def get_child_tables(cur: Cursor, schema: str, name: str) -> List[tuple]:
cur.execute(
"""
SELECT TABLE_NAME, CONSTRAINT_NAME, COLUMN_NAME
FROM ALL_CONS_COLUMNS
WHERE OWNER = :schema
AND CONSTRAINT_NAME IN (
SELECT CONSTRAINT_NAME
FROM ALL_CONSTRAINTS
WHERE CONSTRAINT_TYPE = 'R' -- Referential
AND R_CONSTRAINT_NAME IN (
SELECT CONSTRAINT_NAME
FROM ALL_CONSTRAINTS
WHERE CONSTRAINT_TYPE IN ('P', 'U') -- Primary/Unique
AND OWNER = :schema
AND TABLE_NAME = :name
)
)
""", dict(schema=schema, name=name))
return cur.fetchall()
def fetchCityData(self, con: cx_Oracle.Connection, cur: cx_Oracle.Cursor,
startTime: dt.datetime, endTime: dt.datetime,
tag: str) -> pd.core.frame.DataFrame:
"""fethc weather data of all station of a particular entity
Args:
con (cx_Oracle.Connection): [connection]
cur (cx_Oracle.Cursor): [cursor]
startTime (dt.datetime): [startime]
endTime (dt.datetime): [endTIme]
tag (str): [entityTag]
Returns:
pd.core.frame.DataFrame: [return weather dataframe of all station of a particular entity]
"""
guj, mp, mah, chh, goa, dd, dnh = False, False, False, False, False, False, False
if tag == "WRLDCMP.SCADA1.A0047000":
guj, mp, mah, chh, goa, dd, dnh = True, True, True, True, True, True, True
elif tag == "WRLDCMP.SCADA1.A0046957":
guj = True
elif tag == "WRLDCMP.SCADA1.A0046978":
mp = True
elif tag == "WRLDCMP.SCADA1.A0046980":
mah = True
elif tag == "WRLDCMP.SCADA1.A0046945":
chh = True
elif tag == "WRLDCMP.SCADA1.A0046962":
goa = True
elif tag == "WRLDCMP.SCADA1.A0046948":
dd = True
elif tag == "WRLDCMP.SCADA1.A0046953":
dnh = True
try:
df2 = pd.DataFrame()
if guj:
cur.execute(
'''select time,temperature from solar where city='station_1' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_1'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_2' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_2'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_3' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_3'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_4' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_4'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_5' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_5'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_6' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_6'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_7' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_7'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_8' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_8'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_9' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_9'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
if mp:
cur.execute(
'''select time,temperature from solar where city='station_10' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_10'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_11' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_11'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_12' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_12'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_13' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_13'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_14' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_14'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_15' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_15'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_16' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_16'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
if mah:
cur.execute(
'''select time,temperature from solar where city='station_17' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_17'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_18' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_18'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_19' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_19'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_20' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_20'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_21' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_21'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_22' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_22'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_23' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_23'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_24' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_24'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_25' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_25'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_26' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_26'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_27' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_27'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_28' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_28'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_29' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_29'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_30' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_30'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_31' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_31'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_32' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_32'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_33' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_33'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_34' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_34'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_35' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_35'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_36' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_36'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_37' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_37'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
if chh:
cur.execute(
'''select time,temperature from solar where city='station_38' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_38'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_39' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_39'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_40' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_40'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
if goa:
cur.execute(
'''select time,temperature from solar where city='station_41' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_41'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
if dd:
cur.execute(
'''select time,temperature from solar where city='station_42' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_42'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
cur.execute(
'''select time,temperature from solar where city='station_43' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_43'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
if dnh:
cur.execute(
'''select time,temperature from solar where city='station_44' and (time between :1 and :2 ) order by time''',
(startTime, endTime))
df = pd.DataFrame(cur.fetchall(),
columns=['time', 'station_44'])
df.set_index('time', inplace=True)
df2 = pd.concat([df2, df], axis=1)
# print(df2)
except Exception as e:
print(e)
return pd.DataFrame()
return df2
def _export_pdb2interpro2go2uniprot(cur: cx_Oracle.Cursor, output: str):
# PDBe sequences from UniParc
cur.execute(
"""
SELECT UPI, AC
FROM UNIPARC.XREF
WHERE DBID = 21
AND DELETED = 'N'
"""
)
sequences = {}
for upi, pdb_acc in cur:
if upi in sequences:
sequences[upi]["structures"].add(pdb_acc)
else:
sequences[upi] = {
"structures": {pdb_acc},
"entries": set()
}
# Integrated signatures whose entry is checked and has GO terms
cur.execute(
"""
SELECT METHOD_AC, ENTRY_AC
FROM INTERPRO.ENTRY2METHOD
WHERE ENTRY_AC IN (
SELECT ENTRY_AC
FROM INTERPRO.ENTRY
WHERE CHECKED = 'Y'
INTERSECT
SELECT DISTINCT ENTRY_AC
FROM INTERPRO.INTERPRO2GO
)
"""
)
signatures = dict(cur.fetchall())
# GO terms in InterPro
cur.execute(
"""
SELECT ENTRY_AC, GO_ID
FROM INTERPRO.INTERPRO2GO
WHERE ENTRY_AC IN (
SELECT ENTRY_AC
FROM INTERPRO.ENTRY
WHERE CHECKED = 'Y'
)
"""
)
entries = {}
for entry_acc, go_id in cur:
if entry_acc in entries:
entries[entry_acc].add(go_id)
else:
entries[entry_acc] = {go_id}
# PDBe matches
cur.execute(
"""
SELECT DISTINCT UPI, METHOD_AC
FROM IPRSCAN.MV_IPRSCAN
WHERE UPI IN (
SELECT UPI
FROM UNIPARC.XREF
WHERE DBID = 21
AND DELETED = 'N'
)
"""
)
for upi, signature_acc in cur:
try:
entry_acc = signatures[signature_acc]
except KeyError:
pass
else:
sequences[upi]["entries"].add(entry_acc)
# PDBe taxonomy
structures = pdbe.get_chain_taxonomy(cur)
# UniProt accessions
cur.execute(
"""
SELECT DISTINCT A.AC, B.AC
FROM UNIPARC.XREF A
LEFT OUTER JOIN UNIPARC.XREF B ON A.UPI = B.UPI
WHERE A.DBID = 21
AND A.DELETED = 'N'
AND B.DBID IN (2, 3)
AND B.DELETED = 'N'
"""
)
pdb2uniprot = {}
for pdb_acc, protein_acc in cur:
if not protein_acc:
continue
elif pdb_acc in pdb2uniprot:
pdb2uniprot[pdb_acc].add(protein_acc)
else:
pdb2uniprot[pdb_acc] = {protein_acc}
tmp_path = f"{output}.tmp"
with open(tmp_path, "wt") as fh:
fh.write("#PDBe ID\tchain\tTaxon ID\t"
"InterPro accession\tGO ID\tUniProt accession\n")
for seq in sequences.values():
for pdb_acc in seq["structures"]:
try:
s = structures[pdb_acc]
except KeyError:
# Structure does not exist in PDBe database
continue
pdb_id = s["id"]
chain = s["chain"]
proteins = pdb2uniprot.get(pdb_acc, {''})
for tax_id in s["taxa"]:
for entry_acc in seq["entries"]:
for go_id in entries[entry_acc]:
for protein_acc in proteins:
fh.write(f"{pdb_id}\t{chain}\t{tax_id}\t"
f"{entry_acc}\t{go_id}\t"
f"{protein_acc}\n")
try:
os.remove(output)
except FileNotFoundError:
pass
finally:
os.rename(tmp_path, output)
os.chmod(output, 0o775)
