ModelSEED/Model-SEED-core — Issue #136: ms-update setting permissions incorrectly
Author: aabest
Created: 2012-02-23 18:30:18+00:00
State: open

I just did an "ms-update" and found that commands weren't running after the update completed:

e.g. running mdl-loadmodel yields a "permission denied" error.

Looking at the bin directory, here are the permissions that are automatically set up:

Turing:~/Desktop/ModelSEED/Model-SEED-core/workspace/public/default> ls -l /Users/student/Desktop/ModelSEED/Model-SEED-core/bin
total 368
-rwxrwxr-x 1 student staff 384 Feb 23 13:20 CreateDBScheme
-rwxrwxr-x 1 student staff 202 Feb 23 13:20 ModelDriver
-rwxrwxr-x 1 student staff 208 Feb 23 13:20 QueueDriver
-rwxr-xr-x 1 student staff 883 Feb 23 09:55 ReadMe.txt
-rw-rw-r-- 1 student staff 223 Feb 23 13:20 bc-addbiochemistry
-rw-rw-r-- 1 student staff 217 Feb 23 13:20 bc-loadmedia
-rw-rw-r-- 1 student staff 218 Feb 23 13:20 bc-printmedia
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 fba-checkgrowth
-rw-rw-r-- 1 student staff 212 Feb 23 13:20 fba-fva
-rw-rw-r-- 1 student staff 221 Feb 23 13:20 fba-minimalmedia
-rw-rw-r-- 1 student staff 222 Feb 23 13:20 fba-simphenotypes
-rw-rw-r-- 1 student staff 217 Feb 23 13:20 fba-singleko
-rwxrwxr-x 1 student staff 281 Feb 23 13:20 makeMFAToolkit
-rw-rw-r-- 1 student staff 217 Feb 23 13:20 mdl-addright
-rw-rw-r-- 1 student staff 221 Feb 23 13:20 mdl-autocomplete
-rw-rw-r-- 1 student staff 221 Feb 23 13:20 mdl-changedrains
-rw-rw-r-- 1 student staff 222 Feb 23 13:20 mdl-comparemodels
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 mdl-createmodel
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 mdl-importmodel
-rw-rw-r-- 1 student staff 221 Feb 23 13:20 mdl-inspectstate
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 mdl-loadbiomass
-rw-rw-r-- 1 student staff 218 Feb 23 13:20 mdl-loadmodel
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 mdl-makedbmodel
-rw-rw-r-- 1 student staff 218 Feb 23 13:20 mdl-parsesbml
-rw-rw-r-- 1 student staff 222 Feb 23 13:20 mdl-printcytoseed
-rw-rw-r-- 1 student staff 219 Feb 23 13:20 mdl-printmodel
-rw-rw-r-- 1 student staff 224 Feb 23 13:20 mdl-printmodelgenes
-rw-rw-r-- 1 student staff 218 Feb 23 13:20 mdl-printsbml
-rw-rw-r-- 1 student staff 223 Feb 23 13:20 mdl-reconstruction
-rwxr-xr-x 1 student staff 105 Jan 11 11:32 ms-build-modules
-rwxr-xr-x 1 student staff 144 Jan 11 11:32 ms-config
-rw-rw-r-- 1 student staff 218 Feb 23 13:20 ms-createuser
-rw-rw-r-- 1 student staff 218 Feb 23 13:20 ms-deleteuser
-rwxrwxr-x 1 student staff 78 Feb 23 13:17 ms-goworkspace
-rw-rw-r-- 1 student staff 217 Feb 23 13:20 ms-lasterror
-rw-rw-r-- 1 student staff 221 Feb 23 13:20 ms-listworkspace
-rwxrwxr-x 1 student staff 221 Feb 23 13:20 ms-load-mysql
-rw-rw-r-- 1 student staff 213 Feb 23 13:20 ms-login
-rw-rw-r-- 1 student staff 214 Feb 23 13:20 ms-logout
-rw-rw-r-- 1 student staff 223 Feb 23 13:20 ms-switchworkspace
-rwxrwxr-x 1 student staff 106 Feb 23 13:20 ms-update
-rw-rw-r-- 1 student staff 214 Feb 23 13:20 ms-whoami
-rw-rw-r-- 1 student staff 217 Feb 23 13:20 ms-workspace
-rwxrwxr-x 1 student staff 1551 Feb 23 13:20 source-me.sh
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 sq-blastgenomes
-rw-rw-r-- 1 student staff 220 Feb 23 13:20 util-matrixdist

I manually altered a few... everything works after that. Re-ran the ms-update to see if the permissions issue would occur again... it did.

All of these should be executable, correct?

Thanks,

Aaron