Exemplos de getcursor em Python

Exemplo n.º 1

    def insertOrUpdate(self, session_id, uid):
        with getcursor(self.DBCONN, "insertOrUpdate") as curs:
            curs.execute("""
SELECT id FROM {table}
WHERE session_id = %(session_id)s
""".format(table=self.table), {"session_id": session_id})
            if (curs.rowcount > 0):
                curs.execute("""
UPDATE {table}
SET
uid = %(uid)s
WHERE session_id = %(session_id)s
""".format(table=self.table), {"session_id": session_id,
                               "uid": uid
                               })
            else:
                curs.execute("""
INSERT INTO {table}
(session_id, uid)
VALUES (
%(session_id)s,
%(uid)s
)""".format(table=self.table), {"session_id": session_id,
                                "uid": uid
                                })

Exemplo n.º 2

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def insertOrUpdate(self, url, exists):
        with getcursor(self.DBCONN, "insertOrUpdate") as curs:
            curs.execute(
                """
SELECT exists FROM urlExists
WHERE url = %(url)s
""", {"url": url})
            if (curs.rowcount > 0):
                curs.execute(
                    """
UPDATE urlExists
SET
exists = %(exists)s
WHERE url = %(url)s
RETURNING id;
""", {
                        "url": url,
                        "exists": exists
                    })
            else:
                curs.execute(
                    """
INSERT INTO urlExists
(url, exists)
VALUES (
%(url)s,
%(exists)s
)""", {
                        "url": url,
                        "exists": exists
                    })

Exemplo n.º 3

Arquivo: 18_setup_cart.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "07_setup_cart") as curs:
            setupCart(curs, assembly)

Exemplo n.º 4

Arquivo: 12_cistromePeakIntersections.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    def doRun(args, assembly, curs, tsuffix, jobgen, runDate):
        if args.metadata:
            PI.ImportPeakIntersectionMetadata(curs, assembly, tsuffix, jobgen,
                                              runDate).run()
        elif args.index:
            PI.ImportPeakIntersections(curs, assembly, tsuffix,
                                       runDate).index()
        else:
            m = PI.ImportPeakIntersectionMetadata(curs, assembly, tsuffix,
                                                  jobgen, runDate)
            runDate = m.run()
            ipi = PI.ImportPeakIntersections(curs, assembly, tsuffix, runDate)
            ipi.run()
            ipi.index()

    runDate = Config.cistromePeakIntersectionRunDate
    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "main") as curs:
            if assembly in ["hg38", "mm10"]:
                doRun(args, assembly, curs, "cistromeIntersections",
                      cistrome_peak_metadata, runDate)

Exemplo n.º 5

def run(args, DBCONN):
    printt('***********', "mm10")
    with getcursor(DBCONN, "import DEs") as curs:
        ide = ImportDE(curs)
        if args.index:
            return ide.index()
        ide.setupAll(args.sample)
        ide.index()

Exemplo n.º 6

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def find(self, url):
        with getcursor(self.DBCONN, "findBedOverlap") as curs:
            curs.execute("""
SELECT exists
FROM urlExists
WHERE url = %(url)s
""", {"url": url})
            return curs.rowcount > 0

Exemplo n.º 7

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def find(self, url):
        with getcursor(self.DBCONN, "findBedOverlap") as curs:
            curs.execute(
                """
SELECT exists
FROM urlExists
WHERE url = %(url)s
""", {"url": url})
            return curs.rowcount > 0

Exemplo n.º 8

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def setupDB(self):
        with getcursor(self.DBCONN, "setupDB") as curs:
            curs.execute("""
DROP TABLE IF EXISTS urlExists;
CREATE TABLE urlExists
(id serial PRIMARY KEY,
url text,
exists boolean
    ) """)

Exemplo n.º 9

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def setupDB(self):
        with getcursor(self.DBCONN, "setupDB") as curs:
            curs.execute("""
DROP TABLE IF EXISTS urlExists;
CREATE TABLE urlExists
(id serial PRIMARY KEY,
url text,
exists boolean
    ) """)

Exemplo n.º 10

    def setupDB(self):
        with getcursor(self.DBCONN, "get") as curs:
            curs.execute("""
DROP TABLE IF EXISTS {table};
CREATE TABLE {table}
(id serial PRIMARY KEY,
uid text,
session_id text
) """.format(table=self.table))

Exemplo n.º 11

Arquivo: dbsnps.py Projeto: weng-lab/encyclopedia_v3

    def lookup(self, assembly, rs):
        with getcursor(self.DBCONN, "lookup") as curs:
            curs.execute(
                """
SELECT chrom, chromStart, chromEnd FROM {table}
WHERE name = %(rs)s
""".format(table=self.tableNames[assembly]), {"rs": rs})
            if (curs.rowcount > 0):
                return curs.fetchall()
            return None

Exemplo n.º 12

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "30_cytobands") as curs:
            c = Cytoband(curs, assembly)
            c.run()

Exemplo n.º 13

Arquivo: 38_dcc_cres_beds.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "38_beds") as curs:
            c = DCCCres(curs, assembly)
            c.run()

Exemplo n.º 14

    def fuzzy_lookup(self, assembly, gene):
        with getcursor(self.DBCONN, "lookup") as curs:
            curs.execute("""
SELECT gene FROM {table}
WHERE gene ~ lower(%(gene)s)
""".format(table=self.tableNames[assembly]),
                {"gene": gene})
            if (curs.rowcount > 0):
                return [x[0] for x in curs.fetchall()]
            return None

Exemplo n.º 15

    def lookup(self, assembly, gene):
        with getcursor(self.DBCONN, "lookup") as curs:
            curs.execute("""
SELECT chrom, chromStart, chromEnd FROM {table}
WHERE lower(gene) = lower(%(gene)s)
""".format(table=self.tableNames[assembly]),
                {"gene": gene})
            if (curs.rowcount > 0):
                return curs.fetchall()
            return None

Exemplo n.º 16

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "3_cellTypeInfo") as curs:
            at = AddTSS(curs, assembly)
            at.run()

Exemplo n.º 17

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "35_genes_Details") as curs:
            c = Genes(curs, assembly)
            c.run()

Exemplo n.º 18

def run(args, DBCONN):
    if args.assembly:
        assemblies = [args.assembly]
    assemblies = ["hg19"]  # Config.assemblies

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "31_links") as curs:
            c = Links(curs, assembly)
            c.run()

Exemplo n.º 19

def run(args, DBCONN):
    if args.assembly:
        assemblies = [args.assembly]
    assemblies = ["hg19"]  # Config.assemblies

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "29_tads") as curs:
            g = TADImporter(curs, assembly)
            g.run()

Exemplo n.º 20

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def get(self, url):
        with getcursor(self.DBCONN, "get") as curs:
            curs.execute("""
SELECT exists
FROM urlExists
WHERE url = %(url)s
""", {"url": url})
            if curs.rowcount > 0:
                return curs.fetchone()[0]
            return False

Exemplo n.º 21

Arquivo: 03_pg_cre.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "08_setup_log") as curs:
            pd = PolishData(curs, assembly)
            pd.run()

Exemplo n.º 22

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "04_cellTypeInfo") as curs:
            g = GWASsnps(curs, assembly)
            g.run()

Exemplo n.º 23

Arquivo: 05_genealiases.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "3_cellTypeInfo") as curs:
            aga = ImportGenes(curs, assembly)
            aga.run()
            makeMV(curs, assembly)

Exemplo n.º 24

Arquivo: 25_more_tracks.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        print('***********', assembly)
        pg = PostgresWrapper(DBCONN)
        with getcursor(DBCONN, "dropTables") as curs:
            icg = MoreTracks(curs, assembly, pg)
            icg.run()

Exemplo n.º 25

    def insert(self, session_id, uid):
        with getcursor(self.DBCONN, "get") as curs:
            curs.execute("""
INSERT INTO {table}
(session_id, uid)
VALUES (
%(session_id)s,
%(uid)s
)""".format(table=self.table), {"session_id": session_id,
                                "uid": uid
                                })

Exemplo n.º 26

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def get(self, url):
        with getcursor(self.DBCONN, "get") as curs:
            curs.execute(
                """
SELECT exists
FROM urlExists
WHERE url = %(url)s
""", {"url": url})
            if curs.rowcount > 0:
                return curs.fetchone()[0]
            return False

Exemplo n.º 27

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        printt('***********', assembly)
        with getcursor(DBCONN, "main") as curs:
            ipi = ImportVISTA(curs, assembly)
            ipi.run()
            ipi.index()

Exemplo n.º 28

    def get(self, session_id):
        print(self.table)
        with getcursor(self.DBCONN, "get") as curs:
            curs.execute("""
SELECT uid
FROM {table}
WHERE session_id = %(session_id)s
""".format(table=self.table), {"session_id": session_id})
            uid = curs.fetchone()
            if uid:
                return uid[0]
            return None

Exemplo n.º 29

    def setupDB(self):
        with getcursor(self.DBCONN, "setupDB") as curs:
            curs.execute("""
DROP TABLE IF EXISTS {search};
CREATE TABLE {search}
(id serial PRIMARY KEY,
reAccession text,
assembly text,
uid text NOT NULL,
hubNum integer NOT NULL,
j jsonb
) """.format(search=self.tableSearch))

Exemplo n.º 30

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        with getcursor(DBCONN, "08_setup_log") as curs:
            im = ImportRNAseq(curs, assembly)
            if args.index:
                im.doIndex()
            else:
                im.run()

Exemplo n.º 31

Arquivo: 22_cre_groups.py Projeto: wanliu2019/SCREEN

def run(args, DBCONN):
    assemblies = Config.assemblies
    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        print('***********', assembly)
        with getcursor(DBCONN, "dropTables") as curs:
            icg = ImportCreGroups(curs, assembly)
            icg.run()
            icg.runCts()
        with db_connect_single(os.path.realpath(__file__)) as conn:
            vacumnAnalyze(conn, assembly + "_cre_all", [])

Exemplo n.º 32

    def setupDB(self):
        with getcursor(self.DBCONN, "setupDB") as curs:
            curs.execute("""
DROP TABLE IF EXISTS {search};
CREATE TABLE {search}
(id serial PRIMARY KEY,
assembly text,
assays text,
tissues text,
loci text,
uid text NOT NULL,
assayType integer NOT NULL,
hubNum integer NOT NULL
) """.format(search=self.tableSearch))

Exemplo n.º 33

def run(args, DBCONN):
    assemblies = ["hg19"]  # Config.assemblies

    if args.assembly:
        assemblies = [args.assembly]

    for assembly in assemblies:
        if "hg19" != assembly:
            print("skipping...")
            continue
        printt('***********', assembly)
        with getcursor(DBCONN, "main") as curs:
            ig = ImportGwas(curs, assembly)
            ig.run()

Exemplo n.º 34

Arquivo: 03_genes.py Projeto: weng-lab/encyclopedia_v3

def main():
    args = parse_args()

    if args.local:
        dbs = DBS.localAnnotations()
    else:
        dbs = DBS.pgdsn("Annotations")
    dbs["application_name"] = os.path.realpath(__file__)

    import psycopg2.pool
    DBCONN = psycopg2.pool.ThreadedConnectionPool(1, 32, **dbs)

    with getcursor(DBCONN, "main") as cur:
        setupAll(cur)

Exemplo n.º 35

Arquivo: db_bed_overlap.py Projeto: weng-lab/encyclopedia_v3

    def findBedOverlap(self, assembly, chrom, start, end):
        if assembly not in ["hg19", "mm10"]:
            return []
        with getcursor(self.DBCONN, "findBedOverlap") as curs:
            curs.execute("""
SELECT DISTINCT expID
FROM bedRanges{assembly}
WHERE chrom = %(chrom)s
AND startend && int4range(%(start)s, %(end)s)
""".format(assembly=assembly),
                {"chrom": chrom,
                 "start": start,
                 "end": end})
            return [x[0] for x in curs.fetchall()]

Exemplo n.º 36

Arquivo: db_url_status.py Projeto: weng-lab/encyclopedia_v3

    def insertOrUpdate(self, url, exists):
        with getcursor(self.DBCONN, "insertOrUpdate") as curs:
            curs.execute("""
SELECT exists FROM urlExists
WHERE url = %(url)s
""", {"url": url})
            if (curs.rowcount > 0):
                curs.execute("""
UPDATE urlExists
SET
exists = %(exists)s
WHERE url = %(url)s
RETURNING id;
""", {"url": url,
                    "exists": exists
      })
            else:
                curs.execute("""
INSERT INTO urlExists
(url, exists)
VALUES (
%(url)s,
%(exists)s
)""", {"url": url, "exists": exists})