Group 1: Convert functions in tripal.module file

[laceysanderson]

This was started and almost completed by @shawnawsu. The intent is to convert all functions in the tripal 3 tripal.module file to Drupal 8.

Here is the list of functions from Tripal 3:

• tripal_views_api(): removed
• tripal_init(): replaced by tripal_preprocess_html
• tripal_menu_alter(&$items): check if this was ported
• tripal_menu(): check that this is complete using this tutorial
• tripal_access_user_files($op, $uid, $fid = NULL)
• tripal_accesss_user_collections($uid)
• tripal_users_autocomplete($string): db_select is deprecated
• tripal_access_user_data($uid)
• tripal_permission() check that all permissions were ported
• tripal_theme($existing, $type, $theme, $path): the function exists. We will add theme defn as they are needed.
• tripal_coder_ignore(): check if this is still needed
• tripal_libraries_info()
• tripal_admin_paths()
• tripal_menu_local_tasks_alter(&$data, $router_item, $root_path)
• tripal_shortcut_default_set($account): do we want another dependency to keep these? perhaps we just need to add an if module is installed then do this.
• TripalBundle_load($bundle_type, $reset = FALSE)
• TripalEntity_load($id, $reset = FALSE)
• tripal_import_api()
• tripal_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id): does not yet work
• tripal_form_alter(&$form, $form_state, $form_id): check after TripalField implementation that this works. it removes fields with no widgets from the tripal entity add/edit form.
• tripal_check_new_fields($bundle_name): upgraded although it's called API functions are not.
• tripal_block_info(): Blocks are now plugins
• tripal_block_view($delta = '')
• tripal_block_save($delta = '', $edit = array())
• tripal_block_configure($delta = '')
• tripal_cron(): drupal 8 hook_cron
• tripal_element_info() moved over to classes
• tripal_html5_file_process($element, $form_state, $complete_form)
• tripal_html5_file_validate($element, &$form_state)
• tripal_html5_file_value($element, $input = FALSE, &$form_state)
• tripal_field_display_TripalEntity_alter(&$display, $context)
• tripal_field_group_table_rows_alter(&$element, &$children)

[laceysanderson]

Since this can be a bit overwhelming, I've broken it down into sub-issues with specific documentation:

• Group 1: Upgrade Tripal Core blocks #18 Upgrade Tripal Core blocks
• Group 1: Upgrade menu items #19 Upgrade menu items (only checking needed)
• Group 1: Upgrade Permissions (only checking needed) #20 Upgrade Permissions (only checking needed)
• Group 1: Default Tripal Shortcuts #21 Default Tripal Shortcuts (discussion)
• Group 1: HTML5 File Upload Element #22 Tripal HTML5 file upload form element

Items not broken into issues... if you feel these need their own issue, feel free to create one and tag it with "group 1". Otherwise, feel free to comment in this thread.

• tripal_users_autocomplete($string): db_select is deprecated
• tripal_coder_ignore(): check if this is still needed
• TripalBundle_load($bundle_type, $reset = FALSE): check if this is still needed. Seems to be handled by the Drupal 8 entity api
• TripalEntity_load($id, $reset = FALSE): check if this is still needed. Seems to be handled by the Drupal 8 entity api
• tripal_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id): does not yet work
• tripal_form_alter(&$form, $form_state, $form_id): check after TripalField implementation that this works. it removes fields with no widgets from the tripal entity add/edit form.
• tripal_field_display_TripalEntity_alter(&$display, $context)
• tripal_field_group_table_rows_alter(&$element, &$children)

[ng29]

Heya @laceysanderson ,

I can give it a shot on this. (Though incase any queries will ping ya)

Cheers.

[laceysanderson]

We're happy to have you 😃 Just checking in: how are things going? Any questions?

[ng29]

We're happy to have you 😃 Just checking in: how are things going? Any questions?

@laceysanderson Can i get some more info what needs to be achieved in this issue so that can start it , as it seems kinda Giant rock.

And all functions need to be catered under one PR or in chunks ? .

[laceysanderson]

In comment #17 (comment) I split out a bit of the work into other issues so you don't need to worry about those functions. Instead, for this issue you should focus on the following:

• tripal_users_autocomplete($string): db_select is deprecated
• tripal_coder_ignore(): check if this is still needed
• TripalBundle_load($bundle_type, $reset = FALSE): check if this is still needed. Seems to be handled by the Drupal 8 entity api
• TripalEntity_load($id, $reset = FALSE): check if this is still needed. Seems to be handled by the Drupal 8 entity api
• tripal_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id): does not yet work
• tripal_form_alter(&$form, $form_state, $form_id): check after TripalField implementation that this works. it removes fields with no widgets from the tripal entity add/edit form.
• tripal_field_display_TripalEntity_alter(&$display, $context)
• tripal_field_group_table_rows_alter(&$element, &$children)

As far as how you arrange it, that is completely up to you! Personally, I would start with confirming whether tripal_coder_ignore(), TripalBundle_load() and TripalEntity_load() are even still needed. Next I would look at tripal_users_autocomplete(). The last four seem like they might be related to the field implementation, in which case they cannot be done quite yet. If this ends up being the case then just comment on #28.

[ng29]

In comment #17 (comment) I split out a bit of the work into other issues so you don't need to worry about those functions. Instead, for this issue you should focus on the following:

• tripal_users_autocomplete($string): db_select is deprecated
• tripal_coder_ignore(): check if this is still needed
• TripalBundle_load($bundle_type, $reset = FALSE): check if this is still needed. Seems to be handled by the Drupal 8 entity api
• TripalEntity_load($id, $reset = FALSE): check if this is still needed. Seems to be handled by the Drupal 8 entity api
• tripal_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id): does not yet work
• tripal_form_alter(&$form, $form_state, $form_id): check after TripalField implementation that this works. it removes fields with no widgets from the tripal entity add/edit form.
• tripal_field_display_TripalEntity_alter(&$display, $context)
• tripal_field_group_table_rows_alter(&$element, &$children)

As far as how you arrange it, that is completely up to you! Personally, I would start with confirming whether tripal_coder_ignore(), TripalBundle_load() and TripalEntity_load() are even still needed. Next I would look at tripal_users_autocomplete(). The last four seem like they might be related to the field implementation, in which case they cannot be done quite yet. If this ends up being the case then just comment on #28.

Thanks alot for such detailed explaination, and as far as i understood our main concern is upper 4 functions in your above comment.

Also could you please guide me that from i have to confirm (any link to docs or something) and directory path where these functions need to omitted or any other operation required.

Cheers

[laceysanderson]

Thanks alot for such detailed explaination, and as far as i understood our main concern is upper 4 functions in your above comment.

Exactly :-)

Also could you please guide me that from i have to confirm (any link to docs or something) and directory path where these functions need to omitted or any other operation required.

All the functions should all be in https://github.com/tripal/t4d8/blob/9.x-4.x/tripal/tripal.module (although I see the autocomplete is missing 🤷‍♀️ ) This task requires digging through the new Drupal 8/9 documentation to see if they are still needed. This was the function that they accomplished in Drupal 7:

• tripal_users_autocomplete(): provided an autocomplete for form fields though I'm not sure why we needed a special one for tripal. perhaps it has to do with Chado contacts?
• TripalBundle_load() and TripalEntity_load(): these were related to arguements in hook_menu. Specifically, they ensured that when the bundle_id and/or entity_id were in the path, the appropriate object was loaded and passed to the callback.
• tripal_coder_ignore(): this is an implementation of hook_code_ignore() and was related to ensuring that our own ignore rules for the Drupal code module were picked up. This helps for syntax detecting since we have some API functions which require a certain non-drupal syntax.

[ng29]

Thanks alot for such detailed explaination, and as far as i understood our main concern is upper 4 functions in your above comment.

Exactly :-)

Also could you please guide me that from i have to confirm (any link to docs or something) and directory path where these functions need to omitted or any other operation required.

All the functions should all be in https://github.com/tripal/t4d8/blob/9.x-4.x/tripal/tripal.module (although I see the autocomplete is missing 🤷‍♀️ ) This task requires digging through the new Drupal 8/9 documentation to see if they are still needed. This was the function that they accomplished in Drupal 7:

• tripal_users_autocomplete(): provided an autocomplete for form fields though I'm not sure why we needed a special one for tripal. perhaps it has to do with Chado contacts?
• TripalBundle_load() and TripalEntity_load(): these were related to arguements in hook_menu. Specifically, they ensured that when the bundle_id and/or entity_id were in the path, the appropriate object was loaded and passed to the callback.
• tripal_coder_ignore(): this is an implementation of hook_code_ignore() and was related to ensuring that our own ignore rules for the Drupal code module were picked up. This helps for syntax detecting since we have some API functions which require a certain non-drupal syntax.

Ah, now I am getting somethings in my head... and it needs a high level of concentration to check these out.
But the main problem is that I am not much into Drupal stuff so might not be able to decide the exact use case and regression of omitting some function, too.

So what's your opinion, if we can do it together and you can guide me on slack/another mode.

Cheers

[laceysanderson]

Feel free to ask me questions either here or on slack :-) The easiest one to track down is likely hook_coder_ignore() so I would start there.

[ng29]

Feel free to ask me questions either here or on slack :-) The easiest one to track down is likely hook_coder_ignore() so I would start there.

Okay cool, will see if i got some guts to nail this down

[laceysanderson]

Not Needed:
tripal_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id): handled by fields.
tripal_form_alter(&$form, $form_state, $form_id): TripalField implementation does this.
tripal_field_display_TripalEntity_alter(&$display, $context)
tripal_field_group_table_rows_alter(&$element, &$children)

Remaining:
#21 Default Tripal Shortcuts (discussion)

Since there is only a single thing left and it has it's own issue, I'm closing this.