def comparisonpage(organism, transcriptome):
global user_short_passed
user_short_passed = False
global local
try:
print local
except:
local = False
try:
user = current_user.name
except:
user = None
organism = str(organism)
connection = sqlite3.connect('{}/trips.sqlite'.format(config.SCRIPT_LOC))
connection.text_factory = str
cursor = connection.cursor()
cursor.execute(
"SELECT gwips_clade,gwips_organism,gwips_database,default_transcript from organisms WHERE organism_name = '{}';"
.format(organism))
result = (cursor.fetchone())
gwips_clade = result[0]
gwips_org = result[1]
gwips_db = result[2]
gwips_info = {
"organism": gwips_org,
"clade": gwips_clade,
"database": gwips_db
}
default_tran = result[3]
studyinfo_dict = fetch_study_info(organism)
user_file_dict = {}
if str(request.args.get('files')) != "None":
colors = str(request.args.get('files')).split("_")
for filelist in colors:
all_items = filelist.split(",")
files = []
for item in all_items:
if "#" in item:
color = item
else:
files.append(item)
user_file_dict[color] = files
user_label_dict = {}
if str(request.args.get('labels')) != "None":
colors = str(request.args.get('labels')).split("_")
for label in colors:
all_items = label.split(",")
for item in all_items:
if "#" in item:
color = item
else:
label = item
user_label_dict[color] = label
html_args = {
"user_short": str(request.args.get('short')),
"user_file_dict": user_file_dict,
"user_label_dict": user_label_dict,
"transcript": str(request.args.get('transcript')),
"minread": str(request.args.get('minread')),
"maxread": str(request.args.get('maxread')),
"hili_start": str(request.args.get('hili_start')),
"hili_stop": str(request.args.get('hili_stop')),
"ambig": str(request.args.get('ambig')),
"cov": str(request.args.get('cov')),
"normalize": str(request.args.get('normalize')),
"transcriptome": str(transcriptome)
}
accepted_studies = fetch_studies(user, organism, transcriptome)
file_id_to_name_dict, accepted_studies, accepted_files, seq_types = fetch_files(
accepted_studies)
connection.close()
return render_template('index_compare.html',
studies_dict=accepted_studies,
accepted_files=accepted_files,
gwips_info=gwips_info,
gwips_clade=gwips_clade,
gwips_org=gwips_org,
gwips_db=gwips_db,
organism=organism,
transcriptome=transcriptome,
default_tran=default_tran,
local=local,
html_args=html_args,
file_id_to_name_dict=file_id_to_name_dict,
studyinfo_dict=studyinfo_dict,
seq_types=seq_types)
def interactiveplotpage(organism, transcriptome):
global user_short_passed
user_short_passed = True
global local
try:
print local
except:
local = False
try:
user = current_user.name
except:
user = None
organism = str(organism)
accepted_studies = fetch_studies(user, organism, transcriptome)
file_id_to_name_dict, accepted_studies, accepted_files, seq_types = fetch_files(
accepted_studies)
connection = sqlite3.connect('{}/trips.sqlite'.format(config.SCRIPT_LOC))
connection.text_factory = str
cursor = connection.cursor()
cursor.execute(
"SELECT gwips_clade,gwips_organism,gwips_database,default_transcript from organisms WHERE organism_name = '{}' and transcriptome_list = '{}';"
.format(organism, transcriptome))
result = (cursor.fetchone())
gwips_clade = result[0]
gwips_org = result[1]
gwips_db = result[2]
gwips_info = {
"organism": gwips_org,
"clade": gwips_clade,
"database": gwips_db
}
default_tran = result[3]
studyinfo_dict = fetch_study_info(organism)
user_transcript = request.args.get('tran')
user_readscore = request.args.get('rs')
user_hili = request.args.get('hili')
user_generate_shorturl = request.args.get('genshort')
user_files = request.args.get('files')
user_minread = request.args.get('minread')
user_maxread = request.args.get('maxread')
user_dir = request.args.get('dir')
user_line_graph = request.args.get('lg')
user_ambig = request.args.get('ambig')
user_cov = request.args.get('cov')
user_nuc = request.args.get('nuc')
user_short = request.args.get('short')
user_crd = request.args.get('crd')
if user_files != None:
user_files = user_files.split(",")
user_files = [str(x) for x in user_files]
else:
user_files = []
user_ribo_studies = request.args.get('ribo_studies')
if user_ribo_studies != None:
user_ribo_studies = user_ribo_studies.split(",")
user_ribo_studies = [str(x) for x in user_ribo_studies]
else:
user_ribo_studies = []
user_rna_studies = request.args.get('rna_studies')
if user_rna_studies != None:
user_rna_studies = user_rna_studies.split(",")
user_rna_studies = [str(x) for x in user_rna_studies]
else:
user_rna_studies = []
if user_generate_shorturl == "F":
user_generate_shorturl = False
else:
user_generate_shorturl = True
user_hili_starts = []
user_hili_stops = []
try:
for item in user_hili.split(","):
user_hili_starts.append(int(item.split("_")[0]))
user_hili_stops.append(int(item.split("_")[1]))
except:
user_hili_start = None
user_hili_stop = None
try:
user_minread = int(user_minread)
user_maxread = int(user_maxread)
except:
user_minread = None
user_maxread = None
advanced = 'True'
connection.close()
return render_template('index.html',
gwips_info=gwips_info,
gwips_clade=gwips_clade,
gwips_org=gwips_org,
gwips_db=gwips_db,
organism=organism,
transcriptome=transcriptome,
default_tran=default_tran,
user_transcript=user_transcript,
user_readscore=user_readscore,
user_hili_starts=user_hili_starts,
user_hili_stops=user_hili_stops,
local=local,
studies_dict=accepted_studies,
accepted_files=accepted_files,
user_files=user_files,
user_ribo_studies=user_ribo_studies,
user_rna_studies=user_rna_studies,
user_minread=user_minread,
user_maxread=user_maxread,
user_dir=user_dir,
user_line_graph=user_line_graph,
user_ambig=user_ambig,
user_cov=user_cov,
user_nuc=user_nuc,
user_short=user_short,
user_crd=user_crd,
studyinfo_dict=studyinfo_dict,
advanced=advanced,
seq_types=seq_types)