search

BU-Spark / se-Symbiota-portal

The Symbiota Virtual Flora/Fauna project is an open source software project, with central goal of developing on-line tools that aid in the generation, exploration and management of biodiversity data (collection specimens, observations, images, checklist, keys, etc.). See also: http://bdj.pensoft.net/articles.php?id=1114 and http://symbiota.org/
GNU General Public License v2.0
1 stars 3 forks source link

Investigate symbiota's ingestion functions #44

Closed Tian-Tan closed 5 months ago

Tian-Tan commented 1 year ago

It might make the source of bugs more apparent by fixing symbiota's actual ingestion functions to make it work as intended, and then check the errors in the outcome for bugs.

Tian-Tan commented 1 year ago

Another feature potentially needed: we want to capture the image filename independently of storing the image in case we need to recover the ordering of a batch (aside from the ordinal).

Tian-Tan commented 1 year ago

The "Import/Update Specimen Records" function in the Administration Control Panel was tested and it could not work because our server did not have the "PHP DOMdocument" library installed. Fix needed on server-side to be able to proceed with testing it.

Tian-Tan commented 1 year ago

While the "PHP DOMdocument" problem is being solved, tests have been performed on the batch image ingestion function using the Image Loading function in the "Processing Toolkit" in the Administration Control Panel. An Image Processing Profile called Test1 has been successfully created and a new path for the ingested images /var/www/html/symbiota/content/imglib/HUH has been successfully created too. However, the image processing did not go through and it was stuck on this page: image

Tian-Tan commented 1 year ago

[Mon Aug 14 05:50:18.550859 2023] [php7:warn] [pid 19451] [client 10.0.2.2:59989] PHP Warning: fopen(/var/www/html/symbiota/content/logs/imgProccessing/1_HUH_2023-08-13.log): failed to open stream: Permission denied in /var/www/html/symbiota/classes/ImageLocalProcessor.php on line 100, referer: http://10.210.3.94:8080/collections/specprocessor/index.php [Mon Aug 14 05:50:18.768584 2023] [php7:error] [pid 19451] [client 10.0.2.2:59989] PHP Fatal error: Uncaught Error: Class 'DOMDocument' not found in /var/www/html/symbiota/classes/ImageLocalProcessor.php:376\nStack trace:\n#0 /var/www/html/symbiota/classes/ImageLocalProcessor.php(199): ImageLocalProcessor->processHtml('')\n#1 /var/www/html/symbiota/collections/specprocessor/processor.php(108): ImageLocalProcessor->batchLoadSpecimenImages()\n#2 {main}\n thrown in /var/www/html/symbiota/classes/ImageLocalProcessor.php on line 376, referer: http://10.210.3.94:8080/collections/specprocessor/index.php

The above error was found in the logs, so it looks like it's a mix of PHP DOMdocument and permission errors

Tian-Tan commented 11 months ago

Created a new issue #53 to focus on the PHP DOMdocument errors

Tian-Tan commented 5 months ago

Everything is fixed after the final commit which is d74a61f The solution included:

  1. Migrating everything to containers to fix the PHP DOMdocument errors
  2. Modifying the schema to remove previous dropdown implementations which was causing problems for the site's ingestion functions