Hello Hong, Just to check in again. Did you want to send a screen shot of your directory structure? Or has this been resolved?
Thanks! Best regards, Bridget On Tue, Oct 1, 2019 at 6:56 AM Hong Guan [email protected] [umls-similarity] < [email protected]> wrote: > > > Thank you for quick reply. I was at line 421 of this document > https://metacpan.org/source/BTMCINNES/UMLS-Interface-1..51/INSTALL > <https://metacpan.org/source/BTMCINNES/UMLS-Interface-1.51/INSTALL> > I ran `bash populate_mysql_db.sh` in the META/ directory and got this > error message `populate_mysql_db.sh: line 45: mysql_tables.sql: No such > file or directory` > > Thanks, > Hong > > On Mon, Sep 30, 2019 at 8:40 PM Bridget McInnes [email protected] > [umls-similarity] <[email protected]> wrote: > >> >> >> Hello Hong, >> >> I am not Ted either. Would you provide a little more information: what >> directory are you in? >> >> Best regards, >> >> Bridget >> >> On Mon, Sep 23, 2019 at 9:46 PM Hong Guan [email protected] >> [umls-similarity] <[email protected]> wrote: >> >>> >>> >>> This line >>> $MYSQL_HOME/bin/mysql -u $user -p$password $db_name < mysql_tables.sql >>> >> mysql.log 2>&1 >>> reads the mysql_tables.sql, but I don't see it. >>> >>> Thanks, >>> Hong >>> >>> On Mon, Sep 23, 2019 at 2:03 PM Juliana M Destro [email protected] >>> [umls-similarity] <[email protected]> wrote: >>> >>>> >>>> >>>> I'm not Ted but I think I can help you :-) >>>> >>>> You can get the load scripts in UMLS page: >>>> >>>> https://www.nlm.nih.gov/research/umls/implementation_resources/scripts/index.html >>>> >>>> On Mon, Sep 23, 2019 at 5:17 PM Hong Guan [email protected] >>>> [umls-similarity] <[email protected]> wrote: >>>> >>>>> >>>>> >>>>> Hi Ted, >>>>> >>>>> I am stuck at Stage 5 Step 3 C. When I ran ./populate_mysql_db.sh, I >>>>> got an error message saying "populate_mysql_db.sh: line 45: >>>>> mysql_tables.sql: No such file or directory". I don't see mysql_tables.sql >>>>> in the UMLS/ directory and its sub-directories. What should I do? >>>>> >>>>> Thanks, >>>>> Hong >>>>> >>>>> On Tue, Sep 17, 2019 at 2:13 PM Ted Pedersen [email protected] >>>>> [umls-similarity] <[email protected]> wrote: >>>>> >>>>>> >>>>>> >>>>>> >>>>>> It looks like some Perl modules are missing. These instructions will >>>>>> help install those! >>>>>> >>>>>> https://metacpan.org/source/BTMCINNES/UMLS-Interface-1.51/INSTALL >>>>>> >>>>>> On Tue, Sep 17, 2019 at 2:36 PM Hong Guan [email protected] >>>>>> [umls-similarity] <[email protected]> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> I install UMLS and MySQL 5.7. The error prompt says >>>>>>> >>>>>>> Warning: prerequisite DBD::mysql 0 not found. >>>>>>>> Warning: prerequisite DBI 0 not found. >>>>>>>> Warning: prerequisite Digest::SHA1 2.12 not found. >>>>>>>> Generating a Unix-style Makefile >>>>>>>> Writing Makefile for UMLS::Interface >>>>>>>> Writing MYMETA.yml and MYMETA.json >>>>>>> >>>>>>> >>>>>>> Looks like it recognizes UMLS but not MySQL. What do I do now? >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> On Mon, Sep 16, 2019 at 11:04 AM Ted Pedersen [email protected] >>>>>>> [umls-similarity] <[email protected]> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> The National Library of Medicine has some pretty good instructions >>>>>>>> on how to install UMLS. >>>>>>>> >>>>>>>> https://www..nlm.nih.gov/research/umls/quickstart.html >>>>>>>> <https://www.nlm.nih.gov/research/umls/quickstart.html> >>>>>>>> >>>>>>>> On Mon, Sep 16, 2019 at 1:00 PM [email protected] [umls-similarity] < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I am new to this package. Can anyone tell me how I >>>>>>>>> install UMLS-Similarity from scratch? The system I am using is Ubuntu >>>>>>>>> 18.04. >>>>>>>>> >>>>>>>>> It seems that I need to install UMLS and MySQL before installing >>>>>>>>> UMLS-Similarity. Am I correct? If that is the case, how do I install >>>>>>>>> UMLS? >>>>>>>>> I do know how to install MySQL. >>>>>>>>> >>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Hong Guan >>>>>>> >>>>>>> Research Assistant, Biomedical Informatics >>>>>>> >>>>>>> College of Health Solutions >>>>>>> >>>>>>> Arizona State University >>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> >>>>> Hong Guan, MS >>>>> >>>>> Doctoral Student, Research Assistant >>>>> College of Health Solutions, Arizona State University >>>>> >>>>> >>> >>> -- >>> >>> Hong Guan, MS >>> >>> Doctoral Student, Research Assistant >>> College of Health Solutions, Arizona State University >>> >>> > > -- > > Hong Guan, MS > > Doctoral Student, Research Assistant > College of Health Solutions, Arizona State University > > >
