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⬅️ Previous capture (2023-01-29)

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GN1 metadata

If we edit metadata on GN1 it shows a missing PHP.

The problem can be replitated by logging into GN1 and selecting a dataset. Hit the info button and 'edit' next.

Tags

• assigned: pjotrp
• priority: high
• status: overdue
• type: bug
• keywords: GN1, genenetwork1, annotation

Tasks

• [ ] Update guix, guix-bioinformatics for gn1
• [ ] Fix PHP view in Guix
• [ ] Fix CKEDITOR in Guix

Description

Turns out that it is a PHP page that is not working. Also CKEDITOR is not visible.

Info

On lily the file

/gnshare/gn/web/infoshare/manager/investigator.html

is written in PHP(!)

lily has a configuration setting:

• AddType application/x-httpd-php .htm .html

With running PHP 5.5 or 5.6 versions and i added this code to the .htaccess file. Remember both AddHandler and AddType must be present

AddHandler application/x-httpd-ea-php56 .htm .html .shtml
AddType application/x-httpd-php5 .php

Some hints here.

Building genenetwork1

For the python2.4 packages

gaeta:~/guix-past$ guix build -L ~/guix-past/modules/ -L ~/guix-bioinformatics/ genenetwork1

Gets

`thirdparty/htmlgen/polyfunc.py' -> `/gnu/store/hh21dq96kbmby3dks45ngxd6lzx1lx83-python24-htmlgen-GN1-2.5/lib/python2.4/site-packages/htmlgen//polyfunc.py'
phase `install' succeeded after 0.0 seconds
starting phase `add-install-to-pythonpath'
error: in phase 'add-install-to-pythonpath': uncaught exception:
wrong-type-arg "string-append" "Wrong type (expecting ~A): ~S" ("string" #f) (#f)
phase `add-install-to-pythonpath' failed after 0.0 seconds
Backtrace:
           9 (primitive-load "/gnu/store/5x73mpqayj6xi2ag5l8yblvh4hv…")
In guix/build/gnu-build-system.scm:
    906:2  8 (gnu-build #:source _ #:outputs _ #:inputs _ #:phases . #)
In ice-9/boot-9.scm:
  1752:10  7 (with-exception-handler _ _ #:unwind? _ # _)
In srfi/srfi-1.scm:
    634:9  6 (for-each #<procedure 7fffeff39000 at guix/build/gnu-b…> …)
In ice-9/boot-9.scm:
  1752:10  5 (with-exception-handler _ _ #:unwind? _ # _)
In guix/build/gnu-build-system.scm:
   927:23  4 (_)
In guix/build/python-build-system.scm:
   186:28  3 (add-installed-pythonpath (("python" . "/gnu/store…") …) …)
In unknown file:
           2 (string-append "/gnu/store/hh21dq96kbmby3dks45ngxd6lzx…" …)
In ice-9/boot-9.scm:
  1685:16  1 (raise-exception _ #:continuable? _)
  1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
In procedure string-append: Wrong type (expecting string): #f
builder for `/gnu/store/m4cvh8f83ry9saja47ap7bgzmc58gmk1-python24-htmlgen-GN1-2.5.drv' failed with exit code 1
build of /gnu/store/m4cvh8f83ry9saja47ap7bgzmc58gmk1-python24-htmlgen-GN1-2.5.drv failed
View build log at '/var/log/guix/drvs/m4/cvh8f83ry9saja47ap7bgzmc58gmk1-python24-htmlgen-GN1-2.5.drv.gz'.
guix build: error: build of `/gnu/store/m4cvh8f83ry9saja47ap7bgzmc58gmk1-python24-htmlgen-GN1-2.5.drv' failed