Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merge-seek1.15-into-LDH #52

Closed
wants to merge 297 commits into from
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
297 commits
Select commit Hold shift + click to select a range
9f22b38
Add configuration to features in admin panel
kdp-cloud Jan 30, 2024
5064467
Add custom code snippet to the application layout
kdp-cloud Jan 31, 2024
9d2b8bd
Add tracking notice
kdp-cloud Jan 31, 2024
7ba2e7c
Add custom analytics name
kdp-cloud Jan 31, 2024
966ae54
Add integration tests
kdp-cloud Jan 31, 2024
09bf27f
Add unit tests
kdp-cloud Jan 31, 2024
aa3742f
Consolidate analytics constants in a method
kdp-cloud Jan 31, 2024
767d2af
Change the default value to an empty script tag
kdp-cloud Jan 31, 2024
1d7e925
Wrap `custom_analytics_snippet` in a div instead of a script tag. Esc…
kdp-cloud Jan 31, 2024
3349884
Add test for `custom_analytics_snippet`
kdp-cloud Jan 31, 2024
a8316e2
Remove the AssayClass constants
kdp-cloud Feb 1, 2024
cd06baa
Move long key mapping to a constant outside
kdp-cloud Feb 1, 2024
14089f6
Use the definition instead of manual text setting
kdp-cloud Feb 1, 2024
6fdd31f
Use assay_streams method instead of select statement
kdp-cloud Feb 1, 2024
f51826c
Merge pull request #1730 from ELIXIR-Belgium/fix_matomo_tracking
kdp-cloud Feb 1, 2024
23c0daa
Merge pull request #1722 from ELIXIR-Belgium/implement_assay_streams_…
kdp-cloud Feb 1, 2024
f994a36
Replace `is_single_page_assay?` by `is_isa_json_compliant?`
kdp-cloud Jan 23, 2024
a1faa5d
Add fix linkage to isa assays after a new one is created.
kdp-cloud Jan 24, 2024
f8c2200
Order assays by position in assay_stream
kdp-cloud Jan 24, 2024
3e0237b
Create function to find the input attribute
kdp-cloud Jan 25, 2024
8b5db61
Add functions to find the next and previous linked sample type
kdp-cloud Jan 25, 2024
6b06477
Simplify dynamic table helper
kdp-cloud Jan 26, 2024
ce06b7c
Fix sample type linkage when inserting new assays
kdp-cloud Jan 26, 2024
69a4ef6
Rearrange assay positions when inserting or deleting assays
kdp-cloud Jan 26, 2024
61c374f
Move code to private section
kdp-cloud Jan 26, 2024
bdd97c4
simplify assay linkage when deleting
kdp-cloud Jan 26, 2024
af66b53
Split functionality over assay and isa assay
kdp-cloud Jan 26, 2024
e1c7903
Delete ST first, fix linkage later
kdp-cloud Jan 29, 2024
f4b6783
Simplify deletion of linked sampletypes in studies
kdp-cloud Jan 29, 2024
532c9f3
Fix existing assays controller tests
kdp-cloud Jan 29, 2024
88c2053
Fix existing studies_controller tests
kdp-cloud Jan 29, 2024
50dfe2a
Correct sample type linkage
kdp-cloud Jan 30, 2024
4a6c0eb
Fix existing tests
kdp-cloud Jan 30, 2024
8366b9e
Write test for inserting new assay between assay stream and first assay
kdp-cloud Jan 30, 2024
78c3a7e
Write test for inserting an assay between two experimental assays
kdp-cloud Jan 30, 2024
fc4c991
Actually better as a before_action since the sample_type is created b…
kdp-cloud Jan 30, 2024
d2d1a90
Change the button text when inserting an assay between existing assays
kdp-cloud Jan 30, 2024
3f75302
Modify existing tests for inserting assays
kdp-cloud Jan 30, 2024
183c8ed
Disable button when inserting an assay before an assay with samples i…
kdp-cloud Jan 30, 2024
a09434b
Add test for disabled button
kdp-cloud Jan 30, 2024
518b8ce
Test prevent inserting new assay if next assay's sample type has samples
kdp-cloud Jan 30, 2024
d8aec7d
do not rearrange position if not isa json compliant or if assay stream
kdp-cloud Jan 30, 2024
735896e
Fix tests
kdp-cloud Jan 30, 2024
1ef73ff
test assay position after deletion
kdp-cloud Feb 1, 2024
755b553
seed examples for creating extended metadata type for SEEK resources
whomingbird Feb 1, 2024
279695e
clean up seed file
whomingbird Feb 1, 2024
e255e68
Order assay streams by position
kdp-cloud Feb 1, 2024
d9c8af5
Test positions after creating intermediate assays
kdp-cloud Feb 1, 2024
eb5ef8f
fix for handling missing filename in biomodels result #1729
stuzart Jan 31, 2024
2a462b4
fix the exception handling #1729
stuzart Jan 31, 2024
3b45e1f
update simple-spreadsheet-extractor gem to fix #1728
stuzart Feb 1, 2024
4156488
Merge branch 'seek-1.14' into main
stuzart Feb 2, 2024
102aeb9
Fix / simplify unit tests
kdp-cloud Feb 2, 2024
8a6c20c
Fix the existing functional tests
kdp-cloud Feb 2, 2024
cd7198d
version 1.14.2
stuzart Feb 2, 2024
33a4e0c
Test isa asssay positions
kdp-cloud Feb 2, 2024
90b782c
Merge branch 'seek-1.14' into main
stuzart Feb 2, 2024
f7154c1
update class parameter passed to `new_assay_path`
kdp-cloud Feb 2, 2024
a749164
Fix assays controller tests
kdp-cloud Feb 2, 2024
120b852
Merge pull request #1739 from ELIXIR-Belgium/fix_functional_assays_co…
kdp-cloud Feb 2, 2024
433a80c
Bump nokogiri from 1.14.5 to 1.16.2
dependabot[bot] Feb 6, 2024
50e216c
update controller to take and handle a comma separated list of root u…
stuzart Feb 6, 2024
9323541
update the ols root term validation to support comma separated #1690
stuzart Feb 6, 2024
07ab74b
pluralized ols_root_to_uri database field on sample controlled vocabs…
stuzart Feb 6, 2024
186cbde
pluralized root_uris parameter used to fetch terms #1690
stuzart Feb 6, 2024
65c6e47
handle multiple root uris when showing the CV #1690
stuzart Feb 6, 2024
fab6eb2
fix javascript for deleting new terms #1690
stuzart Feb 6, 2024
d839fb1
Merge pull request #1735 from ELIXIR-Belgium/issue_1656_create_an_ass…
kdp-cloud Feb 7, 2024
5a3c22a
Use instance name in large file warning (for git file). Fixes #1733
fbacall Feb 7, 2024
2d64a26
Fix managing git files with `.json` extension responding with JSON in…
fbacall Feb 7, 2024
85c26d7
Monkeypatch MimeNegotiation to ignore format from extension
fbacall Feb 8, 2024
46bdb16
Patch `ignore_format_from_extension` into `ActionController::Base`
fbacall Feb 8, 2024
ad1d8f8
update docker compose to use mysql 8.0 #1743
stuzart Feb 7, 2024
e48f637
Merge pull request #1745 from seek4science/git-response-fix
fbacall Feb 8, 2024
a21c3df
updates to the file view icon (magnifier) to also link to explore for…
stuzart Feb 5, 2024
99c8e3f
Update syntax
kdp-cloud Feb 2, 2024
c238b88
Add link between template attribute and sample attribute by adding a …
kdp-cloud Feb 2, 2024
48c99d7
Add sample type level function
kdp-cloud Feb 5, 2024
3dcd518
Select ISA tags based on the level
kdp-cloud Feb 5, 2024
8e46c0c
Add template attribute id to the template creation modal
kdp-cloud Feb 5, 2024
58ad6b8
Display ISA Tag options depending on the level
kdp-cloud Feb 5, 2024
f36e5f2
Add template attribute id to the sample attribute forms
kdp-cloud Feb 5, 2024
05b76f4
Add template_attribute_id to the controller params
kdp-cloud Feb 5, 2024
6f68473
Add constraint to edit isa tag in sample_type
kdp-cloud Feb 5, 2024
5e8dbc3
test allow editing isa tag constraint
kdp-cloud Feb 6, 2024
abeb4a3
Add `parent_attribute_id` to template_attributes table with index
kdp-cloud Feb 6, 2024
8098e8f
Add relationship to template attributes
kdp-cloud Feb 6, 2024
c9caefd
Fix typo and update schema
kdp-cloud Feb 6, 2024
6247378
Add parent attribute id to templates controller
kdp-cloud Feb 6, 2024
158d943
Add parent_attribute to form and simplify to rely less on JS
kdp-cloud Feb 6, 2024
b2092aa
Avoid error when sample attribute is initialized and title is nil
kdp-cloud Feb 6, 2024
bf17af7
Simplify logic of input row
kdp-cloud Feb 6, 2024
d11c0f8
Add constraints to template attributes and remove complex javascript
kdp-cloud Feb 6, 2024
83e08ab
Add model functions
kdp-cloud Feb 6, 2024
cd8362f
Remove the Add attribute button if template has child templates
kdp-cloud Feb 6, 2024
ae87660
Reimplement isa_tags fixture
kdp-cloud Feb 6, 2024
5cffb9a
Prohibit deleting templates that have child templates
kdp-cloud Feb 9, 2024
c29a34d
Run migrations after rebase
kdp-cloud Feb 12, 2024
b12fd2c
Tets ISA Tag changed
kdp-cloud Feb 12, 2024
1a48180
test editable isa tags in template
kdp-cloud Feb 12, 2024
d903454
Clean up
kdp-cloud Feb 12, 2024
ae505c9
allow sample_controlled_vocab update if can_edit? #1693
stuzart Feb 8, 2024
eeb94b2
also tie sample_controlled_vocab destroy to can_delete? #1693
stuzart Feb 8, 2024
f3647e4
fix integration api tests #1693
stuzart Feb 9, 2024
c97e83e
Better handling of errors resulting from XHR. Fixes #1750
fbacall Feb 15, 2024
170c4c7
Requests from PR
kdp-cloud Feb 15, 2024
2982633
Add test for `inherited_from_template_attribute?`
kdp-cloud Feb 15, 2024
2af4a0c
Merge pull request #1751 from seek4science/issue-1750
fbacall Feb 15, 2024
228fbb8
Fix tests
kdp-cloud Feb 15, 2024
d830144
extended metadata types administer route, action and permissions #1649
stuzart Feb 12, 2024
e7a3c1d
fix the extended metadata types view folder name #1649
stuzart Feb 12, 2024
7d7611b
Revert "fix the extended metadata types view folder name #1649"
stuzart Feb 12, 2024
cfeaff7
start basic table #1649
stuzart Feb 12, 2024
08f358d
started adding ability to enable / disable EMT's #1649
stuzart Feb 12, 2024
4fcc5e3
fixed tests #1649
stuzart Feb 13, 2024
44580db
split table by top level and nested emt #1649
stuzart Feb 13, 2024
8d35464
dont show disabled emt's as an option to use #1649
stuzart Feb 13, 2024
f2296db
dont show extended metadata if it's type is disabled #1649
stuzart Feb 13, 2024
14afac1
add Manage extended metadata types to admin page #1649
stuzart Feb 13, 2024
6609ac4
cannot create new with disabled extended metadata types, but can upda…
stuzart Feb 13, 2024
7f2a370
handle editing an item with disabled extended metadata #1649
stuzart Feb 14, 2024
5316c54
some text, and a warning when disabling a used type is disabled #1649
stuzart Feb 14, 2024
c94f280
update Usage column title to be clearer #1649
stuzart Feb 14, 2024
3952872
do not display the extended types for the current version #1649
stuzart Feb 14, 2024
5e259fb
hide from api if disabled #1649
stuzart Feb 14, 2024
0292a88
Capitalize the Manage* links at the top right of the admin page #1649
stuzart Feb 16, 2024
697fd01
a little styling of table based on PR requests #1649
stuzart Feb 16, 2024
e8138ba
a test for the fainter text for disabled #1649
stuzart Feb 16, 2024
02f5ec3
Remove unused variable
kdp-cloud Feb 20, 2024
657f1a6
Lock inherited sample attributes
kdp-cloud Feb 21, 2024
2395946
Merge pull request #1749 from ELIXIR-Belgium/issue_1737_fix_isa_tags_…
kdp-cloud Feb 21, 2024
46d1995
Making it possible to reorder Sample Attributes in a ISA JSON complia…
kdp-cloud Feb 21, 2024
2e88af7
Add column reordering to the DataTable.js
kdp-cloud Feb 21, 2024
64dacd5
Display the sample metadata in the same order as the sample attribute…
kdp-cloud Feb 22, 2024
0af587d
Add alert in case of error
kdp-cloud Feb 23, 2024
11aa640
Add error handling
kdp-cloud Feb 23, 2024
7a63fa8
Change status key to sampleUploadAction
kdp-cloud Feb 23, 2024
b1bb8d0
Add definition for Single Page + help text.
kdp-cloud Feb 26, 2024
fd2dc33
Add definition for Default View + help text.
kdp-cloud Feb 26, 2024
d58722e
Change buttons
kdp-cloud Feb 26, 2024
7608261
Abstract modals to partial html files
kdp-cloud Feb 26, 2024
343a0fe
Add `projectDefaultPolicy` to show pages
kdp-cloud Feb 26, 2024
5c1326a
Revert to default
kdp-cloud Feb 26, 2024
2910300
Delete auth lookup records asynchronously. Fixes #1628
fbacall Oct 26, 2023
34463d5
Test fix
fbacall Oct 26, 2023
7888d43
optimise the query to delete by asset_id, but leave by user_id as it …
stuzart Feb 16, 2024
c5ff4ff
adjusted the batch sizes #1628
stuzart Feb 20, 2024
51b3223
a job to delete a batch of samples #1628
stuzart Feb 20, 2024
7f2bc8f
test updates #1628
stuzart Feb 20, 2024
52b9721
Merge pull request #1763 from ELIXIR-Belgium/fix_batch_upload_dynamic…
kdp-cloud Feb 28, 2024
a07e400
Merge pull request #1761 from ELIXIR-Belgium/issue_1756_fix_sample_at…
kdp-cloud Feb 28, 2024
c4c00d0
fix test susceptible to random failures
stuzart Feb 28, 2024
9c84d27
Add nf-core scraper
fbacall Jan 4, 2024
812607f
Add option to scrape all tags, not just latest
fbacall Jan 15, 2024
30fc252
Update nextflow logo
fbacall Jan 16, 2024
968ef4f
Bump rails from 6.1.7.6 to 6.1.7.7
dependabot[bot] Feb 28, 2024
000df83
Remove redundant code
fbacall Feb 28, 2024
cb3c9ce
Allow Galaxy instance to be specified per workflow
fbacall Aug 17, 2022
c12e9fa
Update to use direct TRS URL import method in Galaxy
fbacall May 16, 2023
12e2985
Fix Galaxy TRS import URL
fbacall May 16, 2023
6a8bc3d
Fix `superclass mismatch for class ...` when running all tests
fbacall May 16, 2023
c839a4f
Remove spurious params
fbacall May 16, 2023
3171d3d
Extract workflow execution instance URL
fbacall May 16, 2023
7415fa6
Update factory calls
fbacall Feb 28, 2024
5e7c61a
Merge pull request #1767 from seek4science/nfcore-scraper
fbacall Feb 28, 2024
fe3c237
Fix metadata not being pulled from base extractor in ROLike
fbacall Feb 28, 2024
69c56b7
Use `Git::Blob`s instead of `File`s in extractors called from `GitRep…
fbacall Feb 28, 2024
fb7fa84
Merge pull request #1764 from ELIXIR-Belgium/make_single_pages_name_v…
kdp-cloud Feb 29, 2024
9af40ab
Tolerate blob not being found
fbacall Feb 29, 2024
eb2fa35
Bump yard from 0.9.27 to 0.9.35
dependabot[bot] Feb 28, 2024
07dcbb8
`Git::Blob#path` is not the local file path
fbacall Feb 29, 2024
2e4b96c
Update Galaxy workflow endpoints
fbacall Feb 29, 2024
c7d822b
Escape `?` in regex
fbacall Mar 1, 2024
d18adb0
Bump yard from 0.9.35 to 0.9.36
dependabot[bot] Mar 1, 2024
c2e115b
Fix blank project ID breaking projects selector
fbacall Feb 29, 2024
322076f
Formatting
fbacall Mar 1, 2024
350d196
Seed Minimal starter templates as upgrade task
kdp-cloud Mar 5, 2024
a75ee56
Also include investigations where is_isa_json_compliant is nil
kdp-cloud Mar 5, 2024
b48860b
Fix assay streams upgrade task
kdp-cloud Mar 5, 2024
a3e3e97
Update Workflow RO-Crate generation to match 1.0 spec
fbacall Mar 5, 2024
eed66e7
Update blob size because of RO-Crate metadata changes
fbacall Mar 5, 2024
6493c70
Merge pull request #1770 from seek4science/galaxy-link-rebased
fbacall Mar 5, 2024
7e610f3
Merge pull request #1773 from ELIXIR-Belgium/fix_seek_upgrade_tasks
kdp-cloud Mar 6, 2024
97168a7
Display template_attribute even if Sample Controlled vocab is `nil`.
kdp-cloud Mar 6, 2024
e04dcf5
Add generic attribute validation to template_attribute model
kdp-cloud Mar 6, 2024
146c257
Make an exception Isa Json compliant sample attributes and template a…
kdp-cloud Mar 6, 2024
03bd537
update github actions for cache, checkout, and setup-java - due to de…
stuzart Feb 28, 2024
e587a7b
Initial attempt at custom OIDC provider
fbacall Mar 7, 2024
f94e51a
Add sample_attribute_types to tests
kdp-cloud Mar 8, 2024
109209f
Replace isa_tag by isa_tag_id
kdp-cloud Mar 8, 2024
4d1f2d8
Add test for defining input template attributes
kdp-cloud Mar 8, 2024
55322ec
Revert isa_tag_id to isa_tag
kdp-cloud Mar 8, 2024
45c6cf5
Add test for registered samples attributes
kdp-cloud Mar 8, 2024
180ce85
Add test for preventing the user to make controlled vocabulary templa…
kdp-cloud Mar 8, 2024
4f0c539
1. Allowing users with edit rights to delete their uploaded fulltext …
whomingbird Mar 8, 2024
d26e9b5
Add test for preventing the user to make controlled vocabulary list t…
kdp-cloud Mar 8, 2024
8273d68
Allow custom OIDC provider to be configured
fbacall Mar 8, 2024
06db35b
Change hard coded 'Single Page' text to variable.
kdp-cloud Mar 11, 2024
b5f689d
Bump json-jwt from 1.15.3 to 1.15.3.1
dependabot[bot] Mar 6, 2024
6519496
Merge pull request #1782 from seek4science/seek-1.14-publication
whomingbird Mar 11, 2024
b78584d
Allow OIDC provider to be given custom login button image
fbacall Mar 11, 2024
b6a5177
Improve omniauth failure error message. Fixes #756
fbacall Mar 11, 2024
623e59a
Redirect to root after successful omniauth login following a failure.…
fbacall Mar 11, 2024
07fcfa9
Merge remote-tracking branch 'origin/seek-1.14' into main
stuzart Mar 12, 2024
4caba75
Mock auth needs to be a symbol apparently
fbacall Mar 12, 2024
8b83927
Merge pull request #1778 from seek4science/workflow-crate-updates
fbacall Mar 13, 2024
27aa3e5
Provide redirect URI etc. info next to each omniauth provider #1415
fbacall Mar 13, 2024
1119d48
Add legacy option to LS Login settings. Fixes #1030
fbacall Mar 13, 2024
948d354
Don't use legacy `/identities/auth/...` route for redirect URIs going…
fbacall Mar 13, 2024
2c5048f
flag content blob to be deleted after asset deleted, and filter from …
stuzart Mar 11, 2024
5005cb2
Set LS Login legacy mode for existing users
fbacall Mar 14, 2024
f80240d
Prefer `omniauth_method_name`
fbacall Mar 14, 2024
0a479c0
Makes more sense
kdp-cloud Mar 15, 2024
b2a8389
Don't take into account sample attributes
kdp-cloud Mar 15, 2024
4ff34f8
add write api for extended metadata feature
whomingbird Mar 15, 2024
babd0f1
test WriteAPI for Extended Metadata with Study model
whomingbird Mar 15, 2024
ee7627c
add updated example json files
whomingbird Mar 15, 2024
37d36c5
test WriteAPI for Extended Metadata with Project model
whomingbird Mar 15, 2024
305142e
Merge pull request #1787 from seek4science/oidc-provider
fbacall Mar 15, 2024
8ea97d3
Merge pull request #1781 from ELIXIR-Belgium/fix_controlled_vocabs_in…
kdp-cloud Mar 15, 2024
7361723
test WriteAPI for Extended Metadata with Document model
whomingbird Mar 15, 2024
33445ea
update schemas.yml for the rest resources which support Extended Meta…
whomingbird Mar 15, 2024
c2687cf
add extendedMetadataAttributeMap for extended metadata in schema
whomingbird Mar 18, 2024
6ef2745
Merge pull request #1789 from seek4science/extended_metadata_write_api
whomingbird Mar 18, 2024
f1f3d90
job to remove deleted content blobs every 24 hours #1788
stuzart Mar 14, 2024
8c37c5e
clear names for variables and methods #1788
stuzart Mar 14, 2024
04b83ad
convert float sample attributes from string when serializing #1791
stuzart Mar 19, 2024
c1e4b4d
expanded max sample and sample type to include int, bool and float #1791
stuzart Mar 19, 2024
d00c448
removed unnecessary assertion in test #1791
stuzart Mar 19, 2024
b680f6d
beginnings of an integration test for sitemaps #1794
stuzart Mar 20, 2024
9547c71
some refactoring and make /sitemap.xml available with a sym link #1794
stuzart Mar 20, 2024
1f18599
test some of the content #1794
stuzart Mar 20, 2024
fb2ba4b
tests to skip disabled, and only include visible #1794
stuzart Mar 20, 2024
8507781
test site.xml #1794
stuzart Mar 20, 2024
277bfe9
rubocop #1794
stuzart Mar 20, 2024
fcf49e7
trigger sitemap build during docker startup
stuzart Mar 20, 2024
e1ba088
add the changeref and priority to resource sitemap
stuzart Mar 20, 2024
0fbbbf7
set the individual resource changefreq to weekly #1794
stuzart Mar 20, 2024
05e8694
avoid error being logged for routes not linked to a controller #1794
stuzart Mar 20, 2024
cbf25f4
clear the util cache to prevent disabled types appearing #1794
stuzart Mar 20, 2024
f70d3c1
there was already a method to clear the cache #1794
stuzart Mar 20, 2024
bce6286
try clearing the cache before and after and _enabled config is change…
stuzart Mar 20, 2024
d96f00d
fix test after resolving caching problem #1794
stuzart Mar 21, 2024
ac7684d
final tweaks and tidying up #1794
stuzart Mar 21, 2024
9341fb3
control seek and supercronic logging for docker #1797
stuzart Mar 22, 2024
641fd77
switch to the 1.15-dev image
stuzart Mar 22, 2024
a0c8de6
changed the env variable to RAILS_LOG_LEVEL #1797
stuzart Mar 25, 2024
f99a7b6
Bump stringio from 3.0.1 to 3.0.1.1
dependabot[bot] Mar 25, 2024
6cc5c2a
Bump rdoc from 6.5.0 to 6.5.1.1
dependabot[bot] Mar 25, 2024
f6387cf
Merge remote-tracking branch 'Seek-1.14/seek-1.15' into merge-seek1.1…
ReneHaensel Mar 26, 2024
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
2 changes: 1 addition & 1 deletion .github/workflows/ansible-install.yml
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:

steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Configure ansible for local install
working-directory: /home/runner/work/seek/seek/script/ansible/
Expand Down
32 changes: 5 additions & 27 deletions .github/workflows/docker-image.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,8 @@ on:
- main
- workflow
- workflowhub
- seek-1.11
- seek-1.12
- seek-1.13
- master-ibisba-demonstrator
- ruby-3
- full-test-suite

pull_request:

jobs:
Expand All @@ -23,25 +20,6 @@ jobs:
if: ${{ github.event.workflow_run.conclusion == 'success' }}
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v2
- id: generate-image-tag
name: Generate Image Tag
env:
ref_name: "${{ github.ref_name }}"
head_ref: "${{ github.head_ref }}"
run: |
ref_name="${head_ref:-${ref_name/main/latest}}"
echo "::set-output name=imageTag::${ref_name#v}"
- name: Login to Container Registry
uses: docker/login-action@v1
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Build and Push
uses: docker/build-push-action@v2
with:
context: .
push: true
tags: ghcr.io/${{ github.repository }}:${{ steps.generate-image-tag.outputs.imageTag }}
- uses: actions/checkout@v4
- name: Build the Docker image
run: docker build . --file Dockerfile --tag test-image:$(date +%s)
6 changes: 3 additions & 3 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -66,9 +66,9 @@ jobs:
sudo apt install -y graphicsmagick graphviz libcurl4-gnutls-dev libreoffice poppler-utils build-essential \
git imagemagick libgmp-dev python3.9-dev python3.9-distutils python3-pip
- name: Checkout code
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Setup Java
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: 'temurin'
java-version: '11' # The JDK version to make available on the path.
Expand All @@ -77,7 +77,7 @@ jobs:
with:
bundler-cache: true # runs 'bundle install' and caches installed gems automatically
- name: Cache pip
uses: actions/cache@v3
uses: actions/cache@v4
with:
# This path is specific to Ubuntu
path: ~/.cache/pip
Expand Down
10 changes: 5 additions & 5 deletions Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ gem 'hpricot', '~>0.8.2'
gem 'libxml-ruby', '~>2.9.0', require: 'libxml'
gem 'uuid', '~>2.3'
gem 'RedCloth', '>=4.3.0'
gem 'simple-spreadsheet-extractor', '~> 0.18.0'
gem 'simple-spreadsheet-extractor', '0.18.1'
gem 'open4'
gem 'sample-template-generator', '~>0.7'
gem 'rmagick', '5.3.0'
Expand Down Expand Up @@ -54,14 +54,14 @@ gem 'will_paginate', '~> 3.1'
gem 'yaml_db'
gem 'rails_autolink'
gem 'rfc-822'
gem 'nokogiri', '~> 1.14.3'
gem 'nokogiri', '~> 1.16.2'
#necessary for newer hashie dependency, original api_smith is no longer active
gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b'
gem 'rdf-virtuoso', '>= 0.2.0'
gem 'terrapin'
gem 'lograge'
gem 'psych'
gem 'stringio', '3.0.1' #locked to the default version for ruby 3.1
gem 'stringio', '3.0.1.1' #locked to the default version for ruby 3.1
gem 'validate_url'
gem "attr_encrypted", "~> 3.0.0"
gem 'libreconv'
Expand Down Expand Up @@ -163,6 +163,8 @@ gem 'net-ftp'

gem 'licensee'

gem "sitemap_generator", "~> 6.3"

group :production do
gem 'passenger'
end
Expand Down Expand Up @@ -207,5 +209,3 @@ group :test, :development do
gem 'teaspoon'
gem 'teaspoon-mocha'
end

gem "sitemap_generator", "~> 6.3"
Loading