search

ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
Other
19 stars 10 forks source link

error using loadmodelfromfile #45

Closed mdejongh closed 13 years ago

mdejongh commented 13 years ago

I scp'ed my iYusMp.149 model from bio* to my desktop, then ran

bin/loadmodelfromfile -name "iYusMp.149" -genome "272634.1"

Got the following error log (note that the id used below has an extra ".149" on it)

ModelDriver encountered an unrecoverable error:

""Could not find model specification file: /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/data/MS\ ModelFiles/iYusMp.149.149.tbl!"" at /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/\ FIGMODEL.pm line 133 ModelSEED::FIGMODEL::FIGMODELERROR('Could not find model specification file: /Users/dejongh\ /Deskt...') called at /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/FIGMODEL.pm li\ ne 2545 ModelSEED::FIGMODEL::import_model_file('ModelSEED::FIGMODEL=HASH(0x7fbcac03fe50)', 'HASH(0x\ 7fbcae21a6b0)') called at /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDrive\ r.pm line 4513 ModelSEED::ModelDriver::loadmodelfromfile('ModelSEED::ModelDriver=HASH(0x7fbcac040198)', 'l\ oadmodelfromfile', 'HASH(0x7fbcae21a5c0)') called at /Users/dejongh/Desktop/ModelSEED/Model-SEED-co\ re/lib/ModelSEED/ModelDriver.pl line 121 main::ANON() called at /System/Library/Perl/Extras/5.12/Try/Tiny.pm line 76 eval {...} called at /System/Library/Perl/Extras/5.12/Try/Tiny.pm line 67 Try::Tiny::try('CODE(0x7fbcac0401f8)', 'Try::Tiny::Catch=REF(0x7fbcae1a41d0)') called at /U\ sers/dejongh/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDriver.pl line 124 require /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/lib/ModelSEED/ModelDriver.pl calle\ d at /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/config//ModelSEEDbootstrap.pm line 26 main::run() called at -e line 3

I reran using

bin/loadmodelfromfile -name "iYusMp" -genome "272634.1"

and didn't get any errors log, but did get the following message:

Processing argument: loadmodelfromfile Adding new model iYusMp.149 for mdejongh into database [PPOBackend.pm 246]Database error: DBD::mysql::st execute failed: Unknown column 'defaultStudyMedi\ a' in 'field list' at /Users/dejongh/Desktop/ModelSEED/Model-SEED-core/lib/PPO/PPOBackend.pm line 2\ 29. Successfully imported iYusMp into Model SEED as iYusMp.149!

devoid commented 13 years ago

Matt, I think this fixes the first issue. For the defaultStudyMedia, I'm guessing a database update will deal with that. So I'm closing this issue. Reopen it if you are still getting errors.

mdejongh commented 13 years ago

How do I do a "database update"?

On Mon, Oct 31, 2011 at 7:37 PM, Scott Devoid reply@reply.github.com wrote:

Matt, I think this fixes the first issue. For the defaultStudyMedia, I'm guessing a database update will deal with that. So I'm closing this issue. Reopen it if you are still getting errors.

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/issues/45#issuecomment-2584949

Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

devoid commented 13 years ago

Good question... if you haven't made any data changes that you want to save: drop your existing database: rm data/ModelDB/ModelDB.db or mysql < "DROP DATABASE ModelDB"

download: http://bioseed.mcs.anl.gov/~devoid/FIG/ModelDB-sqlite.tgz or http://bioseed.mcs.anl.gov/~devoid/FIG/ModelDB-mysql.tgz

extract: tar -xzf ModelDB-suffix.tgz -C path/to/data/ and load into database: sqlite3 data/ModelDB/ModelDB.db < ModelDB/ModelDB.sqlite

mysql < ModelDB/ModelDB.mysql

If you have changes that you've made, we need to wait until we get APIs to talk back to the "master-core" in the bio systems.

~ Scott

On Mon, Oct 31, 2011 at 6:42 PM, mdejongh < reply@reply.github.com>wrote:

How do I do a "database update"?

On Mon, Oct 31, 2011 at 7:37 PM, Scott Devoid reply@reply.github.com wrote:

Matt, I think this fixes the first issue. For the defaultStudyMedia, I'm guessing a database update will deal with that. So I'm closing this issue. Reopen it if you are still getting errors.

Reply to this email directly or view it on GitHub:

https://github.com/ModelSEED/Model-SEED-core/issues/45#issuecomment-2584949

Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

Reply to this email directly or view it on GitHub: https://github.com/ModelSEED/Model-SEED-core/issues/45#issuecomment-2584991

mdejongh commented 13 years ago

The download links you gave me are broken.