Any way you can you test it with passing in parameters mdbArgs to use
a non-local mysql instance? If you have that capability, that would be
great.
On May 25, 6:19 am, Namshin Kim <n...@rna.kr> wrote:
> Hmm... I tested again and it worked. And, new lines are successfully added
> to the mysql table.
>
> [deepr...@s47 ~]$ python>>> from pygr import metabase
> >>> mdb = metabase.MetabaseList()
> >>> mdb = metabase.MySQLMetabase('test.pygr', mdb, createLayer='test')
> >>> mdb = metabase.MetabaseList('mysql:test.pygr')
> >>> mdb.dir()
>
> ['0version', 'PYGRLAYERNAME']>>> from pygr.seqdb import SequenceFileDB
> >>> g = SequenceFileDB('hg18')
> >>> g.__doc__ = 'hg18'
> >>> mdb.add_resource("Bio.Seq.Genome.HUMAN.hg18", g)
> >>> mdb.commit()
> >>> mdb.dir()
>
> ['0root', '0version', 'Bio.Seq.Genome.HUMAN.hg18', 'PYGRLAYERNAME']
>
>
>
> [deepr...@s47 ~]$ python>>> from pygr import metabase
> >>> mdb = metabase.MetabaseList('mysql:test.pygr')
> >>> mdb.dir()
>
> ['0root', '0version', 'Bio.Seq.Genome.HUMAN.hg18', 'PYGRLAYERNAME']
>
>
>
> On Tue, May 25, 2010 at 10:53 AM, Kenny Daily <kmda...@gmail.com> wrote:
> > OK! I got this to work. But when I try to add something, I get no
> > warnings, errors, or exceptions, but it doesn't add any rows to the
> > tables. Then when I set up the MetabaseList again (leaving the
> > interpreter), the resource I've added is gone.
>
> > from pygr import metabase
> > from pygr import seqdb
>
> > mdb = metabase.MetabaseList()
> > rdb = metabase.MySQLMetabase(tablename="worldbase.worldbaseindex
> > my.host.edu user pass", mdb=mdb, createLayer="baldig",
> > host="my.host.edu", port=5000)
>
> > ## created this already, tables exist
> > mdb = metabase.MetabaseList("mysql:worldbase.worldbaseindex",
> > mdbArgs=dict(host="my.host.edu", db="worldbase", port=5000,
> > user="user", passwd="pass"))
>
> > g = seqdb.SequenceFileDB("/path/to/sacCer2.fa")
> > g.__doc__ = "Yeast genome"
>
> > ## no errors!
> > mdb.add_resource("Bio.Seq.Genome.YEAST.sacCer2", g)
> > mdb.commit()
> > mdb.dir()
> > Out[30]: ['0root', '0version', 'Bio.Seq.Genome.YEAST.sacCer2',
> > 'PYGRLAYERNAME']
>
> > Then exit the shell....
>
> > from pygr import metabase
>
> > ## created this already, tables exist
> > mdb = metabase.MetabaseList("mysql:worldbase.worldbaseindex",
> > mdbArgs=dict(host="my.host.edu", db="worldbase", port=5000,
> > user="user", passwd="pass"))
> > mdb.dir()
> > Out[3]: ['0version', 'PYGRLAYERNAME']
>
> > Database contents:
> > mysql> select * from worldbaseindex_schema;
> > Empty set (0.00 sec)
>
> > mysql> select * from worldbaseindex;
> > +---------------+----------+-----------+------+---------------------
> > +-------------+---------------+-----------+---------+
> > | pygr_id | location | docstring | user | creation_time |
> > pickle_size | security_code | info_blob | objdata |
> > +---------------+----------+-----------+------+---------------------
> > +-------------+---------------+-----------+---------+
> > | 0version | 0.1.0 | NULL | NULL | NULL
> > | NULL | NULL | NULL | a |
> > | PYGRLAYERNAME | baldig | NULL | NULL | 2010-05-24 17:14:21
> > | NULL | NULL | NULL | a |
> > +---------------+----------+-----------+------+---------------------
> > +-------------+---------------+-----------+---------+
> > 2 rows in set (0.01 sec)
>
> > Kenny
>
> > On May 24, 5:01 pm, Namshin Kim <n...@rna.kr> wrote:
> > > I am not sure whether this is correct usage because many things changed
> > > since I used MySQL as metabase.
>
> > > >>> import os
> > > >>> from pygr import metabase
> > > >>> mdb = metabase.MetabaseList() # open dummy metabase
> > > >>> mdb = metabase.MySQLMetabase('test.pygr', mdb, createLayer='test')
>
> > /data1/deepreds/projects/Pygr_Project/pygr/build/lib.linux-x86_64-2.5/pygr/
> > metabase.py:333:
> > > Warning: Unknown table 'pygr'
> > > self.cursor.execute('drop table if exists %s' % self.tablename)
>
> > /data1/deepreds/projects/Pygr_Project/pygr/build/lib.linux-x86_64-2.5/pygr/
> > metabase.py:343:
> > > Warning: Unknown table 'pygr_schema'
> > > self.cursor.execute('drop table if exists %s' % schemaTable)
>
> > > # database created.
> > > mysql> desc pygr;
> > > +---------------+--------------+------+-----+---------+-------+
> > > | Field | Type | Null | Key | Default | Extra |
> > > +---------------+--------------+------+-----+---------+-------+
> > > | pygr_id | varchar(255) | NO | PRI | NULL | |
> > > | location | varchar(255) | NO | PRI | NULL | |
> > > | docstring | varchar(255) | YES | | NULL | |
> > > | user | varchar(255) | YES | | NULL | |
> > > | creation_time | datetime | YES | | NULL | |
> > > | pickle_size | int(11) | YES | | NULL | |
> > > | security_code | bigint(20) | YES | | NULL | |
> > > | info_blob | text | YES | | NULL | |
> > > | objdata | text | NO | | NULL | |
> > > +---------------+--------------+------+-----+---------+-------+
> > > 9 rows in set (0.00 sec)
>
> > > mysql> desc pygr_schema;
> > > +-----------+--------------+------+-----+---------+-------+
> > > | Field | Type | Null | Key | Default | Extra |
> > > +-----------+--------------+------+-----+---------+-------+
> > > | source_id | varchar(255) | NO | MUL | NULL | |
> > > | target_id | varchar(255) | YES | | NULL | |
> > > | edge_id | varchar(255) | YES | | NULL | |
> > > +-----------+--------------+------+-----+---------+-------+
> > > 3 rows in set (0.00 sec)
>
> > > >>> mdb = metabase.MetabaseList('mysql:test.pygr') # open THAT metabase
> > > again for re-use
> > > >>> mdb.dir()
>
> > > ['0version', 'PYGRLAYERNAME']
>
> > > On Tue, May 25, 2010 at 8:49 AM, Kenny Daily <kmda...@gmail.com> wrote:
> > > > But what is the 'mdb' object in this line:
>
> > > > rdb = metabase.MySQLMetabase('pygrdata.index', mdb,
> > > > createLayer='leelab')
>
> > > > Since you are saying to create something of the same name only after I
> > > > create this! What am I missing?
>
> > > > Kenny
>
> > > > On May 23, 4:21 am, Namshin Kim <n...@rna.kr> wrote:
> > > > > rdb = metabase.MySQLMetabase('pygrdata.index', mdb,
> > createLayer='leelab')
>
> > > > > I guess you are talking about one-liner above. 'pygrdata' is a
> > database
> > > > name
> > > > > and 'index' is a table name. And 'leelab' is a layer name. Thus, you
> > > > should
> > > > > be able to create table on pygrdata database.
>
> > > > > After you create metabase.MySQLMetabase, you can access using usual
> > > > > metabase.
>
> > > > > mdb = metabase.MetabaseList('mysql:pygrdata.index')
>
> > > > > Or you can set WORLDBASEPATH to be mysql:pygrdata.index
>
> > > > > On Fri, May 21, 2010 at 9:36 AM, Kenny Daily <kmda...@gmail.com>
> > wrote:
> > > > > > Is there a mysql metabase example somewhere? I only saw the
> > one-liner
> > > > > > in the module documentation.
>
> > > > > > The example in the module documentation shows I need to create a
> > > > > > metabase.Metabase. But looking at this code, it seems that this
> > calls
> > > > > > metabase.MySQLMetabase if something on the worldbase path is a
> > mysql
> > > > > > database! I'm also not sure what to use as the resourceCache.
> > Finally,
> > > > > > how would I reconnect to this? Do I need a script such as what is
> > in
> > > > > > the __init__.py?
>
> > > > > > Also, the database server uses a non-standard port - can I pass
> > this
> > > > > > through kwargs so it gets to the mysql_connect?
>
> > > > > > Thanks!
>
> > > > > > Kenny
>
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