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bvalot / pyMLST

whole genome MLST analysis
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got an unexpected keyword argument 'name' #14

Closed famiji closed 1 year ago

famiji commented 1 year ago

Hi I install this too by mamba when i try to import database, i receive a sql error

wgmlst import Cp.db "Clostridium perfringens" --force
[INFO: 2023-03-02 11:51:43,558] One element found : Clostridium perfringens
[INFO: 2023-03-02 11:51:43,558] Downloading the core genome...
Traceback (most recent call last):
  File "/home/fmj/miniconda3/envs/pymlst/bin/wgmlst", line 10, in <module>
    sys.exit(wg())
             ^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/commands/import.py", line 57, in cli
    with pymlst.open_wg(os.path.abspath(database)) as mlst:
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/contextlib.py", line 137, in __enter__
    return next(self.gen)
           ^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/core.py", line 40, in open_wg
    mlst = WholeGenomeMLST(file, ref)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/core.py", line 442, in __init__
    self.__database = DatabaseWG(file, ref)
                      ^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/core.py", line 63, in __init__    engine = utils.get_updated_engine(file, 'wg')
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/common/utils.py", line 143, in get_updated_engine
    check_type(conn, module)
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/common/utils.py", line 113, in check_type
    set_type(conn, mlst_type)
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/common/utils.py", line 126, in set_type
    conn.execute(
TypeError: Connection.execute() got an unexpected keyword argument 'name'

Could you help me finding the mistake i do?

cheers.

bvalot commented 1 year ago

Hi,

I have no problem with your command on my installation. Do you have internet in this computer? Because the command download the database from cgsmlt.org. Or do you have permission on the folder you want to create the database?

wgmlst import Cp.db "Clostridium perfringens" --force
[INFO: 2023-03-02 08:56:08,657] One element found : Clostridium perfringens
[INFO: 2023-03-02 08:56:08,657] Downloading the core genome...
[INFO: 2023-03-02 08:56:11,085] Reverse-complemented genes: 926
[INFO: 2023-03-02 08:56:11,085] Database initialized

Benoit

famiji commented 1 year ago

I'm sure I have no problems connecting to the network and creating files Is there a problem with dependency？

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bvalot commented 1 year ago

No idea.

Download this file: wget https://raw.githubusercontent.com/bvalot/pyMLST/master/tests/data/wg/cgmlst_schema.fasta

and try this command: wgMLST create E.coli.db cgmlst_schema.fasta

famiji commented 1 year ago

I try it, this is the result.

(pymlst) fmj@qood:~$ wget https://raw.githubusercontent.com/bvalot/pyMLST/master/tests/data/wg/cgmlst_schema.fasta
--2023-03-02 16:27:26--  https://raw.githubusercontent.com/bvalot/pyMLST/master/tests/data/wg/cgmlst_schema.fasta
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.108.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2367809 (2.3M) [text/plain]
Saving to: ‘cgmlst_schema.fasta’

cgmlst_schema.fasta                 100%[===================================================================>]   2.26M  62.3KB/s    in 62s

2023-03-02 16:33:17 (37.3 KB/s) - ‘cgmlst_schema.fasta’ saved [2367809/2367809]

(pymlst) fmj@qood:~$ wgMLST create E.coli.db cgmlst_schema.fasta
Traceback (most recent call last):
  File "/home/fmj/miniconda3/envs/pymlst/bin/wgMLST", line 10, in <module>
    sys.exit(wg())
             ^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/commands/create.py", line 33, in cli
    with pymlst.open_wg(os.path.abspath(database)) as mlst:
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/contextlib.py", line 137, in __enter__
    return next(self.gen)
           ^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/core.py", line 40, in open_wg
    mlst = WholeGenomeMLST(file, ref)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/core.py", line 442, in __init__
    self.__database = DatabaseWG(file, ref)
                      ^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/wg/core.py", line 63, in __init__
    engine = utils.get_updated_engine(file, 'wg')
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/common/utils.py", line 143, in get_updated_engine
    check_type(conn, module)
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/common/utils.py", line 113, in check_type
    set_type(conn, mlst_type)
  File "/home/fmj/miniconda3/envs/pymlst/lib/python3.11/site-packages/pymlst/common/utils.py", line 126, in set_type
    conn.execute(
TypeError: Connection.execute() got an unexpected keyword argument 'name'
bvalot commented 1 year ago

ok, same problem.

You seems to use 3.11 python version. I think this is the same problem as indicate in 12

Can you try to install pymlst on python 3.9 environnement?

famiji commented 1 year ago
bvalot commented 1 year ago

Can you try to install pymlst on python 3.9 environnement?

bvalot commented 1 year ago

conda create -n "pymlst3.9" python=3.9 pymlst

famiji commented 1 year ago

I followed your advice, but failed again

bvalot commented 1 year ago

you need to activate the good environnement conda activate pymlst3.9

Can you report the result of this command: which wgMLST

famiji commented 1 year ago

/home/fmj/miniconda3/envs/pymlst3.9/bin/wgMLST

bvalot commented 1 year ago

Normally, it must work with this version of python.

Can you report this command result: python --version

famiji commented 1 year ago

Python 3.9.16

bvalot commented 1 year ago

And you have the same error with the import command?

famiji commented 1 year ago

Yes,it still error. Although we haven't found the problem yet, thank you for your patience and timely response.

famiji commented 1 year ago

a new error appear

[INFO: 2023-03-02 16:55:24,099] One element found : Clostridium perfringens
[INFO: 2023-03-02 16:55:24,099] Downloading the core genome...
Traceback (most recent call last):
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/common/web.py", line 231, in get_cgmlst_file
    iterator = next(SeqIO.parse(os.path.join(fas_tmp, fasta), 'fasta'))
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/Bio/SeqIO/__init__.py", line 605, in parse
    return iterator_generator(handle)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/Bio/SeqIO/FastaIO.py", line 223, in __init__
    super().__init__(source, mode="t", fmt="Fasta")
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/Bio/SeqIO/Interfaces.py", line 45, in __init__
    self.stream = open(source, "r" + mode)
OSError: [Errno 24] Too many open files: '/tmp/tmp81po3jrs/fas/CPF_RS01715.fasta'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/fmj/miniconda3/envs/pymlst3.92/bin/wgmlst", line 10, in <module>
    sys.exit(wg())
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/wg/commands/import.py", line 52, in cli
    skipped = web.get_cgmlst_file(url, tmp)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/common/web.py", line 237, in get_cgmlst_file
    return skipped
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/tempfile.py", line 830, in __exit__
    self.cleanup()
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/tempfile.py", line 834, in cleanup
    self._rmtree(self.name)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/tempfile.py", line 816, in _rmtree
    _shutil.rmtree(name, onerror=onerror)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/shutil.py", line 730, in rmtree
    onerror(os.open, path, sys.exc_info())
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/shutil.py", line 727, in rmtree
    fd = os.open(path, os.O_RDONLY)
OSError: [Errno 24] Too many open files: '/tmp/tmp81po3jrs'
bvalot commented 1 year ago

The first problem is link to the change of SQLachemy library from 1.4 to 2.0 version.

Try the command : wgMLST create E.coli.db cgmlst_schema.fasta

famiji commented 1 year ago 
(pymlst3.92) fmj@qood:~$ wgMLST create E.coli.db cgmlst_schema.fasta
Usage: wgMLST create [OPTIONS] DATABASE COREGENE
Try 'wgMLST create -h' for help.

Error: Database alreadly exists, use --force to override it
(pymlst3.92) fmj@qood:~$ wgMLST create E.coli.db cgmlst_schema.fasta --force
Traceback (most recent call last):
  File "/home/fmj/miniconda3/envs/pymlst3.92/bin/wgMLST", line 10, in <module>
    sys.exit(wg())
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/wg/commands/create.py", line 33, in cli
    with pymlst.open_wg(os.path.abspath(database)) as mlst:
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/contextlib.py", line 119, in __enter__
    return next(self.gen)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/wg/core.py", line 40, in open_wg
    mlst = WholeGenomeMLST(file, ref)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/wg/core.py", line 442, in __init__
    self.__database = DatabaseWG(file, ref)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/wg/core.py", line 63, in __init__
    engine = utils.get_updated_engine(file, 'wg')
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/common/utils.py", line 143, in get_updated_engine
    check_type(conn, module)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/common/utils.py", line 113, in check_type
    set_type(conn, mlst_type)
  File "/home/fmj/miniconda3/envs/pymlst3.92/lib/pypy3.9/site-packages/pymlst/common/utils.py", line 126, in set_type
    conn.execute(
TypeError: execute() got an unexpected keyword argument 'name'
bvalot commented 1 year ago

OK, this is the same problem of SQLAlchemy library. You can try to downgrade SQLAlchemy version to 1.4 series

I'm looking for modify pyMLST for compatibility to SQLAlchemy >2.0

famiji commented 1 year ago

I executed the following command and the result was successful

 mamba install SQLAlchemy=1.4
 ulimit -n 2048
 wgmlst import Cp.db "Clostridium perfringens" --force

Thank you again for your patience, timely and professional reply

bvalot commented 1 year ago

good.

I can check to update to SQLAlchemy 2.0 with no pression.