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Merge seek 1.15.1 into LDH#56

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ReneHaensel merged 148 commits intomainnfdi4health/ldh:mainfrom merge-seek-1.15.1intoLDHnfdi4health/ldh:merge-seek-1.15.1intoLDHCopy head branch name to clipboardJul 9, 2024

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Commits

Commits on May 8, 2024

• Add 'assets/manage_specific_attributes' for assay streams

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• Hide assay design in case of assay stream

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• new AuthLookupMaintenanceJob to check consistency, runs priority 3 on the authlookup queue every 8 hours #1866

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• skip users that are already queued when checking, probably a newly registered user #1866

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• skip any types that are present in the queue #1866

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• updated schedule test #1866

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• check each type, rather than just taking the first failing type #1866

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• queue authupdate for user only after person_id is associated #1866

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• updated to to check job is queued after registration #1866

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• give UserAuthLookupUpdateJob a longer timeout of 30 mins, and do in batches of 8000 #1866

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• also skip if person is on the queue, and added test to check for anonymous user checks #1866

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• use each instead of find_each, due to an issue when combined with offset and limit #1866

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• Merge pull request #1871 from ELIXIR-Belgium/issue_1868_fix_assay_stream_permissions

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Commits on May 13, 2024

• upgrade tweaks WIP #1861

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• finished improving the upgrade tasks for updating samples #1861

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• removed upgrade tasks from 1.14 #1861

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• don't queue reindexing items or jobs, or create follow on jobs, if solr_enabled is false #1874

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Commits on May 15, 2024

• internationalize the names in the search types

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• Add test

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• Restore the internalisation settings afterwards

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• Issue 1783 fix add new button (#1872)

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• Merge pull request #1881 from ELIXIR-Belgium/issue_1879_fix_search_options

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Commits on May 16, 2024

• Rewrite can_create? function in more clear way.

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• Filter out administered projects in a very very messy way

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• Make current_person available as helper method and simplify logic.

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• Hide 'Add new attribute button' when it's a new form and shows the button when an existing template is shown.

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• update version numbers for 1.15.0

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• Only lock attribute fields when template is applied on a sample type

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• Make sure template attributes can be removed, even when inherrited and/or mandatory

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• Add tests for the Add new attribute button

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Commits on May 22, 2024

• Add authorised_assay_assets function to data_files_helper

  

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• Only show authorised assays when extracting samples

  

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Commits on May 23, 2024

• add test for project selector

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• Add 'disabled' class instead of disabled prop. This ensures the value can be set but not changed.

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• Make is_title and required attributes read-only if inherited

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• Replace 'disabled' prop with bootstrap class

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• make isa_json_compliant sample_type editable when project member instead

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• Add sample type constraint test for allow_required? of inherited sample attributes

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Commits on May 24, 2024

• Remove all logic from the views and transfer to controller

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• Simplify controller

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• Better errors when not allowed to edit

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• Remove JS that causes the default policy prompt to show twice

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• Remove investigation list partial that conflicts with default policy prompt

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• Prepopulate the investigation ID when assigning @isa_study

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• Simplification + better error messages

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• Skip value if ID is blank

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• Rename registeredSamplesObjectsInput

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• Replace drop-down with objects input with limit of 1 for registered sample attributes

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Commits on May 27, 2024

• Fix tests

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• Remove the data-dismiss attribute and add a function that hides the modal

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• Add functionality for cancel button

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• Make terms unique within a sample controlled vocab

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• Add id as a hidden field to also pass the ID to the controller when updating the CV

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• Revert last two commits

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Commits on May 29, 2024

• Merge pull request #1897 from ELIXIR-Belgium/fix_registered_sample_attribute

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• Revert changes

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• Add function to stop the propagation of the data-dismiss of the inner modals

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• Add static backdrop to the batch permissions modal

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• Group all helper methods together

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• Merge pull request #1884 from ELIXIR-Belgium/fix_template_creation_permissions

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Commits on May 30, 2024

• Merge pull request #1898 from ELIXIR-Belgium/fix_batch_sharing_permissions_in_single_page

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• Merge pull request #1896 from ELIXIR-Belgium/issue_1891_fix_isa_json_compliant_assay_creation

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Commits on May 31, 2024

• Add hidden id fields to the CV terms form and add a uniqueness clause to the validation

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• Update data_files_controller.rb

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• Destroy existing sample_persistence_task if re-extracting

  

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• Simplify assay linkage

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• Make use of :is_input? instead

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• Simplification + update even when not authorized

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• Add unit test for uniqueness clause

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• Fix current controller tests

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• Add test for duplicated CV terms

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Commits on Jun 3, 2024

• Pass errors to partials

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• Merge pull request #1906 from ELIXIR-Belgium/fix_cv_terms

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• Merge pull request #1904 from ELIXIR-Belgium/fix_add_assay_between_assays

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• Add test for unauthorized samples [JSON response]

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• typo

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• Set empty cells to nil

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• Skip id and uuid columns when comparing metadata

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• Fix existing tests

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• Add thead and tbody elements

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• Test the rendered HTML

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• Redirect to correct item in SP view

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Commits on Jun 5, 2024

• Bump actionpack from 6.1.7.7 to 6.1.7.8

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• fix nokogiri version mismatch

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Commits on Jun 6, 2024

• Typo fix

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• fix pid uri validation, and handle gracefully in short_pid for existing entries #1865

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• fix factory pid to conform to fixed validation #1865

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• replace space with - instead of _ #1865

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• Account for git in contains_downloadable_items?. Fixes #1915

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• Merge pull request #1909 from ELIXIR-Belgium/minor_fix_sample_batch_upload

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Commits on Jun 7, 2024

• Merge pull request #1916 from seek4science/fix-contains-downloadable-items

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Commits on Jun 10, 2024

• Bump nf-core rnaseq fixture

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• Attempt to get git tags in order of creation

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• make sure policy copied when persisting extracted samples #1899

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• fix tests by removing forced raise of exception #1899

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• enhance test to check for permissions #1899

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• double check policy/permissions are true copies and not referencing each other #1899

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• skip validations when saving the Policy #1899

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• Ignore disabled/archived repos

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• test the impact on running time when turning off config caching during tests #1917

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• Revert "test the impact on running time when turning off config caching during tests #1917"

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• always clear the cache when calling with_config_value in tests #1917

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Commits on Jun 11, 2024

• Merge pull request #1919 from seek4science/git-tag-order-1.15

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• Add publish button error handling.

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• Update publish button error handling.

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• Update _buttons.html.erb

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• Update publish button error handling.

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Commits on Jun 12, 2024

• Update MDS Code

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Commits on Jun 17, 2024

• when bives fails, correctly catch the exception and report just the STDERR message from the large error message #1921

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• readd raise exception, commented out during testing #1921

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• report the arguments when a job fails #1889

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Commits on Jun 18, 2024

• Handle mentions or about being single values

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• Merge pull request #1924 from seek4science/fix-ro-crate-parse

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Commits on Jun 19, 2024

• Make the template extractor job fail

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• Remove the file after processing

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• Fix current test

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• Translate to html

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• linting

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• Include template count test

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• typo

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• Simplify

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• Create template only if no errors occur

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• Add a test for an invalid json

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• Create ISA tags at setup

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• Updated the code to disable the publish button when there is no metadata.

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Commits on Jun 20, 2024

• Remove all files in directory after extraction

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• Rename fixture

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• Add tests when invalid ISA tags are used

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• Use FileUtils instead of raw shell commands

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• update version to 1.15.1

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• rebuilt api examples from a clean test db

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Commits on Jun 21, 2024

• not lose temporary access code in the URL when switching between versions or clicking on the "Back to Model" button. issue #1926:

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Commits on Jun 24, 2024

• Updated the code to update project on CSH.

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• Fix a bug in the code.

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• Merge pull request #1930 from seek4science/issue-1926

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• Fix a bug in the code.

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• fix bug error handling

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Commits on Jun 25, 2024

• Fix typo

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• Clear cache

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Commits on Jun 26, 2024

• Set SampleAttribute title manually

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Commits on Jun 28, 2024

• Merge pull request #1931 from ELIXIR-Belgium/fix_populate_templates_job

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Commits on Jul 2, 2024

• add an alert message to remind users to confirm addin the Remote URL

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Commits on Jul 3, 2024

• fix typo

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Commits on Jul 4, 2024

• Merge pull request #1938 from seek4science/improve-model-creation-UI

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• update Seeds Resource identifier

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• remove the double checking and updating of the mime type #1820

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Commits on Jul 9, 2024

• Merge remote-tracking branch 'SEEK/seek-1.15' into merge-seek-1.15.1

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• Merge branch 'main' into merge-seek-1.15.1intoLDH

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