[Biopython-dev] [Bug 2849] New: PyGresql PostgreSQL driver support for BioSQL is broken

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2849

           Summary: PyGresql PostgreSQL driver support for BioSQL is broken
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: cymon.cox at gmail.com


cymon at gyra:~/git/github-master/Tests$ python test_BioSQL.py
GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ERROR
GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ERROR
GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ERROR
GenBank file to BioSQL and back to a GenBank file, arab1. ... ERROR
GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ERROR
GenBank file to BioSQL and back to a GenBank file, noref. ... ERROR
GenBank file to BioSQL and back to a GenBank file, one_of. ... ERROR
GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ERROR
Make sure can't import records with same ID (in one go). ... ERROR
Make sure can't import a single record twice (in one go). ... ERROR
Make sure can't import a single record twice (in steps). ... ERROR
Make sure all records are correctly loaded. ... ERROR
Make sure can't reimport existing records. ... ERROR
Indepth check that SeqFeatures are transmitted through the db. ... ERROR
Make sure can load record into another namespace. ... ERROR
Load SeqRecord objects into a BioSQL database. ... ERROR
Get a list of all items in the database. ... ERROR
Test retrieval of items using various ids. ... ERROR
Check can add DBSeq objects together. ... ERROR
Check can turn a DBSeq object into a Seq or MutableSeq. ... ERROR
Make sure Seqs from BioSQL implement the right interface. ... ERROR
Check SeqFeatures of a sequence. ... ERROR
Make sure SeqRecords from BioSQL implement the right interface. ... ERROR
Check that slices of sequences are retrieved properly. ... ERROR
GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ERROR
GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ERROR
GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ERROR
GenBank file to BioSQL, then again to a new namespace, arab1. ... ERROR
GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ERROR
GenBank file to BioSQL, then again to a new namespace, noref. ... ERROR
GenBank file to BioSQL, then again to a new namespace, one_of. ... ERROR
GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ...
ERROR

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, NC_000932.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 409, in test_NC_000932
    self.loop(os.path.join(os.getcwd(), "GenBank", "NC_000932.gb"), "gb")
  File "test_BioSQL.py", line 443, in loop
    count = db.load(original_records)
  File "/home/cymon/git/github-master/BioSQL/BioSeqDatabase.py", line 479, in
load
    db_loader.load_seqrecord(cur_record)
  File "/home/cymon/git/github-master/BioSQL/Loader.py", line 50, in
load_seqrecord
    bioentry_id = self._load_bioentry_table(record)
  File "/home/cymon/git/github-master/BioSQL/Loader.py", line 559, in
_load_bioentry_table
    bioentry_id = self.adaptor.last_id('bioentry')
  File "/home/cymon/git/github-master/BioSQL/BioSeqDatabase.py", line 168, in
last_id
    return self.dbutils.last_id(self.cursor, table)
  File "/home/cymon/git/github-master/BioSQL/DBUtils.py", line 96, in last_id
    cursor.execute(sql)
  File "/usr/lib/python2.6/dist-packages/pgdb.py", line 259, in execute
    self.executemany(operation, (params,))
  File "/usr/lib/python2.6/dist-packages/pgdb.py", line 289, in executemany
    raise DatabaseError("error '%s' in '%s'" % (msg, sql))
DatabaseError: error 'ERROR:  currval of sequence "bioentry_pk_seq" is not yet
defined in this session
' in 'select currval('bioentry_pk_seq')'

======================================================================

etc, etc, etc...

Same error until we get to:

======================================================================
ERROR: Make sure can't import records with same ID (in one go).
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 344, in setUp
    create_database()
  File "test_BioSQL.py", line 56, in create_database
    server.adaptor.autocommit()
  File "/home/cymon/git/github-master/BioSQL/BioSeqDatabase.py", line 172, in
autocommit
    return self.dbutils.autocommit(self.conn, y)
  File "/home/cymon/git/github-master/BioSQL/DBUtils.py", line 101, in
autocommit
    raise NotImplementedError("pgdb does not support this!")
NotImplementedError: pgdb does not support this!

======================================================================
ERROR: Make sure can't import a single record twice (in one go).
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 344, in setUp
    create_database()
  File "test_BioSQL.py", line 56, in create_database
    server.adaptor.autocommit()
  File "/home/cymon/git/github-master/BioSQL/BioSeqDatabase.py", line 172, in
autocommit
    return self.dbutils.autocommit(self.conn, y)
  File "/home/cymon/git/github-master/BioSQL/DBUtils.py", line 101, in
autocommit
    raise NotImplementedError("pgdb does not support this!")
NotImplementedError: pgdb does not support this!

======================================================================


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