Exemple #1
0
    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()
Exemple #2
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    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})
Exemple #3
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    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()
Exemple #4
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 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
Exemple #5
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    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."}
Exemple #6
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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()
Exemple #7
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    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
Exemple #8
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    def multi_meas_delete(self, p_id, s_id, mail, key):
        '''
        deleted ALL the measurements for a given sample
        /!\ IRREVERSIBLE /!\
        '''
        try:
            project = DBSession.query(Projects).filter(Projects.id == p_id).first()
            sample = DBSession.query(Samples).filter(Samples.id == s_id).first()
            user = DBSession.query(User).filter(User._email == mail).first()
            #checking
            print "--- Check your inputs... ---"
            if project is None:
                print "Project " + str(p_id) + " not found."
            if sample is None:
                print "Sample " + str(s_id) + " not found."
            if user is None:
                print "Your mail " + mail + " is not recorded in BioRepo."

            if project.id == sample.project_id and user.id == project.user_id:
                print "--- Begin the purge... ---"
                list_meas = sample.measurements
                print "Today, " + str(len(list_meas)) + " will die..."
                print "--------------------------"
                for m in list_meas:
                    list_fus = m.fus
                    for f in list_fus:
                        #delete the file on the server only if it is not used by anyone else anymore
                        if len(f.measurements) == 1 and not (f.path).startswith(HTS_path_data()) and not (f.path).startswith(HTS_path_archive()):
                            path_fu = f.path + "/" + f.sha1
                            mail = user._email
                            mail_tmp = mail.split('@')
                            path_mail = "AT".join(mail_tmp)
                            path_symlink = f.path + "/" + path_mail + "/" + f.sha1
                            DBSession.delete(f)
                            path_symlink = f.path + "/" + path_mail + "/" + f.sha1
                            try:
                                os.remove(path_symlink)
                            except:
                                print "---- path_symlink deleted yet ----"
                                pass
                            os.remove(path_fu)
                        elif (f.path).startswith(HTS_path_data()) or (f.path).startswith(HTS_path_archive()):
                            DBSession.delete(f)
                            #TODO send back something to hts to notify that it's not into biorepo anymore
                    print str(m.name) + "(" + str(m.id) + ") ... Sorry ... PAN."
                    DBSession.delete(m)
                    DBSession.flush()
                print "--- They are all died T_T ---"

            else:
                print "It's not your project/sample. The FBI was notified. Run."
        except:
            print_traceback()
            print "Something went wrong...Please, don't cry."
Exemple #9
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    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."}
Exemple #10
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    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)}
Exemple #11
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    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')
Exemple #12
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    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("./")
Exemple #13
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 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)
Exemple #14
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 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
Exemple #15
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    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")
Exemple #16
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    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
Exemple #17
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 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
Exemple #18
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 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
Exemple #19
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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 ''
Exemple #20
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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 ''
Exemple #21
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 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
Exemple #22
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 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)
Exemple #23
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    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)
Exemple #24
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 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
Exemple #25
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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()
Exemple #26
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    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')
Exemple #27
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 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}
Exemple #28
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 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)
Exemple #29
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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()
Exemple #30
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 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}
Exemple #31
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 def create_gone_user(self, mail, key, lab_id, firstname, name, user_mail):
     #utilisation (only for admins) :
     #wget --post-data "key=xxxxxxxxxxxxxxxxxxxxx&[email protected]&lab_id=lab_id&firstname=jean-michel&name=michel&[email protected]" \
     # http://yourdomain.com/biorepo/create_gone_user
     try:
         user = User()
         user.firstname = firstname.capitalize()
         user.name = name.capitalize()
         lab = DBSession.query(Labs).filter(Labs.id == lab_id).first()
         user.labs.append(lab)
         user._email = user_mail
         group = DBSession.query(Group).filter(Group.id == 1).first()
         user.groups.append(group)
         DBSession.add(user)
         DBSession.flush()
         print "Gone/Exterior user created :", user
     except:
         print_traceback()
         print "Gone/Exterior user NOT created --> ERROR"
Exemple #32
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    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
Exemple #33
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 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)
Exemple #34
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    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)
Exemple #35
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 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)
Exemple #36
0
 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)
Exemple #37
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    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)
Exemple #38
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 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)
Exemple #39
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 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)
Exemple #40
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 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
Exemple #41
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 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
Exemple #42
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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
Exemple #43
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 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)
Exemple #44
0
    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
Exemple #45
0
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 ''
Exemple #46
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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 '''
Exemple #47
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    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
Exemple #48
0
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
Exemple #49
0
def create_meas(user, meas, name, description, status_type, type_,
                list_samples, parents, dest_raw, dest_processed):
    #new measurement management
    meas.user_id = user.id
    if name is not None:
        meas.name = name
    if description is not None:
        meas.description = description
    if status_type is not None:
        #fix the issue CheckBox TW1-->TW2
        if not isinstance(status_type, bool):
            if status_type == "on" or status_type.lower() == "public":
                status_type = True
            elif status_type.lower() == "private":
                status_type = False
        meas.status_type = status_type
    if type_ is not None:
        if not isinstance(type_, bool):
            if type_ == "on" or type_.lower() == "raw":
                type_ = True
            elif type_.lower() == "processed":
                type_ = False
        meas.type = type_

    #parents
    l = []
    if parents is None or parents == []:
        meas.children = l
    else:
        #if type(parents) is str or unicode or just 1 value in the list:
        if type(parents) is unicode or type(parents) is str or len(
                parents) == 1:
            if type(parents) is list:
                for x in parents:
                    me = DBSession.query(Measurements).filter(
                        Measurements.id == x).first()
                    l.append(me)
            else:
                for x in parents.split(','):
                    me = DBSession.query(Measurements).filter(
                        Measurements.id == x).first()
                    l.append(me)
        else:
            for x in parents:
                me = DBSession.query(Measurements).filter(
                    Measurements.id == x.id).first()
                l.append(me)
        meas.parents = l

    #get the sample information
    if list_samples:
        list_samples_id = list_samples
    else:
        list_samples_id = None

    #replace the for loop to test all the samples
    if list_samples_id is not None:
        if not isinstance(list_samples_id, list):
            list_samples_id = list_samples_id.split(',')
        samples2 = DBSession.query(Samples).filter(
            Samples.id.in_(list_samples_id)).all()

    else:
        samples2 = []
    meas.samples = samples2

    if not os.path.exists(dest_raw):
        os.mkdir(dest_raw)

    if not os.path.exists(dest_processed):
        os.mkdir(dest_processed)

    return meas
Exemple #50
0
 def setdefaultkey(self):
     uid = str(uuid.uuid4())
     while DBSession.query(User).filter(User.key == uid).first():
         uid = str(uuid.uuid4())
     return uid
Exemple #51
0
 def by_email_address(cls, email):
     """Return the user object whose email address is ``email``."""
     return DBSession.query(cls).filter(cls.email == email).first()
Exemple #52
0
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
Exemple #53
0
    def public_link(self, sha1, *args, **kw):
        #get the measurements selected id
        m_id = kw.get('m_id', None)
        f = DBSession.query(Files_up).filter(Files_up.sha1 == sha1).first()
        #if used with BAM_visualisation
        if f is None:
            try:
                tmp = sha1.split('.')
                sha1 = tmp[0]

                if len(tmp) == 2:
                    f = DBSession.query(Files_up).filter(
                        Files_up.sha1 == sha1).first()
                elif len(tmp) == 3:
                    f_bam = DBSession.query(Files_up).filter(
                        Files_up.sha1 == sha1).first()
                    fullname = f_bam.filename
                    name_tmp = fullname.split('.')
                    name = name_tmp[0]
                    f = DBSession.query(Files_up).filter(
                        Files_up.filename == name + ".bam.bai").first()
                if f is None:
                    flash(
                        "Sorry, your URL seems to be wrong. File corresponding to sha1 : "
                        + str(sha1) + " and m_id : " + str(m_id) +
                        " does not exist.", "error")
                    raise abort(403)

            except:
                flash("Sorry, this file is not referenced into BioRepo.",
                      "error")
                raise abort(403)
        list_meas = f.measurements
        for m in list_meas:
            if len(list_meas) == 1:
                if m.status_type:
                    path_fu = f.path + "/" + f.sha1
                    extension = f.extension
                    filename = f.filename
                    file_size = os.path.getsize(path_fu)
                    if dico_mimetypes.has_key(extension):
                        response.content_type = dico_mimetypes[extension]
                    else:
                        response.content_type = 'text/plain'
                    response.headers['X-Sendfile'] = path_fu
                    response.headers[
                        'Content-Disposition'] = 'attachement; filename=%s' % (
                            filename)
                    response.content_length = '%s' % (file_size)
                    return None
                else:
                    flash(
                        "Sorry, this file is not allowed to be extracted out of BioRepo.",
                        "error")
                    raise abort(403)
            #/!\lil hack : the same file can be used by several (or same) user in public AND private, and for this case it's tested in helpers.py
            else:
                meas = DBSession.query(Measurements).filter(
                    Measurements.id == m_id).first()
                list_fus = meas.fus
                if len(list_fus) == 1 and meas.status_type:
                    for other_f in list_fus:
                        sha1 = other_f.sha1
                        path_fu = other_f.path + "/" + sha1
                        extension = other_f.extension
                        filename = other_f.filename
                        file_size = os.path.getsize(path_fu)
                        if dico_mimetypes.has_key(extension):
                            response.content_type = dico_mimetypes[extension]
                        else:
                            response.content_type = 'text/plain'
                        response.headers['X-Sendfile'] = path_fu
                        response.headers[
                            'Content-Disposition'] = 'attachement; filename=%s' % (
                                filename)
                        response.content_length = '%s' % (file_size)
                        return None
                elif not meas.status_type:
                    flash(
                        "Sorry, this file is not allowed to be extracted out of BioRepo.",
                        "error")
                    raise abort(403)
                else:
                    flash("Problem with the attached file", "error")
                    raise abort(403)
Exemple #54
0
 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()
Exemple #55
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    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
Exemple #56
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    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)}
Exemple #57
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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
Exemple #58
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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