pip installs broken version of code

[gszep]

pip installs broken version of code

[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

[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.

[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)