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PostgreSQL.py
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PostgreSQL.py
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import psycopg2
import json
class DBException(Exception):
pass
def connect(dbname):
import credentials
try:
con = psycopg2.connect(host=credentials.hostname, user=credentials.username, password=credentials.password,
dbname=credentials.database)
except psycopg2.Error as e:
raise DBException(e.message)
return con
def create_tables(cur, con):
# don't create tables here
# use file postgreSQL_schema.sql to init db
#
# you will need to search and replace 'username' in the sql file,
# replacing it with the role name you use to access the database
return True
def new_upload(inj_list, cur, con):
try:
cur.execute("""
INSERT INTO uploads (
user_id,
filename,
origin,
upload_time
)
VALUES (%s, %s, %s, CURRENT_TIMESTAMP) RETURNING id AS upload_id""", inj_list)
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
rows = cur.fetchall()
return rows[0][0]
def get_random_id(upload_id, cur, con):
try:
cur.execute("SELECT random_id FROM uploads WHERE id = " + str(upload_id) + ";")
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
rows = cur.fetchall()
return rows[0][0]
def write_mzid_info(peak_list_file_names,
spectra_formats,
analysis_software,
provider,
audits,
samples,
analyses,
protocol,
bib,
upload_id, cur, con):
try:
cur.execute("""UPDATE uploads SET
peak_list_file_names = (%s),
spectra_formats = (%s),
analysis_software = (%s),
provider = (%s),
audits = (%s),
samples = (%s),
analyses = (%s),
protocol = (%s),
bib = (%s)
WHERE id = (%s);""",
(peak_list_file_names,
spectra_formats,
analysis_software,
provider,
audits,
samples,
analyses,
protocol,
bib,
upload_id))
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_other_info(upload_id, crosslinks, ident_count, ident_file_size, upload_warnings, cur, con):
try:
cur.execute("""UPDATE uploads SET contains_crosslinks = (%s), ident_count = (%s), ident_file_size = (%s)
, upload_warnings = (%s)
WHERE id = (%s);""", (crosslinks, ident_count, ident_file_size, json.dumps(upload_warnings), upload_id))
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_error(upload_id, error_type, error, cur, con):
try:
cur.execute("""UPDATE uploads SET error_type = %s
, upload_error = %s
WHERE id = %s;""", (error_type, error, upload_id))
con.commit()
cur.execute("DELETE FROM db_sequences WHERE upload_id = " + str(upload_id) + ";")
con.commit()
cur.execute("DELETE FROM peptides WHERE upload_id = '" + str(upload_id) + "';")
con.commit()
cur.execute("DELETE FROM peptide_evidences WHERE upload_id = " + str(upload_id) + ";")
con.commit()
cur.execute("DELETE FROM modifications WHERE upload_id = " + str(upload_id) + ";")
con.commit()
cur.execute("DELETE FROM spectra WHERE upload_id = " + str(upload_id) + ";")
con.commit()
cur.execute("DELETE FROM spectrum_identifications WHERE upload_id = " + str(upload_id) + ";")
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
# def write_protocols(inj_list, cur, con):
# return True
def write_db_sequences(inj_list, cur, con):
try:
cur.executemany("""
INSERT INTO db_sequences (
id,
accession,
protein_name,
description,
sequence,
upload_id
)
VALUES (%s, %s, %s, %s, %s, %s) """, inj_list)
# con.commit()
#
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_meta_data(*args):
pass
def write_peptides(inj_list, cur, con):
try:
cur.executemany("""
INSERT INTO peptides (
id,
seq_mods,
link_site,
crosslinker_modmass,
upload_id,
crosslinker_pair_id
)
VALUES (%s, %s, %s, %s, %s, %s)""", inj_list)
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_modifications(inj_list, cur, con):
try:
cur.executemany("""
INSERT INTO modifications (
id,
upload_id,
mod_name,
mass,
residues,
accession
)
VALUES (%s, %s, %s, %s, %s, %s)""", inj_list)
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_peptide_evidences(inj_list, cur, con):
try:
cur.executemany("""
INSERT INTO peptide_evidences (
peptide_ref,
dbsequence_ref,
protein_accession,
pep_start,
is_decoy,
upload_id
)
VALUES (%s, %s, %s, %s, %s, %s)""", inj_list)
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_spectra(inj_list, cur, con):
try:
cur.executemany("""
INSERT INTO spectra (
id,
peak_list,
peak_list_file_name,
scan_id,
frag_tol,
upload_id,
spectrum_ref,
precursor_mz,
precursor_charge
)
VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s)""", inj_list)
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True
def write_spectrum_identifications(inj_list, cur, con):
try:
cur.executemany("""
INSERT INTO spectrum_identifications (
id,
upload_id,
spectrum_id,
pep1_id,
pep2_id,
charge_state,
rank,
pass_threshold,
ions,
scores,
exp_mz,
calc_mz,
meta1,
meta2,
meta3
) VALUES (%s, %s, %s, %s, %s, %s, %s, %s , %s, %s, %s, %s, %s, %s, %s)""", inj_list)
con.commit()
except psycopg2.Error as e:
raise DBException(e.message)
return True