Hi Bridget, Here's the screen shot of the META/ directory. Can you schedule a phone call meeting?
Thanks, Hong On Wed, Oct 2, 2019 at 9:29 AM Bridget McInnes [email protected] [umls-similarity] <[email protected]> wrote: > > > 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 >> >> > -- Hong Guan, MS Doctoral Student, Research Assistant College of Health Solutions, Arizona State University
