jianwei-zhang/lims

Laboratory Information Management System

LIMS

Laboratory Information Management System

We developed a web-based LIMS to manage and analyze genomic data at different levels from both wet and dry lab experiments.

Read LIMS Docs to learn more about how to install and use this system.

How to cite?

Zhang, J. et al. Genome Puzzle Master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics, 2016, 32 (20): 3058-3064

lims's Issues

creating new genome fails

creating New Genome from General/New Genome failes.
from var/log/apache2/error.log:

[Fri Aug 13 09:21:43 2021] genomeSave.cgi: DBD::mysql::st execute failed: Incorrect integer value: '' for column 'id' at row 1 at /var/www/cgi-bin/lims/genomeSave.cgi line 439, line 58.
[Fri Aug 13 09:21:56 2021] genomeSave.cgi: Filehandle STDOUT reopened as GEN0 only for input at /usr/share/perl5/Bio/Root/IO.pm line 268, line 58.
[Fri Aug 13 09:21:56 2021] genomeSave.cgi: DBD::mysql::st execute failed: Incorrect integer value: '' for column 'id' at row 1 at /var/www/cgi-bin/lims/genomeSave.cgi line 531,

Can't locate URI/Escape/XS.pm

Describe the bug
A clear and concise description of what the bug is.
I am sure I have installed URI/Escape/XS.pm in cpan and add the lib path in perl5lib, but when I access lims, it still throw an error:

To Reproduce
Steps to reproduce the behavior:
After following the standard process in https://jianwei-zhang.github.io/LIMS/INSTALL.html

Expected behavior
A clear and concise description of what you expected to happen.
Open the main page of LIMS

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Linux master 3.10.0-693.el7.x86_64 #1 SMP Thu Jul 6 19:56:57 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
• Browser [e.g. chrome]
• Version [latest]

Additional context
Add any other context about the problem here.
I think it is about perl version and perl module.

literar braces to be excaped for perl 2.26 and higher

With perl 2.26.1 I am getting

Unescaped left brace in regex is illegal here in regex; marked by <-- HERE in m/$commoncfg->{ <-- HERE HTDOCS}/ at /var/www/cgi-bin/lims/index.cgi line 36.

this is apparently related to https://perldoc.perl.org/5.26.0/perldelta#Unescaped-literal-%22%7B%22-characters-in-regular-expression-patterns-are-no-longer-permissible

the error of lims.sql

When i run command "source /LIMS-master/sql/lims.sql", I got ERROR 1064.

It seems like a syntax error.
I think maybe "note longtext COMMENT," could change to "note longtext COMMENT '',".