ggonnella / fastsubtrees Goto Github PK

RUN pip install 'ntmirror @ git+https://github.com/ggonnella/fastsubtrees/#subdirectory=ntmirror'
RUN ntmirror-download ntdumpdir
RUN pip install 'fastsubtrees @ git+https://github.com/ggonnella/fastsubtrees'

docker run fastsubtrees test
docker run fastsubtrees benchmark
docker run fastsubtrees ...

fastsubtrees$ docker exec fastsubtrees benchmarks
# Downloading the NCBI taxonomy dump...
# Building the fastsubtrees NCBI taxonomy tree...
2022-10-11 08:09:41 INFO: Constructing tree from NCBI taxonomy dump file ntdumpdir/nodes.dmp
2022-10-11 08:09:41 INFO: Constructing temporary parents table...
2022-10-11 08:09:41 INFO: Reading data from file "ntdumpdir/nodes.dmp" ...
2447844it [00:01, 1349487.11it/s]
2022-10-11 08:09:43 INFO: Constructing subtree sizes table...
2984676it [00:06, 451387.87it/s]
2022-10-11 08:09:50 INFO: Constructing tree data and index...
100%|██████████| 2984676/2984676 [05:57<00:00, 8351.77it/s]  
2022-10-11 08:15:47 SUCCESS: Tree data structure constructed
2022-10-11 08:15:47 SUCCESS: Tree constructed
2022-10-11 08:15:47 SUCCESS: Tree written to file "ncbi-taxonomy.tree"

 pip install fastsubtrees
Defaulting to user installation because normal site-packages is not writeable
Collecting fastsubtrees
  Downloading fastsubtrees-1.1-py3-none-any.whl (17 kB)
Collecting tqdm>=4.57.0
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 3.6 MB/s eta 0:00:00
Collecting sh>=1.14.2
  Downloading sh-1.14.3.tar.gz (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.9/62.9 kB 6.2 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting loguru>=0.5.1
  Downloading loguru-0.6.0-py3-none-any.whl (58 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.3/58.3 kB 5.0 MB/s eta 0:00:00
Collecting docopt>=0.6.2
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py) ... done
Collecting ntmirror>=1.2
  Downloading ntmirror-1.2-py3-none-any.whl (10 kB)
Collecting schema>=0.7.4
  Downloading schema-0.7.5-py2.py3-none-any.whl (17 kB)
Requirement already satisfied: PyYAML>=6.0 in /usr/lib/python3.10/site-packages (from fastsubtrees) (6.0)
Collecting mariadb
  Downloading mariadb-1.1.4.zip (97 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.4/97.4 kB 7.5 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [19 lines of output]
      /bin/sh: line 1: mariadb_config: command not found
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-mj6twek8/mariadb_db9a53888c2a40b99114f01c2c82d527/setup.py", line 27, in <module>
          cfg = get_config(options)
        File "/tmp/pip-install-mj6twek8/mariadb_db9a53888c2a40b99114f01c2c82d527/mariadb_posix.py", line 62, in get_config
          cc_version = mariadb_config(config_prg, "cc_version")
        File "/tmp/pip-install-mj6twek8/mariadb_db9a53888c2a40b99114f01c2c82d527/mariadb_posix.py", line 28, in mariadb_config
          raise EnvironmentError(
      OSError: mariadb_config not found.
      
      This error typically indicates that MariaDB Connector/C, a dependency which
      must be preinstalled, is not found.
      If MariaDB Connector/C is not installed, see installation instructions
      If MariaDB Connector/C is installed, either set the environment variable
      MARIADB_CONFIG or edit the configuration file 'site.cfg' to set the
       'mariadb_config' option to the file location of the mariadb_config utility.
      
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

 root@d8798c592652:/fastsubtrees/docker# ./start-example-app
Dash is running on http://0.0.0.0:8050/

 * Serving Flask app 'start' (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: on
./start-example-app: line 15:   823 Killed                  ./start.py
root@d8798c592652:/fastsubtrees/docker# Traceback (most recent call last):
  File "/fastsubtrees/genomes-attributes-viewer/start.py", line 171, in <module>
    app.run_server(debug=True, host='0.0.0.0')
  File "/usr/local/lib/python3.10/dist-packages/dash/dash.py", line 2033, in run_server
    self.server.run(host=host, port=port, debug=debug, **flask_run_options)
  File "/usr/local/lib/python3.10/dist-packages/flask/app.py", line 920, in run
    run_simple(t.cast(str, host), port, self, **options)
  File "/usr/local/lib/python3.10/dist-packages/werkzeug/serving.py", line 1000, in run_simple
    _rwr(
  File "/usr/local/lib/python3.10/dist-packages/werkzeug/_reloader.py", line 418, in run_with_reloader
    ensure_echo_on()
  File "/usr/local/lib/python3.10/dist-packages/werkzeug/_reloader.py", line 398, in ensure_echo_on
    termios.tcsetattr(sys.stdin, termios.TCSANOW, attributes)
termios.error: (5, 'Input/output error')

fastsubtrees$ pytest
==================================================================== test session starts =====================================================================
platform linux -- Python 3.10.7, pytest-7.1.3, pluggy-1.0.0
rootdir: /home/konrad/tmp/fastsubtrees
collected 10 items / 1 error                                                                                                                                 

=========================================================================== ERRORS ===========================================================================
________________________________________________________ ERROR collecting tests/test_fastsubtrees.py _________________________________________________________
ImportError while importing test module '/home/konrad/tmp/fastsubtrees/tests/test_fastsubtrees.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_fastsubtrees.py:6: in <module>
    from tests.reference_results import *
E   ModuleNotFoundError: No module named 'tests'
====================================================================== warnings summary ======================================================================
ntmirror/tests/test_dbload_cli.py:8
  /home/konrad/tmp/fastsubtrees/ntmirror/tests/test_dbload_cli.py:8: PytestUnknownMarkWarning: Unknown pytest.mark.script_launch_mode - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.script_launch_mode('subprocess')

ntmirror/tests/test_dbload_cli.py:21
  /home/konrad/tmp/fastsubtrees/ntmirror/tests/test_dbload_cli.py:21: PytestUnknownMarkWarning: Unknown pytest.mark.script_launch_mode - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.script_launch_mode('subprocess')

ntmirror/tests/test_downloader_cli.py:20
  /home/konrad/tmp/fastsubtrees/ntmirror/tests/test_downloader_cli.py:20: PytestUnknownMarkWarning: Unknown pytest.mark.script_launch_mode - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.script_launch_mode('subprocess')

ntmirror/tests/test_downloader_cli.py:33
  /home/konrad/tmp/fastsubtrees/ntmirror/tests/test_downloader_cli.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.script_launch_mode - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.script_launch_mode('subprocess')

ntmirror/tests/test_downloader_cli.py:46
  /home/konrad/tmp/fastsubtrees/ntmirror/tests/test_downloader_cli.py:46: PytestUnknownMarkWarning: Unknown pytest.mark.script_launch_mode - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
    @pytest.mark.script_launch_mode('subprocess')

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================== short test summary info ===================================================================
ERROR tests/test_fastsubtrees.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
================================================================ 5 warnings, 1 error in 0.17s ================================================================

Callback error updating ..boxplot.figure...boxplot.style...histogram.figure...histogram.style...add-comparison.disabled..

Traceback (most recent call last):
  File "/fastsubtrees/genomes-attributes-viewer/start.py", line 140, in update_figure
    boxplot_dict[id + ')'] = []
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

root@d8798c592652:/fastsubtrees# fastsubtrees-attr-query ncbi-taxonomy.tree GC_content 1129
2022-10-11 03:51:44 SUCCESS: Tree loaded from file "ncbi-taxonomy.tree"
2022-10-11 03:51:44 INFO: Subtree of node 1129 has size 1762
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~$ cd tmp/fastsubtrees/docker 
docker$ docker build . -t fastsubtrees
[+] Building 90.4s (22/30)                                                                                                                                    
 => [internal] load build definition from Dockerfile                                                                                                     0.9s
 => => transferring dockerfile: 1.59kB                                                                                                                   0.0s
 => [internal] load .dockerignore                                                                                                                        0.8s
 => => transferring context: 2B                                                                                                                          0.0s
 => resolve image config for docker.io/docker/dockerfile:1                                                                                               1.2s
 => CACHED docker-image://docker.io/docker/dockerfile:1@sha256:9ba7531bd80fb0a858632727cf7a112fbfd19b17e94c4e84ced81e24ef1a0dbc                          0.0s
 => [internal] load .dockerignore                                                                                                                        0.0s
 => [internal] load build definition from Dockerfile                                                                                                     0.0s
 => [internal] load metadata for docker.io/library/mariadb:10.6                                                                                          0.7s
 => [ 1/22] FROM docker.io/library/mariadb:10.6@sha256:fa578ca359c2d56d9f194abd69c7603077429adc03a1e28e00bf3ed864e5a162                                 10.7s
 => => resolve docker.io/library/mariadb:10.6@sha256:fa578ca359c2d56d9f194abd69c7603077429adc03a1e28e00bf3ed864e5a162                                    0.0s
 => => sha256:fa578ca359c2d56d9f194abd69c7603077429adc03a1e28e00bf3ed864e5a162 979B / 979B                                                               0.0s
 => => sha256:34b09daa97dd250d4f95430737cf6b92048e45a647b270aedb04ff3d00d638b2 8.28kB / 8.28kB                                                           0.0s
 => => sha256:9bbcda1c9ef5a7c692fcd746e20ff8cf4432fd32e8bf9bb8efe01fa325e83a99 2.62kB / 2.62kB                                                           0.0s
 => => sha256:c994327ef3cc11acbe7e8fa87751b72723e88d9cf38ff3ebf91b05a1a2945548 149B / 149B                                                               0.5s
 => => sha256:40d12c21872a92b0b6dd483317d136caa739fa9b0cbe7d444d0267b0ebfe2adc 2.26MB / 2.26MB                                                           0.4s
 => => sha256:dd18621bd4ea9c95166fdbbfede9511a59701cd8000726cf6e8a6f6b429617f7 2.49kB / 2.49kB                                                           0.4s
 => => extracting sha256:c994327ef3cc11acbe7e8fa87751b72723e88d9cf38ff3ebf91b05a1a2945548                                                                0.0s
 => => sha256:582572716dc8228c293bb77ede11deb84fb1c1f137618356e61ba11ff48b45fa 325B / 325B                                                               0.7s
 => => sha256:f0857ffe38ff40e8be228e963b996397db15ccf67118527159f4e458621113e2 88.49MB / 88.49MB                                                         2.0s
 => => extracting sha256:40d12c21872a92b0b6dd483317d136caa739fa9b0cbe7d444d0267b0ebfe2adc                                                                0.2s
 => => sha256:e3f76ad8eca3132254de759ea88d7ea655129f6e170b4d426d76d1843f38260c 3.49kB / 3.49kB                                                           0.8s
 => => sha256:edffdfb1bdec3b59b6b56bbe6cd2c8296939ffddb4bece07e3dee8cd6cef4e7b 7.05kB / 7.05kB                                                           0.9s
 => => extracting sha256:dd18621bd4ea9c95166fdbbfede9511a59701cd8000726cf6e8a6f6b429617f7                                                                0.0s
 => => extracting sha256:582572716dc8228c293bb77ede11deb84fb1c1f137618356e61ba11ff48b45fa                                                                0.0s
 => => extracting sha256:f0857ffe38ff40e8be228e963b996397db15ccf67118527159f4e458621113e2                                                                7.0s
 => => extracting sha256:e3f76ad8eca3132254de759ea88d7ea655129f6e170b4d426d76d1843f38260c                                                                0.1s
 => => extracting sha256:edffdfb1bdec3b59b6b56bbe6cd2c8296939ffddb4bece07e3dee8cd6cef4e7b                                                                0.0s
 => [internal] load build context                                                                                                                        0.3s
 => => transferring context: 194B                                                                                                                        0.0s
 => [ 2/22] RUN apt-get update -y                                                                                                                        2.5s
 => [ 3/22] RUN apt-get install -y software-properties-common                                                                                           26.9s
 => [ 4/22] RUN add-apt-repository -y ppa:deadsnakes/ppa                                                                                                 4.0s 
 => [ 5/22] RUN apt-get install -y python3.8 python3-pip wget curl git time                                                                             17.4s 
 => [ 6/22] RUN ln -s /usr/bin/python3.8 /usr/bin/python                                                                                                 0.6s 
 => [ 7/22] RUN wget https://downloads.mariadb.com/MariaDB/mariadb_repo_setup                                                                            0.8s 
 => [ 8/22] RUN chmod +x mariadb_repo_setup                                                                                                              0.5s 
 => [ 9/22] RUN ./mariadb_repo_setup --mariadb-server-version=mariadb-10.6                                                                               4.6s 
 => [10/22] RUN apt-get install -y libmariadb3 libmariadb-dev                                                                                            2.6s 
 => [11/22] RUN pip install mariadb pytest PyYAML sqlalchemy sh pytest-console-scripts                                                                   4.9s 
 => [12/22] RUN pip install schema snacli                                                                                                                6.4s 
 => [13/22] RUN pip install 'ntmirror @ git+https://github.com/ggonnella/fastsubtrees/#subdirectory=ntmirror'                                            4.4s 
 => ERROR [14/22] RUN ntmirror-download ntdumpdir                                                                                                        0.8s 
------                                                                                                                                                        
 > [14/22] RUN ntmirror-download ntdumpdir:                                                                                                                   
#21 0.692 2022-10-07 10:14:33 | ERROR |                                                                                                                       
#21 0.692                                                                                                                                                     
#21 0.692   RAN: /usr/bin/curl ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz -o ntdumpdir/taxdump.tar.gz -w '%{size_download}' -R                        
#21 0.692                                                                                                                                                     
#21 0.692   STDOUT:
#21 0.692 0
#21 0.692 
#21 0.692   STDERR:
#21 0.692   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
#21 0.692                                  Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
#21 0.692 curl: (7) Failed to connect to ftp.ncbi.nih.gov port 21: Connection refused
#21 0.692 
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