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Home Page: http://biii.eu
License: GNU General Public License v2.0
BIII development repository
Home Page: http://biii.eu
License: GNU General Public License v2.0
http://biii.eu/tag-me-
Note that this page appears only for confirmed taggers)
The fields to sort the Tools and find the one to curate are exposed to the user for search, but the search design/aspect is not ergonomic. I found no way to play on this.
The same apply to the "batch tagging" possibility (hidden page for admins only).
The following error appears for every CRON run.
Could not delete temporary file "temporary://neubiaslogo_Beq_icon.ico" during garbage collection
Need to work with sql-cli to get rid of this.
https://www.drupal.org/project/drupal/issues/2802803
As others have mentioned if you're just trying to clean out a handful of entries, they exist in the file_managed table. You can do so with phpmyadmin or if you don't have that installed you can do 'drush sql-cli' to get into an sql command interface, and then remove the offending entry with something like
delete from file_managed where filename = "LaKelly.jpg";
edit:
or if you want to clear all listings that pertain to a certain folder (which in my case was long gone), you'd do
delete from file_managed WHERE uri LIKE '%wp-content%';
back up your database before trying the above. Looks like in my case although the logs only showed the first 100 or so error messages, Drupal was trying to delete 3700 files that no longer existed.
Check if any module/view/page/block/etc unused to be uninstall to speed up the site
the two serach should be coherent in the display
example: http://biii.eu/all-content?type=All&field_type_target_id=All&field_has_biological_terms_target_id%5B%5D=4243 VS http://biii.eu/search?search_api_fulltext=microtubule
Purpose : displaying the bio Imaging edam terms associated to a biological Search to support the message "One of the purpose of BISE is to help both scientists by transparently linking a biological term to image processing notions, for example Centromere to Spot Detection, or microtubule to filament tracing resulting in the possibility for the researchers to dive into different knowledge and skills without actually needing to know or learn these foreign vocabularies. "
the view http://biii.eu/training-view should be named list of training.
Now with EDAM alpha04 in BIII/BISE:
There have been 1 concept that changed from Operation to Topic in EDAM alpha05, and changed ID!:
And 2 removed:
Interactive segmentation. Replace by Interaction level attribute in BISE/BIII:
- PartSeg, The Allen Cell Structure Segmenter, Interactive watershed, Orbit, FlyLimbTracker, SuRVoS, QuimP, QuPath, FibrilTool, ilastik - Carving
Local thresholding. Consider other concept underneath & including Image segmentation:
- clij - GPU-acceleration for ImageJ
Related: #44, edamontology/edam-bioimaging#14
Note for long term:
(not part of this issue or relevant today, but keep in mind when designing sustainable updating)
In Bio.Tools it turned out that it's needed to keep the annotations with old versions of EDAM, too. Of course marked as obsolete, but not removed once EDAM is updated. This hasn't been done and users are unhappy about it.
when did this "overlay" advanced search (http://test.biii.eu/all-content?field_type_target_id=All&field_has_function_target_id=4097&field_has_topic_target_id_1=All&field_has_interaction_level_target_id=All&field_license_openness_target_id=All&field_has_programming_language_target_id=All&title_1=), it returned three items of MaMuT, when clicking in, they all point to the same page. why showing three times?
minimal list of test to be performed before accepting pulling to master:
site refer to local installation :
test 1 site/soft should return a json formatted list of software
To be continued...
for example skeletonisation search should return ncutw sifwtare, it is only in the 'function'/operation tag which should be indexed.
It shows only new entry cretaed by a tagger, but not the one modified from somebody else or any comment done. It is then underestimating the work of taggers. (example) http://biii.eu/user/1 when I did modify Acquiarium entry)
Dear team,
@PerrineGilloteaux @miura @czhci,
I added about 9 new workflows and a bunch of components/collections on bise this week (used in BIAFLOWS) and I noticed a few issues and undesired behavior when adding them.
previous workflow step
autocompletes to existing biii.eu nodes, but it should (I assume) trace back to existing steps in the workflow being described.current workflow step
if read that way (considering what I just wrote in 1) ) should be renamed as current workflow component/process and this indeed must autocomplete to an existing biii.eu node, which should Ideally link to a component.I can give as an example a workflow that has a simple overview of what it does and does not have steps associated to a certain biii.eu (I consider this acceptable but not ideal) below. it should show how 1) affects the way we add the workflows and why I think this should be fixed.
in this example, I could not associate the step order since they are not associated with biii.eu nodes. but I would add the workflow as steps 12 and 34 running in parallel, then 5 getting results of 2 and 4 to run.
Please let me know if additional clarification is needed. I hope these comments help.
Cheers,
Leandro.
Theme "Zircon" is not supported anymore. As our theme is based on Zircon, we need to replace it with another theme.
For more details, see the web page of zircon.
Quote:
This module is unsupported due to a security issue the maintainer didn’t fix. See Zircon - Critical - Unsupported - SA-CONTRIB-2018-037 for details.
If you want to use this module, your options are:
EDAM is a directed acyclic graph (DAG).
BIII/BISE EDAM widget doesn't show all the "occurences" of a concept with multiple "parents".
E.g.:
In Updating the Site (routine procedure!), the mention to lando start , (to launcg the app ) is missing.
Can you add it saying also that http://bisescratch.lndo.site/ should now be available in the navigator?
protection of natural persons with regard to the processing of personal data and on the free movement of such data: General Data Protection Regulation :
https://ec.europa.eu/info/law/law-topic/data-protection/reform/rules-business-and-organisations/principles-gdpr/what-data-can-we-process-and-under-which-conditions_en
We need to add these information (why we ask it, what would be display, etc..) on the registration page.
It seems that a lot of images of the entries of bii.eu are not shown anymore, like if the link to them is missing
Hi @miura and @vcaldas we (at least Alban, my self and Florian) are completely lost with git: Origin vs Upstream, where are my commit gone, why are then appearing on your name, how can I cancel local modification not committed. Can you help us with a specific wiki page about the procedure?
For example I did 2 commit (one about the first proposal for training model, that i now need to edit based on the first feedback), and one for beeing able to launch the routine procedure of edam updates (everytime a new version go out), but I do not manage to get them back locally, neither to ask for merge.
The script should contain:
Git setup
Lando download
Lando installation
This issue comes from 2 bugs in the taxonomy_menu , only one has been fixed by patch so better to stick to taxonomy menu 3.3 (see composer json commit in fork from me and Chong), will be "pull requested soon"
I saw your additions to "training material" type in dev
branch. It seems that it's already functioning to some extent, but is it OK to create a new branch cambridge
and keep those test-changes there? I will also put the dev
into original status without those additions. This is for practical reason, that it's quite a work for merging new changes in dev
from master
excluding those changes.
Let's also keep the test.biii.eu at cambridge
branch (= what it is now and for further testing of training material node fields), and for adding other new changes we can pull from the dev
branch in test.biii.eu and merge them into cambridge
.
This page should be reviewed. This page only disaply for confirmed taggers (the only ones who can modified somebody else entry), which is good. Now it allow a search (ugly Pb #1 : to be enhanced (sorter) see #90 ) , but it should also display the total number of tool not meeting the minimal criteria and allow to click on this number to go to the list of it. This issue will be closed when this feature will be added:
-number of tools filling the requirements of a detailed but not yet comprehensive description
-number of tools have only a sparse description and need curation
Definition of these minimal criteria here : http://biii.eu/howtocurate
On any page, links are not visible since they are in the same color and font as any text. For the usability it is very important that evering clickeable is visble at first sight (such as function and topic in a sofwtare entry)
The website encountered an unexpected error. Please try again later.
Drupal\Core\Entity\EntityStorageException: SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '377-0-0-en' for key 'PRIMARY': INSERT INTO {comment__comment_body} (entity_id, revision_id, bundle, delta, langcode, comment_body_value, comment_body_format) VALUES (:db_insert_placeholder_0, :db_insert_placeholder_1, :db_insert_placeholder_2, :db_insert_placeholder_3, :db_insert_placeholder_4, :db_insert_placeholder_5, :db_insert_placeholder_6); Array
(
[:db_insert_placeholder_0] => 377
[:db_insert_placeholder_1] => 377
[:db_insert_placeholder_2] => comment
[:db_insert_placeholder_3] => 0
[:db_insert_placeholder_4] => en
[:db_insert_placeholder_5] => <p>test</p>
[:db_insert_placeholder_6] => basic_html
)
in Drupal\Core\Entity\Sql\SqlContentEntityStorage->save() (line 783 of core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorage.php).
Drupal\Core\Database\Statement->execute(Array, Array) (Line: 625)
Drupal\Core\Database\Connection->query('INSERT INTO {comment__comment_body} (entity_id, revision_id, bundle, delta, langcode, comment_body_value, comment_body_format) VALUES (:db_insert_placeholder_0, :db_insert_placeholder_1, :db_insert_placeholder_2, :db_insert_placeholder_3, :db_insert_placeholder_4, :db_insert_placeholder_5, :db_insert_placeholder_6)', Array, Array) (Line: 358)
Drupal\Core\Database\Driver\mysql\Connection->query('INSERT INTO {comment__comment_body} (entity_id, revision_id, bundle, delta, langcode, comment_body_value, comment_body_format) VALUES (:db_insert_placeholder_0, :db_insert_placeholder_1, :db_insert_placeholder_2, :db_insert_placeholder_3, :db_insert_placeholder_4, :db_insert_placeholder_5, :db_insert_placeholder_6)', Array, Array) (Line: 32)
Drupal\Core\Database\Driver\mysql\Insert->execute() (Line: 1304)
Drupal\Core\Entity\Sql\SqlContentEntityStorage->saveToDedicatedTables(Object, , Array) (Line: 886)
Drupal\Core\Entity\Sql\SqlContentEntityStorage->doSaveFieldItems(Object) (Line: 578)
Drupal\Core\Entity\ContentEntityStorageBase->doSave(NULL, Object) (Line: 429)
Drupal\Core\Entity\EntityStorageBase->save(Object) (Line: 774)
Drupal\Core\Entity\Sql\SqlContentEntityStorage->save(Object) (Line: 390)
Drupal\Core\Entity\Entity->save() (Line: 376)
Drupal\comment\CommentForm->save(Array, Object)
call_user_func_array(Array, Array) (Line: 111)
Drupal\Core\Form\FormSubmitter->executeSubmitHandlers(Array, Object) (Line: 51)
Drupal\Core\Form\FormSubmitter->doSubmitForm(Array, Object) (Line: 589)
Drupal\Core\Form\FormBuilder->processForm('comment_comment_form', Array, Object) (Line: 318)
Drupal\Core\Form\FormBuilder->buildForm('comment_comment_form', Object) (Line: 48)
Drupal\Core\Entity\EntityFormBuilder->getForm(Object) (Line: 249)
Drupal\comment\Controller\CommentController->getReplyForm(Object, Object, 'field_give_feedback_on_this_soft', NULL)
call_user_func_array(Array, Array) (Line: 123)
Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->Drupal\Core\EventSubscriber{closure}() (Line: 582)
Drupal\Core\Render\Renderer->executeInRenderContext(Object, Object) (Line: 124)
Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->wrapControllerExecutionInRenderContext(Array, Array) (Line: 97)
Drupal\Core\EventSubscriber\EarlyRenderingControllerWrapperSubscriber->Drupal\Core\EventSubscriber{closure}() (Line: 151)
Symfony\Component\HttpKernel\HttpKernel->handleRaw(Object, 1) (Line: 68)
Symfony\Component\HttpKernel\HttpKernel->handle(Object, 1, 1) (Line: 57)
Drupal\Core\StackMiddleware\Session->handle(Object, 1, 1) (Line: 47)
Drupal\Core\StackMiddleware\KernelPreHandle->handle(Object, 1, 1) (Line: 99)
Drupal\page_cache\StackMiddleware\PageCache->pass(Object, 1, 1) (Line: 78)
Drupal\page_cache\StackMiddleware\PageCache->handle(Object, 1, 1) (Line: 50)
Drupal\ban\BanMiddleware->handle(Object, 1, 1) (Line: 59)
Drupal\httpbl\HttpblMiddleware->handle(Object, 1, 1) (Line: 47)
Drupal\Core\StackMiddleware\ReverseProxyMiddleware->handle(Object, 1, 1) (Line: 52)
Drupal\Core\StackMiddleware\NegotiationMiddleware->handle(Object, 1, 1) (Line: 23)
Stack\StackedHttpKernel->handle(Object, 1, 1) (Line: 693)
Drupal\Core\DrupalKernel->handle(Object) (Line: 19)
http://biii.eu/taxonomy/term/3568: when it comes to a list like this (e.g. after any search, and then click on any term, we will get such list), when we would like to click the item to reach its own page, the only place to do this is "read more", which makes sense, but it is not in an obvious place to reach easily. fix this?
Script to fetch the latest updates and update the local environment.
we should add their corresponding pages: training material (XX), software (XX), etc.
I updated the development wiki page
https://github.com/NeuBIAS/bise/wiki/BISE-development#development-custom-theme-bise
I separated it into three big sections
This is just to notify - and there still are many typos but please ignore those at the moment. By the way, internal linking does not work - is there a good way to anchor sections?
When Editing menu, they are not track by config-export. We need to find a way to track this
If the work in that branch is done, we should delete it.
Should I delete it?
illustrative image currently is only available as file. it would be great to be able to provide the image location URL
Either doing a view for Search for training with field displayed adapted, either adding Topics Covered from Training in the field operation displayed in the table.
Topics covered use the bio Imaging edam ontology, but is not searchable in Advanced serch, and not displayed in the result view.
http://biii.eu/2d-image-processing-and-data-analysis-matlab
http://biii.eu/all-content?type=book&field_type_target_id=All
Once decided, to be implemented.
Dear *,
I'm following up a discussion during the NEUBIAS conference. There is a search plugin for Fijis search bar, which allows searching in the BISE online database:
https://github.com/scijava/scijava-search/blob/master/src/main/java/org/scijava/search/web/BISESearcher.java
It is at the moment deactivated because of an issue in the website (its HTML is no valid XML) because of a missing slash. Read details here:
https://forum.image.sc/t/search-field-on-menu/6958/7
What do you think about reviving this search plugin? I'd be happy to help, but I need support by a developer on server side to put this slash there...
Cheers,
Robert
what links here | what_links_here
EVA block is disabled. Please someone demo it locally, so we can discuss the content and behavior.
A possible candidate theme, to replace Zircon is in the newmockup
branch. Please test and comment.
There seems to be some solution to it.
https://www.drupal.org/project/zircon/issues/2952980
If the problem persists after upgrading Zircon to the latest version, the patch above should be applied.
Some fields are not visible to anaonymous (not logged in) users: for example requires, programming language. I do not think it make sense.
@florian-levet @PerrineGilloteaux @vcaldas
please comment.
Kota
20181023
Up until October 2018 Taggathon, taxonomy terms incuding BISE ontology was handled in the following way.
By using an add-on package "structure sync", it's possible to export taxonomy terms as yml file and handle them just like other settings.
Expexted workflow is as following
drush export-taxonomies
and it will be ready to be exported as files (changes at this stage only happens within the database)drush config:status
(short form drush cst
). If there is difference, you should see structure_sync.data.yml in the list.drush cex
(config:export) will update structure_sync.data.yml
file according to the updates in the database.git add .
& git commit - m "taxnonomy updated"
or so will add these changes to the version tracking.git push origin <branch name>
dev
branch. Wait (or insist) someone else to merge the PR.What Florian can do from now on, is these 7 steps. Extract taxonomy from Webprotege and update your local drupal database using the python script. Then follow step 1 to 6 to push the changes to the Github repo.
git pull upstream dev
pulled any change in structure_sync.data.yml
, If this happened, then taxonomy term has changed and you need to do the following.drush cim
(config:import) to update your local database using updated yml file.drush import-taxonomies
to update taxonomy.After the user receives the latest dump database,
the script should perfom all the actions to launch Bise
On the home page, the block counting the number of Tools also count the unpublished content, leading to an inbcoherent number of Tools: e.g 140 workflows vs 133 in reality). Idem for all I do not know data which have been curated now, but are still countied. This should count ONLY PUBLISH entries.
purpose: detecting download links broken
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