTSstation
'''
#URL example :
#bbcftools.epfl.ch/bam_viewer/gviews/new?assembly_name=pombe&module=biorepo&file=XTv7U2IYVAgIWqBHyPjC
meas = DBSession.query(Measurements).filter(
Measurements.id == meas_id).first()
list_a_values = []
#get the dynamic values
for val in meas.a_values:
list_a_values.append(val.id)
#check if "assembly" is a dynamic key for this measurement
cpt_test = 0
for a in meas.attributs:
if a.key == "assembly":
cpt_test += 1
#get all the values recorded for this key
list_assemblies = a.values
assembly = ''
for v in list_assemblies:
#check if the Attributs_values object is linked to this measurement
if v.id in list_a_values:
assembly = v.value
if assembly == '':
flash(
"Sorry but you have to set an assembly to this measurement",
"error")
raise redirect("/search")
else:
#TODO replace this when BioRepo and HTS will be connected together
#JUST CATCH THE PATH IN DB AND GIVE IT IN THE URL
#/!\ /archive/projects/epfl-vital-it/biorepo_upload/ /!\
hostname = socket.gethostname().lower()
#because of aliasing
if hostname == "ptbbsrv2.epfl.ch":
hostname = "biorepo.epfl.ch"
bam_file = DBSession.query(Files_up).filter(
Files_up.sha1 == sha1).first()
fullname = bam_file.filename
name_tmp = fullname.split('.')
name = name_tmp[0]
bam_name = self.BAM_visualisation(bam_file, name)
bam_path = bam_file.path
path_to_give = bam_path.split(
"/archive/projects/epfl/biorepo_upload")[1]
raise redirect(
'http://bbcftools.epfl.ch/bam_viewer/gviews/new?assembly_name='
+ assembly + "&module=biorepo&file=" + path_to_give +
"/" + bam_name)
def post_edit(self, *args, **kw):
id_project = kw["IDselected"]
project = DBSession.query(Projects).filter(Projects.id == id_project).first()
if kw['project_name'] == '':
flash("Bad Project : Your project must have a name", "error")
raise redirect("./edit/" + id_project)
project.project_name = kw["project_name"]
project.description = kw["description"]
samples_ids = kw.get("samples", None)
if samples_ids is not None:
if not isinstance(samples_ids, (list, tuple)):
samples_ids = [int(samples_ids)]
else:
#from unicode to integer for comparison
list_tmp = []
for i in samples_ids:
i = int(i)
list_tmp.append(i)
samples_ids = list_tmp
else:
samples_ids = []
#check if sample is not deleted
try:
if kw["selected_samples"] != "[]":
old_selected = [int(x) for x in kw["selected_samples"].replace("[", "").replace("]", "").split(",")]
else:
old_selected = []
except:
flash("Samples id error, please contact the administrator to report your bug", 'error')
print "Something changed with this Turbogears version.... controllers/project.py l180 --> JSON solution is better"
raise redirect("./")
list_names = []
for o in old_selected:
if o not in samples_ids:
sample1 = DBSession.query(Samples).filter(Samples.id == o).first()
list_names.append(str(sample1.name))
if len(list_names) > 0:
flash("If you choose to delete : " + str(list_names).replace("[", "").replace("]", "") + " from the project, this sample will be removed. The sample deletion is not enabled here. Please do it directly in the sample page delete option.", 'error')
raise redirect("./edit/" + id_project)
list_samples = []
for s in samples_ids:
sample = DBSession.query(Samples).filter(Samples.id == s).first()
list_samples.append(sample)
project.samples = list_samples
raise redirect("./")
def gimme_projects_plz(self, mail, *args, **kw):
user = DBSession.query(User).filter(User._email == mail).first()
if user is not None:
user_id = user.id
projects = DBSession.query(Projects).filter(Projects.user_id == user_id).all()
dico_projects_by_user = {}
if len(projects) != 0:
for p in projects:
dico_projects_by_user[p.id] = {"project_name": p.project_name}
else:
dico_projects_by_user = {0: {"project_name": "No projects found into BioRepo for this user"}}
else:
dico_projects_by_user = {"error": str(mail) + " is not regristred in BioRepo"}
return dico_projects_by_user
def change_bis_sample(self, sending_s, reception_s):
'''
Allow to move all the measurements of one sample to an other one
and delete the sending sample after the operation.
Usefull for the "_bis" samples in spreadsheet.
@param principal : sending_s (sample id sending the measurements), reception_s (sample id receptioning the measurements)
'''
try:
# samples queries
from_sample = DBSession.query(Samples).filter(Samples.id == int(sending_s)).first()
to_sample = DBSession.query(Samples).filter(Samples.id == int(reception_s)).first()
# get the measurements lists
from_att = from_sample.attributs
to_att = to_sample.attributs
# lab checking
if from_att[0].lab_id != to_att[0].lab_id:
raise Exception("Samples from different labs. Impossible to move these measurements.")
# get list of measurements objects
meas_to_move = from_sample.measurements
meas_in_place = to_sample.measurements
# move the measurements
for m in meas_to_move:
if m not in meas_in_place:
(to_sample.measurements).append(m)
DBSession.delete(from_sample)
DBSession.add(to_sample)
DBSession.flush()
print "---> Sample " + sending_s + " was deleted and its measurements are now into the sample " + reception_s
except:
print_traceback()
def drop_to_vitalit(self, mail, key, meas_ids):
'''
Copy-paste file(s) attached to the measurement(s) id given in input to a /scratch accessible path for the user
'''
list_ids = list(set(meas_ids.split(',')))
msg = "--- DO NOT REPLY TO THIS MESSAGE PLEASE ---\n\n"
user = DBSession.query(User).filter(and_(User._email == mail, User.key == key)).first()
if user is None:
return {'ERROR': "Your mail or you key is not correct."}
labs = user.labs
user_labs = []
for lab in labs:
user_labs.append(lab.name)
if list_ids is None or len(list_ids) == 0:
return {'ERROR': "You have to give one or several id(s) with the meas_ids key."}
#building dico with paths and filenames
dic_paths = {}
for i in list_ids:
meas = DBSession.query(Measurements).filter(Measurements.id == i).first()
#check lab rights
att_meas = meas.attributs[0]
lab_to_check = DBSession.query(Labs).filter(Labs.id == att_meas.lab_id).first()
if lab_to_check.name not in user_labs:
msg = msg + "ERROR : This measurement (" + str(meas.id) + ") doesn't belong to your lab. You can't access to it.\n"
#check status (public/private)
elif not meas.status_type:
msg = msg + "ERROR : This measurement (" + str(meas.id) + ")is not public. You can't move it from BioRepo."
else:
if len(meas.fus) > 0:
for fu in meas.fus:
path_fu = fu.path + "/" + fu.sha1
filename = fu.filename
dic_paths[filename] = path_fu
#check /scratch repository
public_path = path_dropbox(user_labs[0])
#copy-paste the file(s)
for k, v in dic_paths.iteritems():
try:
src = v
dest = public_path + "/" + k
copyfile(src, dest)
msg = msg + k + " is now accessible here : " + dest + "\n"
except:
print ">>> COPY ERROR WITH " + k
msg = msg + "ERROR " + k + " encountered a problem during the copy-paste process. Contact your admin for this file please.\n"
print_traceback()
#send mail with public path(s)
sendMail(user._email, msg, "[BioRepo] Get your file(s) on Vital-IT /scratch")
def check_value_addition(self, list_type_att, dict_att_values_type,
dict_att_values_db, lab_id):
'''
Checking for value(s) addition
@param principal
@return an updated db
'''
for key_type in list_type_att:
for i in dict_att_values_type[key_type]:
#get the attribut and its value(s)
i_att = DBSession.query(Attributs).filter(
and_(Attributs.lab_id == lab_id,
Attributs.key == key_type)).first()
#warning : i_att_value is a list !
i_att_value = DBSession.query(Attributs_values).filter(
and_(Attributs_values.attribut_id == i_att.id,
Attributs_values.value == i)).all()
try:
flag = False
if i not in dict_att_values_db[key_type] and i != "None":
for existant in i_att_value:
if existant.value == i and existant.deprecated == True:
existant.deprecated = False
DBSession.flush()
flag = True
if existant.value is None:
existant.deprecated = True
DBSession.flush()
if flag == False:
new_value = Attributs_values()
new_value.attribut_id = i_att.id
new_value.value = i
new_value.deprecated = False
DBSession.add(new_value)
DBSession.flush()
except Exception as e:
import sys, traceback
a, b, c = sys.exc_info()
traceback.print_exception(a, b, c)
print "--- error login.py check_value_addition() ---"
print "i --->", i
print "key_type --->", key_type
print "list_type_att --->", list_type_att
print "dict_att_values_type[key_type] -->", dict_att_values_type[
key_type]
print "i_att --> ", i_att
print "i_att_value", i_att_value
def get_UCSC_link(obj_id):
'''
Return a HTML link to UCSC
'''
meas = DBSession.query(Measurements).filter(Measurements.id == obj_id).first()
status = meas.status_type
normal_ext = ["bed", "bedgraph", "wig"]
#binary extension, except bam files
binary_ext = ["bw", "bigwig", "bigbed", "bb"]
if status and len(meas.fus) > 0:
list_fus = meas.fus
for x in list_fus:
f_sha1 = x.sha1
ext = x.extension
#t is type. 1 == normal extension, 2 == binary extension, 3 == bam
if ext.lower() in normal_ext:
return'''
<a class='action UCSC_link' href="%s" target="_blank" title="view in UCSC" style="text-decoration:none" target="_blank"></a> ''' % (url('./public/UCSC_link', params=dict(sha1=f_sha1, meas_id=obj_id, t=1)))
elif ext.lower() in binary_ext:
return'''
<a class='action UCSC_link' href="%s" target="_blank" title="view in UCSC" style="text-decoration:none" target="_blank"></a> ''' % (url('./public/UCSC_link', params=dict(sha1=f_sha1, meas_id=obj_id, t=2)))
elif ext.lower() == "bam":
return'''
<a class='action UCSC_link' href="%s" target="_blank" title="view in UCSC" style="text-decoration:none" target="_blank"></a> ''' % (url('./public/UCSC_link', params=dict(sha1=f_sha1, meas_id=obj_id, t=3)))
return ''
def BAM_visualisation(self, bam_object, filename_without_extension, *args, **kw):
#find the bam.bai file associated
bai = DBSession.query(Files_up).filter(and_(Files_up.filename == filename_without_extension + ".bam.bai", Files_up.extension == "bai")).first()
if bai is None:
flash("Sorry but " + bam_object.filename + " has no .bam.bai associated in BioRepo. Upload it and retry the operation.", "error")
raise redirect(url("/search"))
else:
bai_sha1 = bai.sha1
bam_sha1 = bam_object.sha1
bai_path = bai.path
bam_path = bam_object.path
#build the full paths (bam and bam.bai)
bai_full_path = bai_path + "/" + bai_sha1
bam_full_path = bam_path + "/" + bam_sha1
#creating symlink with good names and good extensions
#for the bam file
bam_dest = bam_path + "/" + bam_sha1 + ".bam"
if os.path.islink(bam_dest):
pass
else:
os.symlink(bam_full_path, bam_dest)
bam_name = bam_sha1 + ".bam"
#for the bai file
bai_dest = bam_path + "/" + bam_sha1 + ".bam.bai"
if os.path.islink(bai_dest):
pass
else:
os.symlink(bai_full_path, bai_dest)
return bam_name
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
admins = tg.config.get('admin.mails')
mail = user.email
if user_lab and mail not in admins:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
projects = [p for p in user.projects if p in lab.projects]
elif mail in admins:
projects = DBSession.query(Projects).all()
else:
projects = None
all_projects = [util.to_datagrid(ProjectGrid(), projects, "Projects Table", len(projects) > 0)]
return dict(page='projects', model='project', form_title="new project", items=all_projects, value=kw)
def get_values_from_attributs_meas(self, att):
'''
for a nice display of several attributs_values.value by one attributs.key
'''
att_values = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == att.id,\
Attributs_values.deprecated == False)).all()
#for the boolean display
if att.widget == "checkbox":
for v in att_values:
if v in self.meas.a_values:
val = check_boolean(v.value)
att_key = att.key
att_key = att_key.replace("_", " ")
if not val:
return "NOT " + att_key
else:
return att_key
#for the others widget's types
else:
list_values = []
for v in att_values:
if v in self.meas.a_values:
if v.value not in list_values:
list_values.append(v.value)
list_values = [l for l in list_values if l]
final = " ; ".join(list_values)
return final
def get_all(self, *args, **kw):
user = handler.user.get_user_in_session(request)
# user attributs
#to block to one specific user
attributs = DBSession.query(Attributs).all()
all_attributs = [util.to_datagrid(attribut_grid, attributs, "Attributs Table", len(attributs) > 0)]
return dict(page='attributs', model='attribut', form_title="new attribut", items=all_attributs, value=kw)
def get_values_from_attributs_meas(self, att):
'''
for a nice display of several attributs_values.value by one attributs.key
'''
att_values = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == att.id,\
Attributs_values.deprecated == False)).all()
#for the boolean display
if att.widget == "checkbox":
for v in att_values:
if v in self.meas.a_values:
val = check_boolean(v.value)
att_key = att.key
att_key = att_key.replace("_", " ")
if not val:
return "NOT " + att_key
else:
return att_key
#for the others widget's types
else:
list_values = []
for v in att_values:
if v in self.meas.a_values:
if v.value not in list_values:
list_values.append(v.value)
list_values = [l for l in list_values if l]
final = " ; ".join(list_values)
return final
def get_UCSC_link(obj_id):
'''
Return a HTML link to UCSC
'''
meas = DBSession.query(Measurements).filter(
Measurements.id == obj_id).first()
status = meas.status_type
normal_ext = ["bed", "bedgraph", "wig"]
#binary extension, except bam files
binary_ext = ["bw", "bigwig", "bigbed", "bb"]
if status and len(meas.fus) > 0:
list_fus = meas.fus
for x in list_fus:
f_sha1 = x.sha1
ext = x.extension
#t is type. 1 == normal extension, 2 == binary extension, 3 == bam
if ext.lower() in normal_ext:
return '''
<a class='action UCSC_link' href="%s" target="_blank" title="view in UCSC" style="text-decoration:none" target="_blank"></a> ''' % (
url('./public/UCSC_link',
params=dict(sha1=f_sha1, meas_id=obj_id, t=1)))
elif ext.lower() in binary_ext:
return '''
<a class='action UCSC_link' href="%s" target="_blank" title="view in UCSC" style="text-decoration:none" target="_blank"></a> ''' % (
url('./public/UCSC_link',
params=dict(sha1=f_sha1, meas_id=obj_id, t=2)))
elif ext.lower() == "bam":
return '''
<a class='action UCSC_link' href="%s" target="_blank" title="view in UCSC" style="text-decoration:none" target="_blank"></a> ''' % (
url('./public/UCSC_link',
params=dict(sha1=f_sha1, meas_id=obj_id, t=3)))
return ''
def delete(self, *args, **kw):
user = handler.user.get_user_in_session(request)
project = DBSession.query(Projects).filter(Projects.id == args[0]).first()
admin = isAdmin(user)
if project.user_id == user.id or admin:
try:
flash("Your project " + str(project.project_name) + " has been deleted with success")
except:
flash("Your project " + (project.project_name) + " has been deleted with success")
DBSession.delete(project)
DBSession.flush()
raise redirect('/projects')
else:
flash("It is not your project -> you are not allowed to delete it", 'error')
raise redirect('/projects')
def BAM_visualisation(self, bam_object, filename_without_extension, *args,
**kw):
#find the bam.bai file associated
bai = DBSession.query(Files_up).filter(
and_(Files_up.filename == filename_without_extension + ".bam.bai",
Files_up.extension == "bai")).first()
if bai is None:
flash(
"Sorry but " + bam_object.filename +
" has no .bam.bai associated in BioRepo. Upload it and retry the operation.",
"error")
raise redirect(url("/search"))
else:
bai_sha1 = bai.sha1
bam_sha1 = bam_object.sha1
bai_path = bai.path
bam_path = bam_object.path
#build the full paths (bam and bam.bai)
bai_full_path = bai_path + "/" + bai_sha1
bam_full_path = bam_path + "/" + bam_sha1
#creating symlink with good names and good extensions
#for the bam file
bam_dest = bam_path + "/" + bam_sha1 + ".bam"
if os.path.islink(bam_dest):
pass
else:
os.symlink(bam_full_path, bam_dest)
bam_name = bam_sha1 + ".bam"
#for the bai file
bai_dest = bam_path + "/" + bam_sha1 + ".bam.bai"
if os.path.islink(bai_dest):
pass
else:
os.symlink(bai_full_path, bai_dest)
return bam_name
def new(self, *args, **kw):
tmpl_context.widget = new_attribut_form
#take the logged user
user = handler.user.get_user_in_session(request)
#take the logged user samples
samples = DBSession.query(Samples).join(Projects).join(User).filter(
User.id == user.id).all()
meas = DBSession.query(Measurements).all()
attributs = DBSession.query(Attributs).all()
tmpl_context.samples = samples
tmpl_context.meas = meas
tmpl_context.attributs = attributs
return dict(page='samples',
value=kw,
title='New Sample',
model='Sample')
def get_user(key, mail):
'''
Get the user with the the given mail,
with the given key.
'''
print key, "------------ key given"
print mail, " ---------- mail given"
return DBSession.query(User).filter(and_(User.email == mail, User.key == key)).first()
def post(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
p = Projects()
if kw['project_name'] == '':
flash("Bad Project : Your project must have a name", "error")
raise redirect("./new")
p.project_name = kw['project_name']
p.user_id = user.id
p.description = kw.get('description', None)
(p.labs).append(lab)
DBSession.add(p)
DBSession.flush()
flash("Project created !")
raise redirect('/projects')
def check_mail(self, mail):
mail = mail.lower()
user = DBSession.query(User).filter(User._email == mail).first()
if user is None:
#send False to the HTSstation method
return {'in_biorepo': False}
else:
#send True to the HTSstation method
return {'in_biorepo': True}
def get_user(key, mail):
'''
Get the user with the the given mail,
with the given key.
'''
print key, "------------ key given"
print mail, " ---------- mail given"
return DBSession.query(User).filter(
and_(User.email == mail, User.key == key)).first()
def get_projects(self):
list_projects = []
for sample in self.samples:
p_id = sample.project_id
project = DBSession.query(Projects).filter(Projects.id == p_id).first()
p_name = project.project_name
if (p_name + " (p_id: " + str(p_id) + ")") not in list_projects:
list_projects.append(p_name + " (p_id: " + str(p_id) + ")")
return ' ; '.join(list_projects)
def check_mail(self, mail):
mail = mail.lower()
user = DBSession.query(User).filter(User._email == mail).first()
if user is None:
#send False to the HTSstation method
return {'in_biorepo': False}
else:
#send True to the HTSstation method
return {'in_biorepo': True}
def get_projects(self):
list_projects = []
for sample in self.samples:
p_id = sample.project_id
project = DBSession.query(Projects).filter(
Projects.id == p_id).first()
p_name = project.project_name
if (p_name + " (p_id: " + str(p_id) + ")") not in list_projects:
list_projects.append(p_name + " (p_id: " + str(p_id) + ")")
return ' ; '.join(list_projects)
def Gviz_link(self, sha1, meas_id, *args, **kw):
'''
redirect to Gviz BAM viewer hosted on HTSstation
'''
#URL example :
#bbcftools.epfl.ch/bam_viewer/gviews/new?assembly_name=pombe&module=biorepo&file=XTv7U2IYVAgIWqBHyPjC
meas = DBSession.query(Measurements).filter(Measurements.id == meas_id).first()
list_a_values = []
#get the dynamic values
for val in meas.a_values:
list_a_values.append(val.id)
#check if "assembly" is a dynamic key for this measurement
cpt_test = 0
for a in meas.attributs:
if a.key == "assembly":
cpt_test += 1
#get all the values recorded for this key
list_assemblies = a.values
assembly = ''
for v in list_assemblies:
#check if the Attributs_values object is linked to this measurement
if v.id in list_a_values:
assembly = v.value
if assembly == '':
flash("Sorry but you have to set an assembly to this measurement", "error")
raise redirect("/search")
else:
#TODO replace this when BioRepo and HTS will be connected together
#JUST CATCH THE PATH IN DB AND GIVE IT IN THE URL
#/!\ /archive/projects/epfl-vital-it/biorepo_upload/ /!\
hostname = socket.gethostname().lower()
#because of aliasing
if hostname == "ptbbsrv2.epfl.ch":
hostname = "biorepo.epfl.ch"
bam_file = DBSession.query(Files_up).filter(Files_up.sha1 == sha1).first()
fullname = bam_file.filename
name_tmp = fullname.split('.')
name = name_tmp[0]
bam_name = self.BAM_visualisation(bam_file, name)
bam_path = bam_file.path
path_to_give = bam_path.split("/archive/projects/epfl/biorepo_upload")[1]
raise redirect('http://bbcftools.epfl.ch/bam_viewer/gviews/new?assembly_name=' + assembly + "&module=biorepo&file=" +
path_to_give + "/" + bam_name)
def check_value_addition(self, list_type_att, dict_att_values_type, dict_att_values_db, lab_id):
'''
Checking for value(s) addition
@param principal
@return an updated db
'''
for key_type in list_type_att:
for i in dict_att_values_type[key_type]:
#get the attribut and its value(s)
i_att = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab_id, Attributs.key == key_type)).first()
#warning : i_att_value is a list !
i_att_value = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == i_att.id,
Attributs_values.value == i)).all()
try:
flag = False
if i not in dict_att_values_db[key_type] and i != "None":
for existant in i_att_value:
if existant.value == i and existant.deprecated == True:
existant.deprecated = False
DBSession.flush()
flag = True
if existant.value is None:
existant.deprecated = True
DBSession.flush()
if flag == False:
new_value = Attributs_values()
new_value.attribut_id = i_att.id
new_value.value = i
new_value.deprecated = False
DBSession.add(new_value)
DBSession.flush()
except Exception as e:
import sys, traceback
a, b, c = sys.exc_info()
traceback.print_exception(a, b, c)
print "--- error login.py check_value_addition() ---"
print "i --->", i
print "key_type --->", key_type
print "list_type_att --->", list_type_att
print "dict_att_values_type[key_type] -->", dict_att_values_type[key_type]
print "i_att --> ", i_att
print "i_att_value", i_att_value
def create_ext_lab(self, mail, key, lab_name):
#utilisation (only for admins) :
#wget --post-data "[email protected]&key=xxxxxxxxxxx&lab_name=bbcf" http://yourdomain.com/biorepo/create_ext_lab
lab_test = DBSession.query(Labs).filter(Labs.name == lab_name).first()
if lab_test is None:
try:
lab = Labs()
lab.name = lab_name
lab.path_raw = path_raw(lab_name)
lab.path_processed = path_processed(lab_name)
lab.path_tmp = path_tmp(lab_name)
DBSession.add(lab)
DBSession.flush()
print "Exterior lab created :", lab_name
except:
print_traceback()
print "Exterior lab NOT created --> ERROR"
else:
print "This lab : ", str(lab_name), " is in the db yet. --> ERROR"
def new(self, **kw):
#get the logged user
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
samples = []
if user_lab is not None:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
projects = [p.id for p in user.projects if p in lab.projects]
for a in attributs:
for s in a.samples:
if s not in samples and s.project_id in projects:
samples.append(s)
new_form = NewProject(action=url('/projects/post')).req()
new_form.child.children[0].placeholder = "Your project name..."
new_form.child.children[1].placeholder = "Your commments here..."
new_form.child.children[2].options = [(sample.id, '%s' % (sample.name)) for sample in samples]
return dict(page='projects', widget=new_form)
def post_delete(self, *args, **kw):
for id in args:
permission = DBSession.query(Permission).filter(Permission.id == id).first()
if permission.name == gl.perm_admin:
flash('Cannot delete admin permission')
redirect('/permissions')
if permission.name == gl.perm_user:
flash('Cannot delete read permission')
redirect('/permissions')
return CrudRestController.post_delete(self, *args, **kw)
def post_delete(self, *args, **kw):
for id in args:
group = DBSession.query(Group).filter(Group.id == id).first()
if group.name == gl.group_admins:
flash('Cannot delete admin group')
redirect('/groups')
if group.name == gl.group_users:
flash('Cannot delete users group')
redirect('/groups')
return CrudRestController.post_delete(self, *args, **kw)
def new(self, *args, **kw):
#take the logged user
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
projects = DBSession.query(Projects).filter(Projects.user_id == user.id).all()
for p in projects:
if p not in lab.projects:
projects.remove(p)
new_form = build_form("new", "sample", None)(action=url('/samples/post')).req()
#static fields
new_form.child.children[0].options = [(project.id, '%s' % project.project_name) for project in projects]
new_form.child.children[1].placeholder = "Your sample name..."
new_form.child.children[2].options = get_list_types(user_lab)
new_form.child.children[3].placeholder = "Your protocole here..."
return dict(page='samples', widget=new_form)
def post_delete(self, *args, **kw):
for id in args:
permission = DBSession.query(Permission).filter(
Permission.id == id).first()
if permission.name == gl.perm_admin:
flash('Cannot delete admin permission')
redirect('/permissions')
if permission.name == gl.perm_user:
flash('Cannot delete read permission')
redirect('/permissions')
return CrudRestController.post_delete(self, *args, **kw)
def hts_boss(self, key):
'''
return dico with sha1 and meas_id from HTSStation files
/!\ Only Fabrice is able to use it
'''
VIP_user = DBSession.query(User).filter(User.id == 9).first()
if key != VIP_user.key:
return {'ERROR': 'Restricted Boss method.'}
dico_id_path = {}
fus = DBSession.query(Files_up).filter(
Files_up.path.like('/data/%')).distinct()
for f in fus:
sha1 = f.sha1
list_meas = f.measurements
for m in list_meas:
m_id = m.id
if sha1 in dico_id_path.keys():
dico_id_path[sha1].append(m_id)
else:
dico_id_path[sha1] = [m_id]
return dico_id_path
def get_user_in_session(request):
'''
Get the user that is performing the current request
@param request: the web request
@type request: a WebOb
'''
if not 'repoze.who.identity' in request.environ:
print "############### abort in handler/user ################"
abort(401)
identity = request.environ['repoze.who.identity']
email = identity['repoze.who.userid']
user = DBSession.query(User).filter(User.email == email).first()
return user
def get_all(self, *args, **kw):
user = handler.user.get_user_in_session(request)
# user attributs
#to block to one specific user
attributs = DBSession.query(Attributs).all()
all_attributs = [
util.to_datagrid(attribut_grid, attributs, "Attributs Table",
len(attributs) > 0)
]
return dict(page='attributs',
model='attribut',
form_title="new attribut",
items=all_attributs,
value=kw)
def manage_fu_from_HTS(existing_fu, meas, filename, sha1, url_path, hts_path):
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE FROM HTS--------"
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
fu.path = hts_path
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
else:
fu.extension = "not specified"
fu.sha1 = sha1
fu.url_path = url_path
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
return fu
def get_values_from_attributs_sample(self, att):
'''
for a nice display of several attributs_values.value by one attributs.key
'''
att_values = DBSession.query(Attributs_values).filter(and_(Attributs_values.attribut_id == att.id,\
Attributs_values.deprecated == False)).all()
list_values = []
#for the boolean display
if att.widget == "checkbox":
for v in att_values:
for s in self.samples:
try:
if v in self.s.a_values:
val = check_boolean(v.value)
att_key = att.key
att_key = att_key.replace("_", " ")
if not val:
word = "NOT " + att_key
if word not in list_values:
list_values.append(word)
else:
if att_key not in list_values:
list_values.append(att_key)
#exception at the beginning of a lab when one or several checkbox doesn't get values yet
except:
att_key = att.key
att_key = att_key.replace("_", " ")
word = "NOT " + att_key
if word not in list_values:
list_values.append(word)
else:
if att_key not in list_values:
list_values.append(att_key)
#for the others widget's types
else:
for v in att_values:
for s in self.samples:
if v in s.a_values:
if v.value not in list_values:
list_values.append(v.value)
list_values = [l for l in list_values if l]
final = " ; ".join(list_values)
return final
def get_GViz_link(obj_id):
'''
Return a HTML link to Gviz HTSstation
'''
meas = DBSession.query(Measurements).filter(
Measurements.id == obj_id).first()
status = meas.status_type
if status and len(meas.fus) > 0:
list_fus = meas.fus
for x in list_fus:
f_sha1 = x.sha1
ext = x.extension
if ext.lower() == "bam":
return '''
<a class='action GViz_link' href="%s" target="_blank" title="view in GViz" style="text-decoration:none" target="_blank"></a> ''' % (
url('./public/Gviz_link',
params=dict(sha1=f_sha1, meas_id=obj_id)))
return ''
def get_public_link(obj_id):
'''
Return a HTML public download link.
'''
#TODO : understand and fix the bug...
meas = DBSession.query(Measurements).filter(
Measurements.id == obj_id).first()
status = meas.status_type
f_sha1 = ''
#have to be public
if status and len(meas.fus) > 0:
list_fus = meas.fus
for x in list_fus:
f_sha1 = x.sha1
return '''
<a class='action public_link' href="%s" title="public link for this measurement" style="text-decoration:none"></a> ''' % (
url('./public/public_link', params=dict(sha1=f_sha1, m_id=obj_id)))
else:
return '''
def build_attribut_value(self, s, lab_id, dict_fixed_values_type,
list_fixed_values_type, config):
'''
build Attribut values
@return a list of Attribut values
'''
list_objects_value = []
for att in list_fixed_values_type:
#build a dictionnary of fixed values : {'key':'[value1, value2, value3, ...}'}
list_values = []
list_values = (config.get(s + att, att)).split(',')
dict_fixed_values_type[att] = list_values
for k, list_values in dict_fixed_values_type.iteritems():
att_tmp = DBSession.query(Attributs).filter(
and_(Attributs.key == k), Attributs.lab_id == lab_id).first()
for v in list_values:
attributs_v = Attributs_values()
attributs_v.attribut_id = att_tmp.id
attributs_v.value = v
attributs_v.deprecated = False
list_objects_value.append(attributs_v)
return list_objects_value
def clone_form(user_lab, id_object):
'''
to clone dynamic measurement form
'''
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
#static list ]
list_static = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.TextField(id="name",
label_text="Name :",
placeholder="Measurement name...",
validator=twc.Validator(required=True)),
twf.TextArea(id="description", label_text="Description :"),
twf.MultipleSelectField(
id="samples",
label_text="Your samples : ",
help_text="You can add some of your existing data to this project."
),
twf.CheckBox(
id="status_type",
label_text="Privacy : ",
help_text=
"Check to have it available from outside EPFL (required for UCSC visualisation)"
),
twf.CheckBox(id="type",
label_text="Raw data : ",
help_text="Check if raw data"),
#twf.MultipleSelectField(id="parents", label_text="Parents : ", help_text="Parent(s) of this measurement."),
twd.HidingRadioButtonList(id="upload_way",
label_text='Upload my file via...',
options=('my computer', 'a Vital-IT path',
'a URL'),
mapping={
'my computer': ['upload'],
'a Vital-IT path': ['vitalit_path'],
'a URL': ['url_path', 'url_up'],
}),
twf.FileField(id="upload", help_text='Please provide a data'),
twf.TextField(id="vitalit_path",
label_text="Scratch path",
placeholder="/scratch/el/biorepo/dropbox/"),
twf.TextField(id="url_path",
label_text="File's url",
placeholder="http://www..."),
twf.CheckBox(id="url_up",
label_text="I want to upload the file from this URL : ",
help_text="tick it if you want to download it in BioRepo")
]
list_dynamic = []
if lab is None:
print "----- no dynamic fields detected ---------"
list_fields = [list_static, list_dynamic]
return list_fields
else:
to_clone = DBSession.query(Measurements).filter(
Measurements.id == int(id_object)).first()
tag = "measurements"
if to_clone is not None:
list_dynamic_attributes = to_clone.attributs
for att in list_dynamic_attributes:
if att.deprecated == False:
twf_type = convert_widget(att.widget)
twf_type.id = att.key
list_a_values = att.values
if att.widget == "textfield" or att.widget == "textarea" or att.widget == "hiding_textfield" or att.widget == "hiding_textarea":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
elif att.widget == "checkbox" or att.widget == "hiding_checkbox":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
#dynamic boolean are stored in varchar in the db, we have to cast them in boolean for the display
value_2_display = check_boolean(v.value)
twf_type.value = value_2_display
list_dynamic.append(twf_type)
elif att.widget == "multipleselectfield" or att.widget == "hiding_multipleselectfield":
list_possible_values = []
for v in list_a_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
selected_values = []
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
selected_values.append(v.value)
twf_type.value = selected_values
list_dynamic.append(twf_type)
elif att.widget == "singleselectfield" or att.widget == "hiding_singleselectfield":
list_possible_values = []
for v in list_a_values:
if v.value not in list_possible_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if to_clone in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
else:
print "Your measurement was not found. ID problem. id :", id_object
raise
list_fields = [list_static, list_dynamic]
return list_fields
def by_email_address(cls, email):
"""Return the user object whose email address is ``email``."""
return DBSession.query(cls).filter(cls.email == email).first()
def new_form_parents(user_lab):
'''for new form with parents'''
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
#static lists
list_static_samples = [
twf.SingleSelectField(id="project",
label_text="Your projects : ",
help_text="Select project for this sample",
prompt_text=None),
twf.TextField(id="name",
label_text="Name :",
validator=twc.Validator(required=True)),
twf.SingleSelectField(id="type",
label_text="Type : ",
help_text="Technique used",
prompt_text=None),
twf.TextArea(
id="protocole",
label_text="Protocole :",
)
]
list_static_measurements = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.TextField(id="name",
label_text="Name :",
placeholder="Measurement name...",
validator=twc.Validator(required=True)),
twf.TextArea(id="description", label_text="Description :"),
twf.MultipleSelectField(
id="samples",
label_text="Your samples : ",
help_text="You can add some of your existing data to this project."
),
twf.CheckBox(
id="status_type",
label_text="Privacy : ",
help_text=
"Check to have it available from outside EPFL (required for UCSC visualisation)"
),
twf.CheckBox(id="type",
label_text="Raw data : ",
help_text="Check if raw data"),
twf.MultipleSelectField(id="parents",
label_text="Parents : ",
help_text="Parent(s) of this measurement."),
twd.HidingRadioButtonList(id="upload_way",
label_text='Upload my file via...',
options=('my computer', 'a Vital-IT path',
'a URL'),
mapping={
'my computer': ['upload'],
'a Vital-IT path': ['vitalit_path'],
'a URL': ['url_path', 'url_up'],
}),
twf.FileField(id="upload", help_text='Please provide a data'),
twf.TextField(id="vitalit_path",
label_text="Scratch path",
placeholder="/scratch/el/biorepo/dropbox/"),
twf.TextField(id="url_path",
label_text="File's url",
placeholder="http://www..."),
twf.CheckBox(id="url_up",
label_text="I want to upload the file from this URL : ",
help_text="tick it if you want to download it in BioRepo")
]
list_dynamic_samples = []
list_hiding_samples = []
list_dynamic_measurements = []
list_hiding_meas = []
#catch the dynamic hiding fields
dic_hiding_meas = session.get("hiding_meas", {})
dic_hiding_samples = session.get("hiding_sample", {})
if lab is None:
print "----- no dynamic fields detected ---------"
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
else:
lab_id = lab.id
list_attributs = DBSession.query(Attributs).filter(
Attributs.lab_id == lab_id).all()
if len(list_attributs) > 0:
#lists_construction(list_attributs)
for a in list_attributs:
attribut_key = a.key
deprecated = a.deprecated
fixed_value = a.fixed_value
widget = a.widget
owner = a.owner
#############################
######### NEW SAMPLE ########
#############################
if owner == "sample":
#dynamic
if not deprecated and fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "multipleselectfield" or widget == "singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_dynamic_samples.append(twf_type)
elif widget == "checkbox":
list_dynamic_samples.append(twf_type)
elif widget == "hiding_singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_hiding_samples.append(twf_type)
elif widget == "hiding_checkbox":
list_hiding_samples.append(twf_type)
else:
print widget, "-----ERROR----- ELSE, type samples widget in forms.py"
elif not deprecated and not fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "textfield" or widget == "textarea":
twf_type.placeholder = "Write here..."
list_dynamic_samples.append(twf_type)
elif widget == "checkbox":
list_dynamic_samples.append(twf_type)
elif widget == "hiding_textfield" or widget == "hiding_textarea":
twf_type.placeholder = "Write here..."
list_hiding_samples.append(twf_type)
elif widget == "hiding_checkbox":
list_hiding_samples.append(twf_type)
else:
print widget, "WIDGET SAMPLE NOT FOUND, add an elif please"
raise
elif deprecated:
pass
else:
print "WIDGET SAMPLES ERROR : widget type is not known --> ", widget
raise
################################
######## NEW MEASUREMENT #######
################################
elif owner == "measurement":
#dynamic
#for attributes with fixed values
if not deprecated and fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "multipleselectfield" or widget == "singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_dynamic_measurements.append(twf_type)
elif widget == "hiding_singleselectfield":
list_values = []
list_attributes_values = DBSession.query(
Attributs_values).filter(
Attributs_values.attribut_id ==
a.id).all()
for av in list_attributes_values:
if not av.deprecated and av.value not in list_values:
list_values.append(av.value)
twf_type.options = list_values
list_hiding_meas.append(twf_type)
#elif widget == "checkbox":
#list_dynamic_measurements.append(twf_type)
else:
print widget, "-----ERROR----- ELSE, type measurements widget in forms.py"
raise
#for others attributes
elif not deprecated and not fixed_value:
twf_type = convert_widget(widget)
twf_type.id = attribut_key
if widget == "textfield" or widget == "textarea":
twf_type.placeholder = "Write here..."
list_dynamic_measurements.append(twf_type)
elif widget == "checkbox":
list_dynamic_measurements.append(twf_type)
elif widget == "hiding_textfield" or widget == "hiding_textarea":
twf_type.placeholder = "Write here..."
list_hiding_meas.append(twf_type)
elif widget == "hiding_checkbox":
list_hiding_meas.append(twf_type)
else:
print widget, "WIGDET MEASUREMENT NOT FOUND, add an elif please"
raise
elif deprecated:
pass
#in bugs case
else:
print "WIDGET MEASUREMENTS ERROR : widget type is not known --> ", widget
raise
#TO TEST WITH SEVERAL TWD OBJECTS
#build dynamic dynamic fields
#samples
list_twd_s = []
for k in dic_hiding_samples:
twd_object = twd.HidingRadioButtonList()
twd_object.id = k
dico_mapping = dic_hiding_samples[k]
options = []
for key in dico_mapping.keys():
options.append(key)
twd_object.options = options
twd_object.mapping = dico_mapping
list_twd_s.append(twd_object)
list_dynamic_samples = list_dynamic_samples + list_twd_s + list_hiding_samples
#measurements
list_twd_m = []
for k in dic_hiding_meas:
twd_object = twd.HidingRadioButtonList()
twd_object.id = k
dico_mapping = dic_hiding_meas[k]
options = []
for key in dico_mapping.keys():
options.append(key)
twd_object.options = options
twd_object.mapping = dico_mapping
list_twd_m.append(twd_object)
list_dynamic_measurements = list_dynamic_measurements + list_twd_m + list_hiding_meas
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
else:
print "-----forms.py----- Houston, we have a problem : The lab ", lab.name, " doesn't get any attributes -----"
raise
def edit(self, *args, **kw):
tmpl_context.widget = attribut_edit_form
user = handler.user.get_user_in_session(request)
attribut = DBSession.query(Attributs).filter(
Attributs.id == args[0]).first()
def setdefaultkey(self):
uid = str(uuid.uuid4())
while DBSession.query(User).filter(User.key == uid).first():
uid = str(uuid.uuid4())
return uid
def to_json_test(self):
static_fields = {
'Description':
self.meas.description,
'User':
self.get_name(),
'Measurements':
self.get_meas_name(),
'description':
self.meas.description,
'Created':
self.date.strftime(date_format),
'Samples':
' ; '.join(['%s' % (sample.name) for sample in self.samples]),
'Projects':
self.get_projects(),
'Type':
self.get_sample_type(),
'DataType':
self.get_measurement_type(),
'scroll_info':
genshi.Markup(self.get_img_scroll()),
'Attachment':
self.get_extension,
'Actions':
get_info_link(self.id) + get_dl_link(self.id) +
get_public_link(self.id) + get_UCSC_link(self.id) +
get_GViz_link(self.id) + get_SPAN_id(self.id)
}
#find None statics fields to change the display in datatables
for sf in static_fields.keys():
if static_fields[sf] is None or static_fields[sf] == "":
static_fields[sf] = None
dyn_in_searchgrid = session.get("search_grid_fields", [])
labo = session.get("current_lab")
for d in dyn_in_searchgrid:
new = d.replace("_", " ")
dyn_in_searchgrid.remove(d)
dyn_in_searchgrid.append(new)
meas_dynamic_fields = {}
samples_dynamic_fields = {}
attributs_meas = [
a.to_json() for a in self.meas.attributs if not a.deprecated
]
list_avalues_meas = self.meas.a_values
for avm in list_avalues_meas:
for am in attributs_meas:
key = am["key"].replace("_", " ")
if str(am["id"]) == str(avm.attribut_id):
if am["widget"] != "checkbox" and am[
"widget"] != "hiding_checkbox":
meas_dynamic_fields[key] = avm.value
else:
if check_boolean(avm.value):
meas_dynamic_fields[key] = key
else:
meas_dynamic_fields[key] = "NOT " + str(key)
attributs_samples = self.get_attributs_samples_json()
if len(self.samples) < 2:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s[
"widget"] != "hiding_checkbox":
samples_dynamic_fields[key] = avs.value
else:
if check_boolean(avs.value):
samples_dynamic_fields[key] = key
else:
samples_dynamic_fields[key] = "NOT " + str(
key)
else:
for s in self.samples:
list_avalues_samples = s.a_values
for avs in list_avalues_samples:
for a_s in attributs_samples:
key = a_s["key"].replace("_", " ")
if str(a_s["id"]) == str(avs.attribut_id):
if a_s["widget"] != "checkbox" and a_s[
"widget"] != "hiding_checkbox":
if key not in samples_dynamic_fields.keys():
samples_dynamic_fields[key] = [avs.value]
else:
if avs.value not in samples_dynamic_fields[
key]:
samples_dynamic_fields[key].append(
avs.value)
else:
if check_boolean(avs.value):
if key not in samples_dynamic_fields.keys(
):
samples_dynamic_fields[key] = [key]
else:
samples_dynamic_fields[key].append(key)
else:
if key not in samples_dynamic_fields.keys(
):
samples_dynamic_fields[key] = [
"NOT " + str(key)
]
else:
samples_dynamic_fields[key].append(
"NOT " + str(key))
for k in samples_dynamic_fields.keys():
samples_dynamic_fields[k] = " ; ".join(
samples_dynamic_fields[k])
#Sorting dynamic fields with conf file to display in searchgrid
dyn_fields = {}
for k in samples_dynamic_fields:
if k in dyn_in_searchgrid:
dyn_fields[k.capitalize()] = samples_dynamic_fields[k]
for key in meas_dynamic_fields:
if key in dyn_in_searchgrid:
dyn_fields[key.capitalize()] = meas_dynamic_fields[key]
#for the empty fields
for k in dyn_in_searchgrid:
if k.capitalize() not in dyn_fields.keys():
k_db = k.replace(" ", "_")
lab = DBSession.query(Labs).filter(Labs.name == labo).first()
lab_id = lab.id
k_obj = DBSession.query(Attributs).filter(
and_(Attributs.key == k_db,
Attributs.lab_id == lab_id)).first()
if k_obj.widget != "checkbox" and k_obj.widget != "hiding_checkbox":
dyn_fields[k.capitalize()] = None
else:
dyn_fields[k.capitalize()] = ["NOT " + str(k)]
final = dict(static_fields.items() + dyn_fields.items())
return final
def build_search_grid(measurements):
search_grid = BootstrapGrid()
#static end
end_fields = [('Attachment', lambda obj: genshi.Markup(obj.get_extension)),
('Description', "description"), ("Date", "created"),
("Action", lambda obj: genshi.Markup(
get_info_link(obj.id) + get_dl_link(obj.id) +
get_public_link(obj.id) + get_UCSC_link(obj.id) +
get_GViz_link(obj.id) + get_SPAN_id(obj.id)))]
#static and dynamic fields
fields = []
fields_static = [("", "scroll_info"), ("User", "user"), ("Projects", lambda obj:genshi.Markup(obj.projects_display)), ("Samples", lambda obj:genshi.Markup(
obj.samples_display)), ("Type", lambda obj:genshi.Markup(obj.sample_type)),\
("Measurements", lambda obj:genshi.Markup(obj.name)), ("DataType", lambda obj:genshi.Markup(obj.measurement_type))]
fields_dyn = []
list_searchable = []
positions_not_searchable = []
hidden_list = []
lab_id = None
if not isinstance(measurements, list):
measurements = [measurements]
if len(measurements) > 0:
meas = measurements[0]
#dyn meas
for att in meas.attributs:
#get the lab_id
lab_id = att.lab_id
vals = lambda obj, a=att: obj.get_values_from_attributs_meas(a)
fields_dyn.append((att.key, vals))
if att.searchable == True:
list_searchable.append(att.key)
#dyn sample
if len(meas.samples) > 0:
sample = (meas.samples)[0]
for att in sample.attributs:
val = lambda obj, a=att: obj.get_values_from_attributs_sample(a
)
fields_dyn.append((att.key, val))
if att.searchable == True:
list_searchable.append(att.key)
############## CUSTOMIZE THE SEARCH GRID BY LAB #######################
#/!\ the grid begins at 0
#to customize hidden fields by lab
lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
movable_fields = fields_static + fields_dyn
if lab:
if lab.name == "ptbb":
pass
elif lab.name == "updub":
pass
elif lab.name == "lvg":
#move some field in the grid
for f in movable_fields:
if f[0] == "flag_final":
new_list = value_travel_into_da_list(
movable_fields, movable_fields.index(f),
len(movable_fields))
movable_fields = new_list
for f in movable_fields:
if f[0] == "quality":
new_list = value_travel_into_da_list(
movable_fields, movable_fields.index(f),
len(movable_fields))
movable_fields = new_list
#hide Samples name
for f in movable_fields:
if f[0] == "Samples":
i = movable_fields.index(f)
hidden_list.append(i)
for f in movable_fields:
if f[0] == "ab_source":
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "upnae":
fields_to_hide = ["replica_id", "drug_dose", "lane_id", "paired_end_id", "strand",\
"source", "machine", "starting_material", "treatment", "paired_end", "polya", "strand_specific",\
"viewpoint", "protein_bait", "technical_replica_id", "feeding_type", "light_condition"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "stutz":
fields_to_hide = ["article_title", "strain", "time_point", "antibody", "treatment_time",\
"phase", "medium", "background"]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
elif lab.name == "shore":
fields_to_hide = [
"article_title", "year", "time_point", "sequencing_method",
"treatment_time", "phase"
]
for f in movable_fields:
if f[0] in fields_to_hide:
i = movable_fields.index(f)
hidden_list.append(i)
#addition with the 3 common end-fields
fields = movable_fields + end_fields
#build the list (positions_not_searchable) to send to the js for the searchable buttons
for f in fields:
search_grid.fields.append(f)
for i, item in enumerate(search_grid.fields):
if item[0] not in list_searchable:
positions_not_searchable.append(i)
for f in fields_static:
for i, item in enumerate(movable_fields):
#and i not in list_tmp
if f[0] == item[0] and f[
0] != '' and f in fields_static and i in positions_not_searchable:
positions_not_searchable.remove(i)
#build the list (ignored_list) for the ignored fields
total = len(search_grid.fields) - 1
hidden_list.append(total - 2)
#positions_not_searchable = delete the search button of the field
#hidden_list = the field does not appear anymore into the searchgrid and its search button disappears BUT it is still searchable !
return search_grid, hidden_list, positions_not_searchable
def manage_fu(existing_fu, meas, public_dirname, filename, sha1, up_data,
url_path, url_up, dest_raw, dest_processed, tmp_path, lab):
tmpdir_to_delete = os.path.abspath(os.path.join(tmp_path, os.path.pardir))
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE --------"
#create symbolic link
source = existing_fu.path + "/" + sha1
if meas.type:
dest = dest_raw + sha1
#test symlin existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
#test symlink existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
flash(symlink_e + ", measurement created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
#raise redirect("./")
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
#raw test for path orientation
if meas.type:
fu.path = path_raw(lab)
data_dirname = os.path.join(public_dirname, fu.path)
else:
fu.path = path_processed(lab)
data_dirname = os.path.join(public_dirname, fu.path)
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
# root, ext = os.path.splitext(filename)
# DOUBLE_EXTENSIONS = ['tar.gz','tar.bz2','bedGraph.gz','bed.gz']
# if any([filename.endswith(x) for x in DOUBLE_EXTENSIONS]):
# root, first_ext = os.path.splitext(root)
# ext = first_ext + ext
# fu.extension = ext
# else:
# fu.extension = ext
else:
fu.extension = "not specified"
data_path = os.path.join(data_dirname, str(sha1))
fu.sha1 = sha1
fu.url_path = url_path
#writing the file into the server HD
#version browser
try:
with open(data_path, "w") as d:
if up_data is not None:
d.write(up_data.value)
elif url_path is not None and url_up:
u = urllib2.urlopen(url_path)
while True:
buffer = u.read(8192)
if not buffer:
break
d.write(buffer)
else:
print "ERROR"
#version commandline
except:
shutil.move(tmp_path, data_path)
#symlink
source = data_path
if meas.type:
dest = dest_raw + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
if meas.type:
flash(symlink_e + ", raw data was successfully created")
else:
flash(symlink_e + ", processed data was successfully created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
return fu
def index(self, *args, **kw):
user_lab = session.get("current_lab", None)
user_projects = []
u_projects = []
u_samples = []
u_meas = []
u_children = []
u_global = []
dico_final = {}
#TODO : admin view - watch for a dl link
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
lab_users = lab.users
for u in lab_users:
projects = DBSession.query(Projects).filter(
Projects.user_id == u.id).all()
if len(projects) > 0:
for p in projects:
for lab in p.labs:
if lab.name == user_lab:
user_projects.append(p)
for proj in user_projects:
for sample in proj.samples:
if len(sample.measurements) > 0:
for meas in sample.measurements:
if len(meas.children) == 0:
u_meas.append({
"name":
str(meas.name) + "(" +
str(meas.id) + ")"
})
else:
for child in meas.children:
u_children.append({
"name":
str(child.name) + "(" +
str(child.id) + ")"
})
u_meas.append({
"name":
str(meas.name) + "(" +
str(meas.id) + ")",
"children":
u_children
})
u_children = []
u_samples.append({
"name":
str(sample.name) + "(" + str(sample.type) +
")",
"children":
u_meas
})
u_meas = []
else:
u_samples.append({
"name":
str(sample.name + "(" + str(sample.type) +
")")
})
if len(proj.samples) > 0:
u_projects.append({
"name": str(proj.project_name),
"children": u_samples
})
u_samples = []
else:
u_projects.append({"name": str(proj.project_name)})
u_global.append({
"name": u.firstname + " " + u.name,
"children": u_projects
})
u_projects = []
user_projects = []
#uncomment these 4 lines if you want to see every lab users registered in BioRepo
#else:
#u_global.append({"name": u.firstname + " " + u.name})
#u_projects = []
#user_projects = []
dico_final["name"] = user_lab
dico_final["children"] = u_global
return {"data": json.dumps(dico_final)}
def edit_form(user_lab, owner, id_object):
'''
to edit dynamic form
'''
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
#static lists
list_static_samples = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.SingleSelectField(
id="project",
label_text="Your projects : ",
help_text="the project which contains your sample is selected",
prompt_text=None),
twf.TextField(id="name", label_text="Name :", validator=twc.Required),
twf.SingleSelectField(id="type",
label_text="Type : ",
help_text="What technique do you use ?",
prompt_text=None),
twf.TextArea(
id="protocole",
label_text="Protocole :",
),
twf.MultipleSelectField(id="measurements",
label_text="Attached measurement(s) : ")
]
list_static_measurements = [
twf.HiddenField(id="IDselected", label_text="ID selected :"),
twf.TextField(id="name",
label_text="Name :",
placeholder="Measurement name...",
validator=twc.Required),
twf.TextArea(id="description", label_text="Description :"),
twf.MultipleSelectField(
id="samples",
label_text="Your samples : ",
help_text="You can add some of your existing data to this project."
),
twf.CheckBox(
id="status_type",
label_text="Privacy : ",
help_text=
"Check to have it available from outside EPFL (required for UCSC visualisation)"
),
twf.CheckBox(id="type",
label_text="Raw data : ",
help_text="Check if raw data"),
twf.MultipleSelectField(id="parents",
label_text="Parents : ",
help_text="Parent(s) of this measurement."),
twf.LabelField(
id="uploaded",
help_text=
"is attached to this measurement. If you want to change, it's better to delete this measurement and create a new one."
),
twf.TextField(
id="url_path",
help_text=
"If you want to add a new URL, your old URL will be stored into the description",
placeholder="http://www...")
#twf.CheckBox(id="url_up", label_text="I want to upload the file from this URL : ",
#help_text="tick it if you want to download it in BioRepo")
]
list_dynamic_samples = []
list_dynamic_measurements = []
if lab is None:
print "----- no dynamic fields detected ---------"
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
else:
if owner == "sample":
object_edited = DBSession.query(Samples).filter(
Samples.id == int(id_object)).first()
list_dynamic = list_dynamic_samples
tag = "samples"
elif owner == "meas":
object_edited = DBSession.query(Measurements).filter(
Measurements.id == int(id_object)).first()
list_dynamic = list_dynamic_measurements
tag = "measurements"
else:
print "----------------- owner error : ", owner, " <----owner --------------------"
raise
if object_edited is not None:
list_dynamic_attributes = object_edited.attributs
for att in list_dynamic_attributes:
if att.deprecated == False:
twf_type = convert_widget(att.widget)
twf_type.id = att.key
list_a_values = att.values
if att.widget == "textfield" or att.widget == "textarea" or att.widget == "hiding_textfield" or att.widget == "hiding_textarea":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
elif att.widget == "checkbox" or att.widget == "hiding_checkbox":
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
#dynamic boolean are stored in varchar in the db, we have to cast them in boolean for the display
value_2_display = check_boolean(v.value)
twf_type.value = value_2_display
list_dynamic.append(twf_type)
elif att.widget == "multipleselectfield" or att.widget == "hiding_multipleselectfield":
list_possible_values = []
for v in list_a_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
selected_values = []
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
selected_values.append(v.value)
twf_type.value = selected_values
list_dynamic.append(twf_type)
elif att.widget == "singleselectfield" or att.widget == "hiding_singleselectfield":
list_possible_values = []
for v in list_a_values:
if v.value not in list_possible_values:
list_possible_values.append(v.value)
twf_type.options = list_possible_values
for v in list_a_values:
if hasattr(v, tag):
value_object = getattr(v, tag)
if object_edited in value_object:
twf_type.value = v.value
list_dynamic.append(twf_type)
else:
print "Your ", owner, " was not found. ID problem. id :", id_object
raise
list_fields = [
list_static_samples, list_dynamic_samples,
list_static_measurements, list_dynamic_measurements
]
return list_fields
