def readFromMysql(self, db, numId, withSeqs=True):
""" read from mysql database, return None if not found in Db """
#pmcId = pmcId.strip("pmcA")
self.numId = numId
if withSeqs:
self.seqs = {}
recs = util.sql(db, "select fileName, seqId, sequence, context from sequences where numId='%s'" % str(numId))
#if len(recs)==0:
#return None
for r in recs:
filename, seqId, seq, raw = r
self.seqs[seqId]=(filename, seq, raw)
row = util.sql(db, "select pmid, pmcId from refs where numId='%s';" % str(numId))
self.pmid, self.pmcId = row[0]
recs = util.sql(db, "select * from bestGenomes where numId='%s';" % str(numId))
if len(recs)>0:
self.bestGenome = recs[0][1]
else:
self.bestGenomes= None
recs = util.sql(db, "select genomeId, chrom, start, end, numId, seqid, score, groupId from features where numId='%s'; " % str(numId))
self.chainHits = recs
#recs = util.sql(db, "select * from blastHits where numId='%s'" % str(pmcId))
#self.rawHits = IndexedBlastHits(recs)
#recs = util.sql(db, "select * from filtHits where numId='%s'" % str(pmcId))
#self.filtHits = IndexedBlastHits(recs)
#recs = util.sql(db, "select * from blastHitsGenes where numId='%s'" % str(pmcId))
#self.filtGeneHits = IndexedBlastHits(recs)
return True
def process_register():
email = request.form.get("email")
passwd = get_password(email)
if len(passwd) > 0:
return redirect(url_for('register_error', error='already exists'))
pass1 = request.form.get("pass1")
pass2 = request.form.get("pass2")
# validate email
schema = {'email': {'type': 'string', 'regex': '^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$'}}
document = {'email': email}
v = Validator(schema)
if not v.validate(document):
return redirect(url_for('register_error', error='email'))
if not pass1 == pass2:
return redirect(url_for('register_error', error='pass'))
from util import escape_sql_characters
email = escape_sql_characters(email)
pass1 = escape_sql_characters(pass1)
insert_query = f"INSERT INTO user_data (email, password) VALUES ('{email}','{pass1}')"
sql(insert_query, db=db, rollback=True)
return redirect(url_for('register_success'))
def getNumIdsOrthologs(db, orthologs):
orthologIds = ["'" + g + "'" for g in orthologs]
query = "select numId from bestGenes, orthologs where orthologs.geneId in (%s) and bestGenes.geneId=orthologs.geneId;" % ",".join(
orthologIds)
recs = util.sql(db, query)
recs = [str(l[0]) for l in recs]
return recs
def getOrthologs(db, geneIds):
geneIds = ["'" + g + "'" for g in geneIds]
query = "select geneId from orthologs where hsGeneId in (%s);" % ",".join(
geneIds)
recs = util.sql(db, query)
recs = [l[0] for l in recs]
return recs
def getNumIds(db, geneId, asStrings=False):
recs = util.sql(db,
"select numId from bestGenes where geneId='%s';" % geneId)
recs = [l[0] for l in recs]
if asStrings:
recs = [str(x) for x in recs]
return recs
def readFromMysql(self, db, numId, withSeqs=True):
""" read from mysql database, return None if not found in Db """
#pmcId = pmcId.strip("pmcA")
self.numId = numId
if withSeqs:
self.seqs = {}
recs = util.sql(
db,
"select fileName, seqId, sequence, context from sequences where numId='%s'"
% str(numId))
#if len(recs)==0:
#return None
for r in recs:
filename, seqId, seq, raw = r
self.seqs[seqId] = (filename, seq, raw)
row = util.sql(
db, "select pmid, pmcId from refs where numId='%s';" % str(numId))
self.pmid, self.pmcId = row[0]
recs = util.sql(
db, "select * from bestGenomes where numId='%s';" % str(numId))
if len(recs) > 0:
self.bestGenome = recs[0][1]
else:
self.bestGenomes = None
recs = util.sql(
db,
"select genomeId, chrom, start, end, numId, seqid, score, groupId from features where numId='%s'; "
% str(numId))
self.chainHits = recs
#recs = util.sql(db, "select * from blastHits where numId='%s'" % str(pmcId))
#self.rawHits = IndexedBlastHits(recs)
#recs = util.sql(db, "select * from filtHits where numId='%s'" % str(pmcId))
#self.filtHits = IndexedBlastHits(recs)
#recs = util.sql(db, "select * from blastHitsGenes where numId='%s'" % str(pmcId))
#self.filtGeneHits = IndexedBlastHits(recs)
return True
def getNumIdsOrthologs(db, orthologs):
orthologIds = ["'"+g+"'" for g in orthologs]
query = "select numId from bestGenes, orthologs where orthologs.geneId in (%s) and bestGenes.geneId=orthologs.geneId;" % ",".join(orthologIds)
recs = util.sql(db, query)
recs = [str(l[0]) for l in recs]
return recs
def getOrthologs(db, geneIds):
geneIds = ["'"+g+"'" for g in geneIds]
query = "select geneId from orthologs where hsGeneId in (%s);" % ",".join(geneIds)
recs = util.sql(db, query)
recs = [l[0] for l in recs]
return recs
def getIdForSymbol(db, symbol):
recs = util.sql(db, "select geneId from genes where symbol = %s;", symbol)
if len(recs)==0:
return symbol
else:
return recs[0][0]
def getHumanOrthologs(db, geneId):
recs = util.sql(db, "select hsGeneId from orthologs where geneId='%s' " % (geneId))
recs = [l[0] for l in recs]
return recs
def getNumIds(db, geneId, asStrings=False):
recs = util.sql(db, "select numId from bestGenes where geneId='%s';" % geneId)
recs = [l[0] for l in recs]
if asStrings:
recs = [str(x) for x in recs]
return recs
def getIdForSymbol(db, symbol):
recs = util.sql(db, "select geneId from genes where symbol = %s;", symbol)
if len(recs) == 0:
return symbol
else:
return recs[0][0]
def getHumanOrthologs(db, geneId):
recs = util.sql(
db, "select hsGeneId from orthologs where geneId='%s' " % (geneId))
recs = [l[0] for l in recs]
return recs
if not tables['db config']:
config['overwrite']['db_config_modify'] = "True"
if not tables['books']:
config['overwrite']['books_table_modify'] = "True"
config['DEFAULT']['import books'] = "True"
if not tables['users']: config['overwrite']['user_table_modify'] = "True"
if not tables['reviews']: config['overwrite']['reviews_table_modify'] = "True"
print(dict(config['overwrite']))
print("Decisions made.\nWorking on:")
# Creating tables one by one
# db config
print("DB Config table.")
if config['overwrite']['db_config_modify'] == "True":
if tables['db config']:
sql(config['queries']['drop db config'], db=db, rollback=True)
sql(config['queries']['db config'], db=db)
for key in config['overwrite'].keys():
add_var(key, config['overwrite'][key], db=db)
for key in config['overwrite'].keys():
modify_var(key, config['overwrite'][key], db=db)
# Books
print("Books table.")
if config['overwrite']['books_table_modify'] == "True":
if tables['books']:
sql(config['queries']['drop books'], rollback=True)
sql(config['queries']['create books'], db=db)
if config['overwrite']['books_table_modify'] == 'True' or config['DEFAULT'][
'import books'] == 'True':