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I'm getting a simple error but I don't know how to solve it.

While performing make test on this perl package (Linux) https://metacpan.org/pod/UMLS::Interface:

DBI connect('umls;mysql_read_default_group=client;','',...) failed: Access denied for user 'jon'@'localhost' (using password: NO) at /home/jon/UMLS/UMLS-Interface-1.51/blib/lib/UMLS/Interface/CuiFinder.pm line 2465.

I have a password, but I don't know how can I supply it during the installation.

My desire is to make the tests & installation work for both the UMLS Interface/similarity in order to find similarity & relatedness between words. If there exists some web-server that I can query for similarity, it might be a good detour.

Tries:

  1. Trying to install with cpanm

    (base) jon@jon:~/UMLS/UMLS-Interface-1.51$ sudo cpanm UMLS::Interface UMLS::Interface is up to date. (1.51)

Here it looks installed ok, but then I have the same problem with UMLS-SIMILARITY on the make test.

  1. Trying to install with :

    perl Makefile.PL make make test make install

Output:

(base) jon@jon:~/UMLS/UMLS-Interface-1.51$ perl Makefile.PL
Checking if your kit is complete...
Warning: the following files are missing in your kit:
    t/mysql.t
Please inform the author.
Generating a Unix-style Makefile
Writing Makefile for UMLS::Interface
Writing MYMETA.yml and MYMETA.json

And then on the 'make test' I get the database error 

(Access denied for user 'jon'@'localhost' (using password: NO)

  1. I've searched where I can supply config file / mysql password in UMLS-Interface or UMLS-Similarity packages. Didn't find.

  2. I've tried to install DBI & DBD in several methods, all routes gets me to the same error.

  3. I've tried the web-interface: https://metacpan.org/pod/distribution/UMLS-Similarity/utils/query-umls-similarity-webinterface.pl But get the following error:

    (base) jon@jon:~/UMLS/UMLS-Similarity-1.47/utils$ query-umls-similarity-webinterface.pl hand skull Default Settings: --default http://atlas.ahc.umn.edu/ --measure path --sab MSH --rel PAR/CHD User Settings: No user defined settings

    500 Can't connect to atlas.ahc.umn.edu:80http://atlas.ahc.umn.edu//cgi-bin/umls_similarity.cgi?word1=hand&word2=skull&sab=MSH&rel=PAR%2FCHD&similarity=path&button=Compute+Similarity&sabdef=UMLS_ALL&reldef=CUI%2FPAR%2FCHD%2FRB%2FRN&relatedness=vector <>()<>() ^C

  4. I tried on Windows as well.

    DBI connect('umls;mysql_read_default_group=client;','',...) failed: Can't connect to MySQL server on 'localhost' (10061) at E:\umls_perl\UMLS-Interface-1.51\blib\lib/UMLS/Interface/CuiFinder.pm line 2465

How can I solve it? Thanks

jonb
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  • I am not familiar with UMLS, but there are some information on how to install the module in the [INSTALL](https://metacpan.org/source/BTMCINNES/UMLS-Interface-1.51/INSTALL) file. – Håkon Hægland Aug 25 '19 at 09:56
  • I saw it. The step relevant for me is Step 6. But I don't know what to do in order to overcome this problem. I've tried supplying "PREFIX" as suggested in the Step 6 instructions but it didn't solve it... – jonb Aug 25 '19 at 12:53

0 Answers0