A possible candidate theme, to replace Zircon is in the newmockup branch. Please test and comment.

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.

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.

Check if any module/view/page/block/etc unused to be uninstall to speed up the site

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...

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.

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

Collections and Components types do not need (or cannot have) workflow steps, so it's better be limited to the workflow type.

In addition, it's better be folded like other items.

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)

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?

@miura @PerrineGilloteaux

If the work in that branch is done, we should delete it.
Should I delete it?

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"

• Message such as /app/xx not found with lando .
  Solution: restart docker and lando
• Message such as Connection to SQL database impossible (with lando drush cr for example) -> Solution: check your .env and your settings.local.: credential to your local database may not be correct .

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:

• Choose another, actively maintained module instead
• File an issue in the queue with a patch to fix the module and then contact the security team to have your version reviewed and the project handed over to you following the unsupported project process.
• Hire someone to fix the security bug so the module can be re-published and supported (Consider hiring companies listed in the Marketplace)

we should add their corresponding pages: training material (XX), software (XX), etc.

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. "

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.

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)

Taggers page is causing some error:

http://biii.eu/taggers?page=0&sort_by=name&sort_order=ASC

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.

1. previous workflow step autocompletes to existing biii.eu nodes, but it should (I assume) trace back to existing steps in the workflow being described.
2. 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.
3. Step numbers. Shouldn't this be set automatically as they are added/reordered? I would say the template using "Step number: description" should be changed just to "description" and we then should use an automatic step number (I am not sure how feasible this is, so definitely open to discussion).

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.

There have been 1 concept that changed from Operation to Topic in EDAM alpha05, and changed ID!:

• Neuron image analysis. Update entries by adding it as hasTopic in BISE/BIII:
  - Paintera, Rivulet 2, Aivia, CEM, VMTK: Vascular Modeling Toolkit, Neurite Tracer, Simple Tracing DF-Tracing, nctuTW, Reconstruct, JFilament

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.

what links here | what_links_here
EVA block is disabled. Please someone demo it locally, so we can discuss the content and behavior.

for example skeletonisation search should return ncutw sifwtare, it is only in the 'function'/operation tag which should be indexed.

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.:

• Image segmentation is only listed under Image processing, but not also under Image analysis
• Frequency analysis is only shown under Image processing, but not also under Analysis

the view http://biii.eu/training-view should be named list of training.

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.

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.

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)

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

@florian-levet @PerrineGilloteaux @vcaldas

please comment.

Updating the workflow for taxonomy terms

Kota

20181023

Current way of Adding, Editing, Weighting Taxonomy Terms

Up until October 2018 Taggathon, taxonomy terms incuding BISE ontology was handled in the following way.

• Addition: New terms were transferred and added from Webprotege to biii.eu.LocalCopy using python script (Florian's work) - then the updated database is dumped manually, then the dumped file is imported from the biii.eu.
  • Taxonomy terms (EDAM Bioimaging ontology "Functions", "Topics" etc) lives only in database.
• Weighting: Order of taxonomy appearance is also handled only in the database.
• Disadvantage: updating of texonomy terms is NOT independent from other database updates, and not tracked by Git - cannot be easily pushed and pulled.

Recommended update in the workflow

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

Exporting taxonomy updates from database to yml file

1. Adding, Editing, Weighting taxonomy terms in the local biii.eu.
2. Translate the updates to writable format by drush export-taxonomies and it will be ready to be exported as files (changes at this stage only happens within the database)
3. Check that there is difference in the database and yml file: drush config:status (short form drush cst). If there is difference, you should see structure_sync.data.yml in the list.
4. As usual, drush cex (config:export) will update structure_sync.data.yml file according to the updates in the database.
5. git add . & git commit - m "taxnonomy updated" or so will add these changes to the version tracking.
6. git push origin <branch name>
7. In Github, issue a pull request to NEUBIAS/bise 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.

Importing taxonomy updates from file to yml file

1. Check if 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.
2. drush cim (config:import) to update your local database using updated yml file.
3. drush import-taxonomies to update taxonomy.

We need another choice "All". I often need to click 3 times to select all Win, Mac, & Linux.

Some fields are not visible to anaonymous (not logged in) users: for example requires, programming language. I do not think it make sense.

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

Hi @PerrineGilloteaux

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.

Script to fetch the latest updates and update the local environment.

The script should contain:
Git setup
Lando download
Lando installation

@vcaldas

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

• installation procedure
• how to develop
• actual development examples

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?

purpose: detecting download links broken

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?

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).

When Editing menu, they are not track by config-export. We need to find a way to track this

• solution 1: do it directly on the data base (after testing locally) from Florian's Script.
• solution 2: taxonomy terms are content (module structured sync)
  tested by Kota? procedure complex
  Which one should be preferered

After the user receives the latest dump database,
the script should perfom all the actions to launch Bise

Now with EDAM alpha04 in BIII/BISE:

• Operation
  -> Alignment construction
  Here it should continue expanding further to Image registration
  The taxonomy exists correctly in BIII/BISE
  But it cannot be expanded in BIII/BISE

illustrative image currently is only available as file. it would be great to be able to provide the image location URL

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?