pip installs broken version of code

[gszep]

On Windows 10 with Python 3.8.5 I've set up a MySQL database and can successfully connect to it from command prompt

> mysql --user=gszep  --password=station --host=localhost pyuniprot
mysql: [Warning] Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 78
Server version: 8.0.25 MySQL Community Server - GPL

Copyright (c) 2000, 2021, Oracle and/or its affiliates.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql>

successfully connected it to the python library

>pyuniprot mysql
server name/ IP address database is hosted [localhost]:
MySQL/MariaDB user [pyuniprot_user]: gszep
MySQL/MariaDB password [pyuniprot_passwd]: station
database name [pyuniprot]:
character set [utf8]:
Connection was successful

however when attempt to update the database with a small virus

>pyuniprot update --taxids 133704
WARNING: Update is very time consuming and can take several
hours depending which organisms you are importing!

bin was anderes
346934it [00:11, 30587.45it/s]
Traceback (most recent call last):
  File "c:\programdata\miniconda3\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\programdata\miniconda3\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\Scripts\pyuniprot.exe\__main__.py", line 7, in <module>
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\click\core.py", line 1137, in __call__
    return self.main(*args, **kwargs)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\click\core.py", line 1062, in main
    rv = self.invoke(ctx)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\click\core.py", line 1668, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\click\core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\click\core.py", line 763, in invoke
    return __callback(*args, **kwargs)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\cli.py", line 72, in update
    database.update(taxids=taxids, connection=conn, force_download=force_download, silent=silent)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\manager\database.py", line 836, in update
    db.db_import_xml(urls, force_download, taxids, silent)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\manager\database.py", line 160, in db_import_xml
    self.import_xml(xml_gzipped_file_path, taxids, silent)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\manager\database.py", line 233, in import_xml
    self.insert_entries(entry_xml, taxids)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\manager\database.py", line 258, in insert_entries
    self.insert_entry(entry, taxids)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\manager\database.py", line 280, in insert_entry
    taxid = self.get_taxid(entry)
  File "C:\Users\gszep\AppData\Roaming\Python\Python38\site-packages\pyuniprot\manager\database.py", line 628, in get_taxid
    return int(entry.find(query).get('id'))
AttributeError: 'NoneType' object has no attribute 'get'

on an Ubuntu 18.04 with Python 3.6 we get the same error

Import 173479167 lines:   0%|                         | 346934/173479167
[00:01<12:09, 237194.02it/s]

Traceback (most recent call last):
  File "/home/gszep/.local/bin/pyuniprot", line 8, in <module>
    sys.exit(main())
  File "/home/gszep/.local/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/gszep/.local/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/gszep/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/gszep/.local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/gszep/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/cli.py", line 72, in update
    database.update(taxids=taxids, connection=conn, force_download=force_download, silent=silent)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/manager/database.py", line 836, in update
    db.db_import_xml(urls, force_download, taxids, silent)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/manager/database.py", line 160, in db_import_xml
    self.import_xml(xml_gzipped_file_path, taxids, silent)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/manager/database.py", line 233, in import_xml
    self.insert_entries(entry_xml, taxids)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/manager/database.py", line 258, in insert_entries
    self.insert_entry(entry, taxids)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/manager/database.py", line 280, in insert_entry
    taxid = self.get_taxid(entry)
  File "/home/gszep/.local/lib/python3.6/site-packages/pyuniprot/manager/database.py", line 628, in get_taxid
    return int(entry.find(query).get('id'))

[gszep]

the scripts seem to have created some tables though

mysql> SHOW TABLES;
+--------------------------------------+
| Tables_in_pyuniprot                  |
+--------------------------------------+
| pyuniprot_accession                  |
| pyuniprot_alternativefullname        |
| pyuniprot_alternativeshortname       |
| pyuniprot_appuser                    |
| pyuniprot_dbreference                |
| pyuniprot_disease                    |
| pyuniprot_diseasecomment             |
| pyuniprot_ecnumber                   |
| pyuniprot_entry                      |
| pyuniprot_entry__keyword             |
| pyuniprot_entry__pmid                |
| pyuniprot_entry__subcellularlocation |
| pyuniprot_entry__tissueinreference   |
| pyuniprot_feature                    |
| pyuniprot_function                   |
| pyuniprot_keyword                    |
| pyuniprot_organismhost               |
| pyuniprot_othergenename              |
| pyuniprot_pmid                       |
| pyuniprot_sequence                   |
| pyuniprot_subcellularlocation        |
| pyuniprot_tissueinreference          |
| pyuniprot_tissuespecificity          |
| pyuniprot_version                    |
+--------------------------------------+
24 rows in set (0.01 sec)

but all of them have 0 rows except this one

mysql> SELECT * FROM pyuniprot_version;
+----+---------------+--------------+--------------+-------------------+-----------------------+
| id | knowledgebase | release_name | release_date | import_start_date | import_completed_date |
+----+---------------+--------------+--------------+-------------------+-----------------------+
|  1 | Swiss-Prot    | 2021_03      | 2021-06-02   | NULL              | NULL                  |
|  2 | TrEMBL        | 2021_03      | 2021-06-02   | NULL              | NULL                  |
+----+---------------+--------------+--------------+-------------------+-----------------------+
2 rows in set (0.00 sec)

it appears the .xml.gz file is being downloaded correctly but is not imported into the SQL database.

[gszep]

fixed the bug I think this line should be

for entry in entries.iterfind("./entry"):

pip install pyuniprot seems to install a broken version of the code. I now installed the master branch and it seems to work 👍🏼

pip install https://github.com/cebel/pyuniprot/archive/master.zip

[psi-cmd]

@gszep you may keep the issue title, I almost miss out the solution 😂

[psi-cmd]

BTW, the download function was changed to download and extract in latest code, which means if you have downloaded .xml.gz file in ~/.pyuniprot/data with pyuniprot from pypi, you have to decompress it with gzip -d -c uniprot_sprot.xml.gz > uniprot_sprot.xml. to avoid uniprot_sprot.xml not found error. (If you don't want to download twice)