From 4fad05322257218ed8671a2a4f282dfa01a48453 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 11:17:57 +0200 Subject: [PATCH 01/36] Final implementation details for ro-crate posting --- _plugins/api.rb | 53 ++++++++++++++++++++----------------------------- 1 file changed, 22 insertions(+), 31 deletions(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index f838af9b316bcd..d068bb4ba0911e 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -346,11 +346,6 @@ def generate(site) Jekyll::Hooks.register :site, :post_write do |site| # No need to run this except in prod. if Jekyll.env == 'production' - # Import on-demand - require 'securerandom' - require 'zip' - - dir = File.join(site.dest, 'api', 'workflows') # Public tool listing: reorganised if site.data['public-server-tools'] && site.data['public-server-tools']['tools'] @@ -404,6 +399,11 @@ def generate(site) end end + # Import on-demand + require 'securerandom' + require 'zip' + + dir = File.join(site.dest, 'api', 'workflows') # ro-crate-metadata.json TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material| @@ -431,6 +431,9 @@ def generate(site) path = File.join(wfdir, 'ro-crate-metadata.json') Jekyll.logger.debug "[GTN/API/WFRun] Writing #{path}" + # Replace last / with # to make a valid URL + wfurlid = site.config['url'] + site.config['baseurl'] + '/' + workflow['path'].gsub(%r{/workflows/}, '/workflows#') + uuids = workflow['creators'].map do |c| if c.key?('identifier') && !c['identifier'].empty? "https://orcid.org/#{c['identifier']}" @@ -449,31 +452,25 @@ def generate(site) license = workflow['license'] ? "https://spdx.org/licenses/#{workflow['license']}" : 'https://spdx.org/licenses/CC-BY-4.0' crate = { - '@context' => 'https://w3id.org/ro/crate/1.1/context', + '@context' => ['https://w3id.org/ro/crate/1.1/context'], '@graph' => [ - # { - # '@id': './', - # '@type': 'Dataset', - # datePublished: workflow['modified'], - # }, { '@id': 'ro-crate-metadata.json', '@type': 'CreativeWork', about: { - '@id': './' + '@id': wfurlid, + }, + conformsTo: { + '@id': 'https://w3id.org/ro/crate/1.1' }, - conformsTo: [ - { - '@id': 'https://w3id.org/ro/crate/1.1' - }, - { - '@id': 'https://about.workflowhub.eu/Workflow-RO-Crate/' - } - ] }, { - '@id': './', + '@id': wfurlid, '@type': 'Dataset', + name: workflow['name'], + description: 'Galaxy workflow', + version: Gtn::ModificationTimes.obtain_modification_count(workflow['path']).to_s, + license: license, datePublished: workflow['modified'].strftime('%Y-%m-%dT%H:%M:%S.%L%:z'), # hasPart: [ # { @@ -482,7 +479,10 @@ def generate(site) # ], mainEntity: { '@id': "#{wfname}.ga" - } + }, + hasPart: [{ + '@id': "#{wfname}.ga" + }] }, { '@id': "#{wfname}.ga", @@ -492,20 +492,11 @@ def generate(site) ComputationalWorkflow ], author: author_uuids, - license: { - '@id': license, - }, name: workflow['name'], - version: Gtn::ModificationTimes.obtain_modification_count(workflow['path']), programmingLanguage: { '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy' } }, - { - '@id': license, - '@type': 'CreativeWork', - name: workflow['license'], - }, { '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy', '@type': 'ComputerLanguage', From d9696c16375788c36e9a6d7b45aba7f969aa9f00 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Sun, 23 Jun 2024 10:10:41 +0200 Subject: [PATCH 02/36] whatever --- ...67347324e0fd530e5f3a44ffca81fd9f5068ac.txt | 111578 --------------- ...67347324e0fd530e5f3a44ffca81fd9f5068ac.txt | 19179 --- 2 files changed, 130757 deletions(-) delete mode 100644 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shared/images/suffix_trie_4.png -A shared/images/suffix_trie_5.png -A shared/images/suffix_trie_6.png -A shared/images/suffix_trie_7.png -A shared/images/suffix_trie_8.png -A shared/images/suffix_trie_9.png -A shared/images/tophat.png -A shared/images/tophat2.png -A shared/images/tophat_interface.png -A shared/images/tophat_output.png -A shared/images/trie.png -A shared/images/trie_no_end.png -A shared/images/ucsc_dm3.png -A shared/images/vcfallelicprimitives.png -A shared/images/within_norm.png -GTN_GTN:1468271001 - -R100 ChIPseq/ChIPseq.md ChIP-Seq/ChIPseq.md -R100 Data_Sources/Data_Sources.md Dev-Corner/Data-Sources/Data_Sources.md -R100 Data_Sources/images/data_source_integration.png Dev-Corner/Data-Sources/images/data_source_integration.png -GTN_GTN:1468270836 - -R100 genome-annotation/general-introduction/Aspergillus_sequence.fasta Genome-Annotation/general-introduction/Aspergillus_sequence.fasta -R100 genome-annotation/general-introduction/README.md Genome-Annotation/general-introduction/README.md -R100 genome-annotation/general-introduction/Streptomyces_coelicolor_part.genbank Genome-Annotation/general-introduction/Streptomyces_coelicolor_part.genbank -R100 genome-annotation/general-introduction/antismash_full.png Genome-Annotation/general-introduction/antismash_full.png -R100 genome-annotation/general-introduction/augustus.png Genome-Annotation/general-introduction/augustus.png -R100 genome-annotation/general-introduction/augustus_out.png Genome-Annotation/general-introduction/augustus_out.png -R100 genome-annotation/general-introduction/barchart_sequencecomposition.png Genome-Annotation/general-introduction/barchart_sequencecomposition.png -R100 genome-annotation/general-introduction/blast database.png Genome-Annotation/general-introduction/blast database.png -R100 genome-annotation/general-introduction/blastP.png Genome-Annotation/general-introduction/blastP.png -R100 genome-annotation/general-introduction/blastprograms.png Genome-Annotation/general-introduction/blastprograms.png -R100 genome-annotation/general-introduction/fasta_format.png Genome-Annotation/general-introduction/fasta_format.png -R100 genome-annotation/general-introduction/gb_full.png Genome-Annotation/general-introduction/gb_full.png -R100 genome-annotation/general-introduction/gff3_format.png Genome-Annotation/general-introduction/gff3_format.png -R100 genome-annotation/general-introduction/selectlines.png Genome-Annotation/general-introduction/selectlines.png -R100 genome-annotation/general-introduction/work flow_Screenshot from 2015-06-23 09-33-23.png Genome-Annotation/general-introduction/work flow_Screenshot from 2015-06-23 09-33-23.png -GTN_GTN:1468270812 - -R100 Methylation-Seq/Methylation-Seq.md MethylC-Seq/Methylation-Seq.md -GTN_GTN:1468270779 - -R100 rna-seq/rna-seq.md RNA-Seq/rna-seq.md -GTN_GTN:1468270375 - -R100 Galaxy_Introduction/Galaxy_Introduction.md Introduction/Galaxy_Introduction.md -R100 Galaxy_Introduction/images/Interval2Bed_1.png Introduction/images/Interval2Bed_1.png -R100 Galaxy_Introduction/images/SInterval2Bed_2.png Introduction/images/SInterval2Bed_2.png -R100 Galaxy_Introduction/images/rename_history.png Introduction/images/rename_history.png -R100 Galaxy_Introduction/images/sample_workflow.png Introduction/images/sample_workflow.png -R100 Galaxy_Introduction/images/screenshot.jpg Introduction/images/screenshot.jpg -R100 Galaxy_Introduction/images/upload_button.png Introduction/images/upload_button.png -R100 Galaxy_Introduction/slides/Introduction_to_Galaxy_Uni.pdf Introduction/slides/Introduction_to_Galaxy_Uni.pdf -R100 Galaxy_Introduction/slides/Manke_2015.09.21a.pdf Introduction/slides/Manke_2015.09.21a.pdf -R100 Galaxy_Introduction/tables/Galaxy1-GSE37268_mof3.out.hpeak.txt Introduction/tables/Galaxy1-GSE37268_mof3.out.hpeak.txt -R100 Galaxy_Introduction/tables/Galaxy12-unique_gene_names.tabular Introduction/tables/Galaxy12-unique_gene_names.tabular -R100 Galaxy_Introduction/tables/Galaxy2-UCSC_Main_on_Mouse__refGene_genome.bed Introduction/tables/Galaxy2-UCSC_Main_on_Mouse__refGene_genome.bed -R100 Galaxy_Introduction/tables/Galaxy8-Count_genes_on_different_chromosomes.tabular Introduction/tables/Galaxy8-Count_genes_on_different_chromosomes.tabular -R100 Galaxy_Introduction/tables/Galaxy9-Count_genes_on_different_chromosomes.tabular Introduction/tables/Galaxy9-Count_genes_on_different_chromosomes.tabular -GTN_GTN:1460560217 - -A Galaxy_Introduction/images/upload_button.png -GTN_GTN:1460558464 - -A IGV_Introduction/images/callout_1.jpg -A IGV_Introduction/images/callout_2.jpg -A IGV_Introduction/images/callout_3.jpg -A IGV_Introduction/images/callout_4.jpg -A IGV_Introduction/images/callout_5.jpg -A IGV_Introduction/images/callout_6.jpg -A IGV_Introduction/images/callout_7.jpg -GTN_GTN:1460557942 - -A IGV_Introduction/images/icon_backforward.jpg -A IGV_Introduction/images/icon_genome.jpg -A IGV_Introduction/images/icon_genome_dropdown.jpg -A IGV_Introduction/images/icon_popuponoff.jpg -A IGV_Introduction/images/icon_refresh.jpg -A IGV_Introduction/images/icon_region_of_interest.jpg -A IGV_Introduction/images/icon_squish.jpg -A IGV_Introduction/images/icon_zoom.jpg -A IGV_Introduction/images/igv_chromdrop.jpg -A IGV_Introduction/images/searchbox.jpg -GTN_GTN:1460554942 - -A IGV_Introduction/images/ChIP-Seq_bigwig.png -A IGV_Introduction/images/data_range.png -A IGV_Introduction/images/load_encode_RNA-seq_BAM.png -A IGV_Introduction/images/sashimi_plot.png -A IGV_Introduction/images/view_pairs.png -GTN_GTN:1460459040 - -A Data_Sources/images/data_source_integration.png -GTN_GTN:1460369230 - -R100 Galaxy_Introduction/Introduction_to_Galaxy_Uni.pdf Galaxy_Introduction/slides/Introduction_to_Galaxy_Uni.pdf -R100 Galaxy_Introduction/Manke_2015.09.21a.pdf Galaxy_Introduction/slides/Manke_2015.09.21a.pdf -GTN_GTN:1460367850 - -A Galaxy_Introduction/images/Interval2Bed_1.png -A Galaxy_Introduction/images/SInterval2Bed_2.png -A Galaxy_Introduction/images/rename_history.png -A Galaxy_Introduction/images/sample_workflow.png -A Galaxy_Introduction/images/screenshot.jpg -GTN_GTN:1460367097 - -A Galaxy_Introduction/tables/Galaxy12-unique_gene_names.tabular -A Galaxy_Introduction/tables/Galaxy2-UCSC_Main_on_Mouse__refGene_genome.bed -A Galaxy_Introduction/tables/Galaxy8-Count_genes_on_different_chromosomes.tabular -A Galaxy_Introduction/tables/Galaxy9-Count_genes_on_different_chromosomes.tabular -GTN_GTN:1460365652 - -R100 Galaxy_Introduction/tables/Galaxy1-GSE37268_mof3.out.hpeak.txt.interval Galaxy_Introduction/tables/Galaxy1-GSE37268_mof3.out.hpeak.txt -GTN_GTN:1460365318 - -A Galaxy_Introduction/tables/Galaxy1-GSE37268_mof3.out.hpeak.txt.interval -GTN_GTN:1459522661 - -A CONTRIBUTORS.md -GTN_GTN:1459321658 - -A Data_Sources/Data_Sources.md -GTN_GTN:1459321614 - -A IGV_Introduction/IGV_Introduction.md -GTN_GTN:1459320281 - -R100 rna-seq/README.md rna-seq/rna-seq.md -GTN_GTN:1459320229 - -R100 Galaxy_Introduction/README.md Galaxy_Introduction/Galaxy_Introduction.md -GTN_GTN:1459264798 - -A Galaxy_Introduction/Introduction_to_Galaxy_Uni.pdf -A Galaxy_Introduction/Manke_2015.09.21a.pdf -A Galaxy_Introduction/README.md -GTN_GTN:1459246240 - -A useful_literatur/reading_suggestions.md -GTN_GTN:1459238641 - -A Methylation-Seq/Methylation-Seq.md -GTN_GTN:1458644937 - -A Exome-Seq/Exome-Seq.md -GTN_GTN:1458644909 - -R100 ChIPseq.md ChIPseq/ChIPseq.md -GTN_GTN:1458644317 - -A ChIPseq.md -GTN_GTN:1435651101 - -A rna-seq/README.md -GTN_GTN:1435577008 - -A LICENSE.txt -GTN_GTN:1435576550 - -A genome-annotation/general-introduction/README.md -GTN_GTN:1435573329 - -A README.md -A genome-annotation/general-introduction/Aspergillus_sequence.fasta -A genome-annotation/general-introduction/Streptomyces_coelicolor_part.genbank -A genome-annotation/general-introduction/antismash_full.png -A genome-annotation/general-introduction/augustus.png -A genome-annotation/general-introduction/augustus_out.png -A genome-annotation/general-introduction/barchart_sequencecomposition.png -A genome-annotation/general-introduction/blast database.png -A genome-annotation/general-introduction/blastP.png -A genome-annotation/general-introduction/blastprograms.png -A genome-annotation/general-introduction/fasta_format.png -A genome-annotation/general-introduction/gb_full.png -A genome-annotation/general-introduction/gff3_format.png -A genome-annotation/general-introduction/selectlines.png -A genome-annotation/general-introduction/work flow_Screenshot from 2015-06-23 09-33-23.png From 418a1d017db90fbc380cbe12c8834c596606c29e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 11:30:54 +0200 Subject: [PATCH 03/36] Implement upload --- .github/workflows/workflowhub.yml | 49 +++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 .github/workflows/workflowhub.yml diff --git a/.github/workflows/workflowhub.yml b/.github/workflows/workflowhub.yml new file mode 100644 index 00000000000000..8d8e8d1d24d4d8 --- /dev/null +++ b/.github/workflows/workflowhub.yml @@ -0,0 +1,49 @@ +name: "[Cron] Upload workflows to (DEV)WorkflowHub" + +on: + schedule: + # * is a special character in YAML so you have to quote this string + # We'll run this daily at noon. + - cron: '59 12 * * *' + workflow_dispatch: + +jobs: + runner-job: + if: github.repository_owner == 'galaxyproject' + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 200 + + # BEGIN Dependencies + - uses: ruby/setup-ruby@v1 + with: + ruby-version: "3.0" + - uses: actions/cache@v2 + with: + path: | + vendor/bundle + ~/.npm + key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}-node-${{ hashFiles('**/package-lock.json') }} + restore-keys: | + ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}-node- + ${{ runner.os }}-gems- + - name: Install dependencies + run: | + gem install bundler + bundle config path vendor/bundle + bundle install --jobs 4 --retry 3 + bundle pristine ffi + # END Dependencies + + - name: Build Site + run: | + JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material + + - name: Upload workflows + run: | + find _site/training-material/api/workflows/ -name 'rocrate.zip' | xargs -P 1 -I {} curl -L -X POST -H "Authorization: Token $DEV_WFH_TOKEN" -F 'workflow[project_ids][]=63' -F 'ro_crate=@{}' https://dev.workflowhub.eu/workflows/submit + env: + DEV_WFH_TOKEN: ${{ secrets.DEV_WFH_TOKEN }} From 31f7b5661c812318855abd1e93da6bf3d79ca2db Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 11:46:02 +0200 Subject: [PATCH 04/36] use better separable folders --- _plugins/api.rb | 2 +- _plugins/jekyll-topic-filter.rb | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index d068bb4ba0911e..844564b58ee7a2 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -426,7 +426,7 @@ def generate(site) # "test_results"=>nil, # "modified"=>2023-06-07 12:09:36.12 +0200} - wfdir = File.join(dir, wfid, wfname) + wfdir = File.join(dir, workflow['topic_id'], workflow['tutorial_id'], wfname) FileUtils.mkdir_p(wfdir) path = File.join(wfdir, 'ro-crate-metadata.json') Jekyll.logger.debug "[GTN/API/WFRun] Writing #{path}" diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 52c41351a83202..6e46f4b61e90c1 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -585,6 +585,9 @@ def self.resolve_material(site, material) 'wfname' => wfname, 'trs_endpoint' => "#{domain}/#{trs}", 'license' => license, + 'parent_id' => page_obj['id'], + 'topic_id' => page['topic_name'], + 'tutorial_id' => page['tutorial_name'], 'creators' => creators, 'name' => wf_json['name'], 'title' => wftitle, From 14cdb9ff8743d3082e7762c65bdc2b80ca36e891 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 11:51:45 +0200 Subject: [PATCH 05/36] add wfh uploader --- bin/wfh-upload.py | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 bin/wfh-upload.py diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py new file mode 100644 index 00000000000000..39c3b8d62ab39b --- /dev/null +++ b/bin/wfh-upload.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python +import os +import requests +import glob +import time + +crates = glob.glob( + "_site/training-material/api/workflows/**/rocrate.zip", recursive=True +) + +for crate_path in crates: + # _site/training-material/api/workflows/proteomics/proteogenomics-novel-peptide-analysis/galaxy-workflow-mouse_novel_peptide_analysis/rocrate.zip + p = crate_path.split("/") + (topic, tutorial, workflow) = p[4:7] + + payload = { + "ro_crate": (crate_path, open(crate_path, "rb")), + "workflow[project_ids][]": (None, 63), + } + headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"]} + + response = requests.post( + "https://dev.workflowhub.eu/workflows/submit", files=payload, headers=headers + ) + code = response.status_code + if code != 200: + print(f"Error {code} uploading {crate_path}") + print(response.text) + continue + + data = response.json() + wf_id = data["data"]["id"] + print(f"Uploaded {crate_path} as workflow {wf_id}") + # time.sleep(1) From 9e5ace1deac2bfe3f4c67b2d9dcf2d29b202b57e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 11:52:29 +0200 Subject: [PATCH 06/36] better script --- .github/workflows/workflowhub.yml | 8 ++++++-- bin/wfh-upload.py | 0 2 files changed, 6 insertions(+), 2 deletions(-) mode change 100644 => 100755 bin/wfh-upload.py diff --git a/.github/workflows/workflowhub.yml b/.github/workflows/workflowhub.yml index 8d8e8d1d24d4d8..b93241bf4f2b45 100644 --- a/.github/workflows/workflowhub.yml +++ b/.github/workflows/workflowhub.yml @@ -18,9 +18,13 @@ jobs: fetch-depth: 200 # BEGIN Dependencies + - uses: actions/setup-python@v2 + with: + python-version: '3.11' + architecture: 'x64' - uses: ruby/setup-ruby@v1 with: - ruby-version: "3.0" + ruby-version: "3.1" - uses: actions/cache@v2 with: path: | @@ -44,6 +48,6 @@ jobs: - name: Upload workflows run: | - find _site/training-material/api/workflows/ -name 'rocrate.zip' | xargs -P 1 -I {} curl -L -X POST -H "Authorization: Token $DEV_WFH_TOKEN" -F 'workflow[project_ids][]=63' -F 'ro_crate=@{}' https://dev.workflowhub.eu/workflows/submit + python bin/wfh-upload.py env: DEV_WFH_TOKEN: ${{ secrets.DEV_WFH_TOKEN }} diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py old mode 100644 new mode 100755 From 30a0aa9aeffba9c927369bc721fcceff26a46c25 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 12:39:56 +0200 Subject: [PATCH 07/36] formatting --- _plugins/api.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index 844564b58ee7a2..6d0b805b8b10be 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -408,7 +408,6 @@ def generate(site) # ro-crate-metadata.json TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material| material['workflows'].each do |workflow| - wfid = workflow['wfid'] wfname = workflow['wfname'] # {"workflow"=>"galaxy-workflow-mouse_novel_peptide_analysis.ga", # "tests"=>false, @@ -432,7 +431,8 @@ def generate(site) Jekyll.logger.debug "[GTN/API/WFRun] Writing #{path}" # Replace last / with # to make a valid URL - wfurlid = site.config['url'] + site.config['baseurl'] + '/' + workflow['path'].gsub(%r{/workflows/}, '/workflows#') + wfurlid = site.config['url'] + site.config['baseurl'] + '/' + workflow['path'].gsub(%r{/workflows/}, + '/workflows#') uuids = workflow['creators'].map do |c| if c.key?('identifier') && !c['identifier'].empty? From 1f38e89d211aa0cf9c05cbb914a6930228a42961 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 12:53:24 +0200 Subject: [PATCH 08/36] parallelise --- bin/wfh-upload.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 39c3b8d62ab39b..a757be9a462d04 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -1,15 +1,16 @@ #!/usr/bin/env python import os +import sys import requests import glob import time +import multiprocessing crates = glob.glob( "_site/training-material/api/workflows/**/rocrate.zip", recursive=True ) -for crate_path in crates: - # _site/training-material/api/workflows/proteomics/proteogenomics-novel-peptide-analysis/galaxy-workflow-mouse_novel_peptide_analysis/rocrate.zip +def doUpload(crate_path): p = crate_path.split("/") (topic, tutorial, workflow) = p[4:7] @@ -25,10 +26,18 @@ code = response.status_code if code != 200: print(f"Error {code} uploading {crate_path}") - print(response.text) - continue + # sys.stdout.write('!') + return response.text + # sys.stdout.write('.') data = response.json() wf_id = data["data"]["id"] - print(f"Uploaded {crate_path} as workflow {wf_id}") - # time.sleep(1) + return f"Uploaded {crate_path} as workflow {wf_id}" + + +with multiprocessing.Pool(8) as p: + results = p.map(doUpload, crates) + +print() +for result in results: + print(result) From 8ae6eb87182d12c6fd0161f0d3599bb04d2ee8e0 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 22 Apr 2024 13:11:48 +0200 Subject: [PATCH 09/36] save yaml --- bin/wfh-upload.py | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index a757be9a462d04..7b70b3708ebfcb 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +import yaml import os import sys import requests @@ -18,7 +19,7 @@ def doUpload(crate_path): "ro_crate": (crate_path, open(crate_path, "rb")), "workflow[project_ids][]": (None, 63), } - headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"]} + headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"], 'User-Agent': 'github.com/galaxyproject/training-material@1.0'} response = requests.post( "https://dev.workflowhub.eu/workflows/submit", files=payload, headers=headers @@ -26,18 +27,22 @@ def doUpload(crate_path): code = response.status_code if code != 200: print(f"Error {code} uploading {crate_path}") - # sys.stdout.write('!') - return response.text - # sys.stdout.write('.') + print(response.text) + return None data = response.json() wf_id = data["data"]["id"] - return f"Uploaded {crate_path} as workflow {wf_id}" + return (topic, tutorial, workflow, wf_id) -with multiprocessing.Pool(8) as p: +with multiprocessing.Pool(4) as p: results = p.map(doUpload, crates) -print() -for result in results: - print(result) +results = [x for x in results if x is not None] + +data = {} +for (topic, tutorial, workflow, wf_id) in results: + data.setdefault(topic, {}).setdefault(tutorial, {})[workflow] = wf_id + +with open('metadata/workflowhub.yml', 'w') as handle: + yaml.dump(data, handle) From e969800bfc4f76e09ebe70c43b50a20a331c3fe0 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 23 Apr 2024 15:13:36 +0200 Subject: [PATCH 10/36] add pngs to crates --- _plugins/api.rb | 32 +++++++++++++++- _plugins/jekyll-topic-filter.rb | 66 ++++++++++++++++++++++++++++++++- 2 files changed, 95 insertions(+), 3 deletions(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index 6d0b805b8b10be..127f368b6d79bd 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -406,8 +406,11 @@ def generate(site) dir = File.join(site.dest, 'api', 'workflows') # ro-crate-metadata.json + crate_start = Time.now + count = 0 TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material| material['workflows'].each do |workflow| + count += 1 wfname = workflow['wfname'] # {"workflow"=>"galaxy-workflow-mouse_novel_peptide_analysis.ga", # "tests"=>false, @@ -429,6 +432,11 @@ def generate(site) FileUtils.mkdir_p(wfdir) path = File.join(wfdir, 'ro-crate-metadata.json') Jekyll.logger.debug "[GTN/API/WFRun] Writing #{path}" + # We have the `dot` graph code in a variable, we need to pass it to `dot -T png ` on the stdin + dot_path = File.join(wfdir, "graph.dot") + File.write(dot_path, workflow['graph_dot']) + Jekyll.logger.debug "[GTN/API/WFRun] dot -T png #{dot_path} > graph.png" + `dot -T png '#{dot_path}' > '#{File.join(wfdir, 'graph.png')}'` # Replace last / with # to make a valid URL wfurlid = site.config['url'] + site.config['baseurl'] + '/' + workflow['path'].gsub(%r{/workflows/}, @@ -480,9 +488,14 @@ def generate(site) mainEntity: { '@id': "#{wfname}.ga" }, - hasPart: [{ + hasPart: [ + { '@id': "#{wfname}.ga" - }] + }, + { + '@id': "graph.png" + }, + ] }, { '@id': "#{wfname}.ga", @@ -495,8 +508,20 @@ def generate(site) name: workflow['name'], programmingLanguage: { '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy' + }, + image: { + '@id': 'graph.png' } }, + { + '@id': 'graph.png', + '@type': [ + 'File', + 'ImageObject', + 'WorkflowSketch' + ], + contentSize: File.size(File.join(wfdir, 'graph.png')), + }, { '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy', '@type': 'ComputerLanguage', @@ -519,9 +544,12 @@ def generate(site) # - The name of the file as it will appear in the archive # - The original file, including the path to find it zipfile.add('ro-crate-metadata.json', path) + zipfile.add('graph.png', File.join(wfdir, 'graph.png')) zipfile.add("#{wfname}.ga", workflow['path']) end end end + + Jekyll.logger.debug "[GTN/API/WFRun] RO-Crate Metadata written in #{Time.now - crate_start} seconds for #{count} workflows" end end diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 6e46f4b61e90c1..060acf37b47da2 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -455,6 +455,69 @@ def self.mermaid(wf) "flowchart TD\n" + statements.map { |q| " #{q}" }.join("\n") end + def self.graph_dot(wf) + # We're converting it to Mermaid + # flowchart TD + # A[Start] --> B{Is it?} + # B -- Yes --> C[OK] + # C --> D[Rethink] + # D --> B + # B -- No ----> E[End] + # digraph test { + # + # 0[shape=box,style=filled,color=lightblue,label="ℹ️ Input Dataset\nBionano_dataset"] + # 1[shape=box,style=filled,color=lightblue,label="ℹ️ Input Dataset\nHi-C_dataset_R"] + # 3 -> 6 [label="output"] + # 7[shape=box,label="Busco"] + # 4 -> 7 [label="out_fa"] + # 8[shape=box,label="Busco"] + # 5 -> 8 [label="out_fa"] + + statements = [] + wf['steps'].each_key do |id| + step = wf['steps'][id] + chosen_label = mermaid_safe_label(step['label'] || step['name']) + + case step['type'] + when 'data_collection_input' + statements.append "#{id}[shape=box,style=filled,color=lightblue,label=\"ℹ️ Input Collection\\n#{chosen_label}\"]" + when 'data_input' + statements.append "#{id}[shape=box,style=filled,color=lightblue,label=\"ℹ️ Input Dataset\\n#{chosen_label}\"]" + when 'parameter_input' + statements.append "#{id}[shape=box,style=filled,color=lightgreen,label=\"ℹ️ Input Parameter\\n#{chosen_label}\"]" + when 'subworkflow' + statements.append "#{id}[shape=box,style=filled,color=lightcoral,label=\"🛠️ Subworkflow\\n#{chosen_label}\"]" + else + statements.append "#{id}[shape=box,label=\"#{chosen_label}\"]" + end + + step = wf['steps'][id] + step['input_connections'].each do |_, v| + # if v is a list + if v.is_a?(Array) + v.each do |v2| + statements.append "#{v2['id']} -> #{id} [label=\"#{mermaid_safe_label(v2['output_name'])}\"]" + end + else + statements.append "#{v['id']} -> #{id} [label=\"#{mermaid_safe_label(v['output_name'])}\"]" + end + end + + (step['workflow_outputs'] || []) + .reject { |wo| wo['label'].nil? } + .map do |wo| + wo['uuid'] = SecureRandom.uuid.to_s if wo['uuid'].nil? + wo + end + .each do |wo| + statements.append "k#{wo['uuid'].gsub('-', '')}[style=filled,color=lightseagreen,label=\"Output\\n#{wo['label']}\"]" + statements.append "#{id} -> k#{wo['uuid'].gsub('-', '')}" + end + end + + "digraph main {\n" + statements.map { |q| " #{q}" }.join("\n") + "\n}" + end + def self.resolve_material(site, material) # We've already # looked in every /topic/*/tutorials/* folder, and turn these disparate @@ -559,7 +622,7 @@ def self.resolve_material(site, material) workflow_names = workflows.map { |a| a.split('/')[-1] } page_obj['workflows'] = workflow_names.map do |wf| wfid = "#{page['topic_name']}-#{page['tutorial_name']}" - wfname = wf.gsub(/.ga/, '').downcase + wfname = wf.gsub(/.ga/, '').downcase.gsub(/[^a-z0-9]/, '-') trs = "api/ga4gh/trs/v2/tools/#{wfid}/versions/#{wfname}" wf_path = "#{folder}/workflows/#{wf}" wf_json = JSON.parse(File.read(wf_path)) @@ -594,6 +657,7 @@ def self.resolve_material(site, material) 'test_results' => workflow_test_outputs, 'modified' => File.mtime(wf_path), 'mermaid' => mermaid(wf_json), + 'graph_dot' => graph_dot(wf_json), } end end From d2b8ff75bec1992b0812ea6d28368efbc4083c8d Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 24 Apr 2024 16:33:14 +0200 Subject: [PATCH 11/36] aesthetic improvements --- _plugins/jekyll-topic-filter.rb | 24 +++++++++++++++--------- assets/branding/gtn-heart.png | Bin 8793 -> 8781 bytes assets/branding/gtn-logo.png | Bin 47253 -> 47193 bytes assets/branding/gtn-logo@512-bot.png | Bin 0 -> 53261 bytes assets/branding/gtn-logo@512.png | Bin 21515 -> 21491 bytes assets/branding/gtn-workflows.png | Bin 0 -> 12213 bytes 6 files changed, 15 insertions(+), 9 deletions(-) create mode 100644 assets/branding/gtn-logo@512-bot.png create mode 100644 assets/branding/gtn-workflows.png diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 060acf37b47da2..bc65f8a9df3b9a 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -473,22 +473,25 @@ def self.graph_dot(wf) # 8[shape=box,label="Busco"] # 5 -> 8 [label="out_fa"] - statements = [] + statements = [ + 'node [fontname="Atkinson Hyperlegible", shape=box, color=white,style=filled,color=peachpuff,margin="0.2,0.2"];', + 'edge [fontname="Atkinson Hyperlegible"];', + ] wf['steps'].each_key do |id| step = wf['steps'][id] chosen_label = mermaid_safe_label(step['label'] || step['name']) case step['type'] when 'data_collection_input' - statements.append "#{id}[shape=box,style=filled,color=lightblue,label=\"ℹ️ Input Collection\\n#{chosen_label}\"]" + statements.append "#{id}[color=lightblue,label=\"ℹ️ Input Collection\\n#{chosen_label}\"]" when 'data_input' - statements.append "#{id}[shape=box,style=filled,color=lightblue,label=\"ℹ️ Input Dataset\\n#{chosen_label}\"]" + statements.append "#{id}[color=lightblue,label=\"ℹ️ Input Dataset\\n#{chosen_label}\"]" when 'parameter_input' - statements.append "#{id}[shape=box,style=filled,color=lightgreen,label=\"ℹ️ Input Parameter\\n#{chosen_label}\"]" + statements.append "#{id}[color=lightgreen,label=\"ℹ️ Input Parameter\\n#{chosen_label}\"]" when 'subworkflow' - statements.append "#{id}[shape=box,style=filled,color=lightcoral,label=\"🛠️ Subworkflow\\n#{chosen_label}\"]" + statements.append "#{id}[color=lightcoral,label=\"🛠️ Subworkflow\\n#{chosen_label}\"]" else - statements.append "#{id}[shape=box,label=\"#{chosen_label}\"]" + statements.append "#{id}[label=\"#{chosen_label}\"]" end step = wf['steps'][id] @@ -510,11 +513,14 @@ def self.graph_dot(wf) wo end .each do |wo| - statements.append "k#{wo['uuid'].gsub('-', '')}[style=filled,color=lightseagreen,label=\"Output\\n#{wo['label']}\"]" - statements.append "#{id} -> k#{wo['uuid'].gsub('-', '')}" - end + statements.append "k#{wo['uuid'].gsub('-', '')}[color=lightseagreen,label=\"Output\\n#{wo['label']}\"]" + statements.append "#{id} -> k#{wo['uuid'].gsub('-', '')}" + statements.append "k#{wo['uuid'].gsub('-', '')} -> logo" + end end + 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zC32YIKf`j!ozg`T|Gy54_lScr5={CZuso7d6AE>+atH8<@Nxq49?=5+uW*zdEUc~6 ztQ@V~Z2){AWH>(!r>Oof7ylykZ6Qd25U&U)&`GI?0tuk{4~LEu)ZNR%)e7)`X6?%6 zMH3Q5{SOLR3oQzEa`thxwYG5wXn9!L+k$~|P7W5fj!lVt{{+nVKQM@u8`#y>+1=L3 z@xRpiu Date: Sun, 23 Jun 2024 13:20:56 +0200 Subject: [PATCH 12/36] mostly working ro-crate? --- _plugins/api.rb | 141 +----------------- _plugins/gtn.rb | 1 + _plugins/gtn/ro-crate.rb | 208 +++++++++++++++++++++++++++ _plugins/jekyll-topic-filter.rb | 7 +- bin/lint.rb | 6 +- bin/wfh-upload.py | 14 +- faqs/galaxy/workflows_report_view.md | 2 +- 7 files changed, 230 insertions(+), 149 deletions(-) create mode 100644 _plugins/gtn/ro-crate.rb diff --git a/_plugins/api.rb b/_plugins/api.rb index 127f368b6d79bd..1d69fece9c9871 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -6,6 +6,7 @@ require './_plugins/gtn/metrics' require './_plugins/gtn/scholar' require './_plugins/gtn/git' +require './_plugins/gtn/ro-crate' require './_plugins/gtn' ## @@ -401,152 +402,16 @@ def generate(site) # Import on-demand require 'securerandom' - require 'zip' - dir = File.join(site.dest, 'api', 'workflows') + dir = File.join(site.dest, 'api', 'workflows') # ro-crate-metadata.json crate_start = Time.now count = 0 TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material| material['workflows'].each do |workflow| + Gtn::RoCrate.write(dir, workflow, site.config['url'], site.config['baseurl']) count += 1 - wfname = workflow['wfname'] - # {"workflow"=>"galaxy-workflow-mouse_novel_peptide_analysis.ga", - # "tests"=>false, - # "url"=> - # "http://0.0.0.0:4002/training-material/topics/.../workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga", - # "path"=> - # "topics/proteomics/tutorials/.../galaxy-workflow-mouse_novel_peptide_analysis.ga", - # "wfid"=>"proteomics-proteogenomics-novel-peptide-analysis", - # "wfname"=>"galaxy-workflow-mouse_novel_peptide_analysis", - # "trs_endpoint"=> - # "http://0.0.0.0:4002/training-material/api/.../versions/galaxy-workflow-mouse_novel_peptide_analysis", - # "license"=>nil, - # "creators"=>[], - # "name"=>"GTN Proteogemics3 Novel Peptide Analysis", - # "test_results"=>nil, - # "modified"=>2023-06-07 12:09:36.12 +0200} - - wfdir = File.join(dir, workflow['topic_id'], workflow['tutorial_id'], wfname) - FileUtils.mkdir_p(wfdir) - path = File.join(wfdir, 'ro-crate-metadata.json') - Jekyll.logger.debug "[GTN/API/WFRun] Writing #{path}" - # We have the `dot` graph code in a variable, we need to pass it to `dot -T png ` on the stdin - dot_path = File.join(wfdir, "graph.dot") - File.write(dot_path, workflow['graph_dot']) - Jekyll.logger.debug "[GTN/API/WFRun] dot -T png #{dot_path} > graph.png" - `dot -T png '#{dot_path}' > '#{File.join(wfdir, 'graph.png')}'` - - # Replace last / with # to make a valid URL - wfurlid = site.config['url'] + site.config['baseurl'] + '/' + workflow['path'].gsub(%r{/workflows/}, - '/workflows#') - - uuids = workflow['creators'].map do |c| - if c.key?('identifier') && !c['identifier'].empty? - "https://orcid.org/#{c['identifier']}" - else - "##{SecureRandom.uuid}" - end - end - author_uuids = uuids.map { |u| { '@id' => u.to_s } } - author_linked = workflow['creators'].map.with_index do |c, i| - { - '@id' => (uuids[i]).to_s, - '@type' => c['class'], - 'name' => c['name'], - } - end - license = workflow['license'] ? "https://spdx.org/licenses/#{workflow['license']}" : 'https://spdx.org/licenses/CC-BY-4.0' - - crate = { - '@context' => ['https://w3id.org/ro/crate/1.1/context'], - '@graph' => [ - { - '@id': 'ro-crate-metadata.json', - '@type': 'CreativeWork', - about: { - '@id': wfurlid, - }, - conformsTo: { - '@id': 'https://w3id.org/ro/crate/1.1' - }, - }, - { - '@id': wfurlid, - '@type': 'Dataset', - name: workflow['name'], - description: 'Galaxy workflow', - version: Gtn::ModificationTimes.obtain_modification_count(workflow['path']).to_s, - license: license, - datePublished: workflow['modified'].strftime('%Y-%m-%dT%H:%M:%S.%L%:z'), - # hasPart: [ - # { - # '@id': '#assembly-assembly-quality-control' - # } - # ], - mainEntity: { - '@id': "#{wfname}.ga" - }, - hasPart: [ - { - '@id': "#{wfname}.ga" - }, - { - '@id': "graph.png" - }, - ] - }, - { - '@id': "#{wfname}.ga", - '@type': %w[ - File - SoftwareSourceCode - ComputationalWorkflow - ], - author: author_uuids, - name: workflow['name'], - programmingLanguage: { - '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy' - }, - image: { - '@id': 'graph.png' - } - }, - { - '@id': 'graph.png', - '@type': [ - 'File', - 'ImageObject', - 'WorkflowSketch' - ], - contentSize: File.size(File.join(wfdir, 'graph.png')), - }, - { - '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy', - '@type': 'ComputerLanguage', - identifier: { - '@id': 'https://galaxyproject.org/' - }, - name: 'Galaxy', - url: { - '@id': 'https://galaxyproject.org/' - }, - version: '23.1' - } - ] - } - crate['@graph'] += author_linked - File.write(path, JSON.pretty_generate(crate)) - - zip_path = File.join(wfdir, 'rocrate.zip') - Zip::File.open(zip_path, create: true) do |zipfile| - # - The name of the file as it will appear in the archive - # - The original file, including the path to find it - zipfile.add('ro-crate-metadata.json', path) - zipfile.add('graph.png', File.join(wfdir, 'graph.png')) - zipfile.add("#{wfname}.ga", workflow['path']) - end end end diff --git a/_plugins/gtn.rb b/_plugins/gtn.rb index ea45b8b0eb0a24..bfa0a8b45be33d 100644 --- a/_plugins/gtn.rb +++ b/_plugins/gtn.rb @@ -4,6 +4,7 @@ require './_plugins/gtn/contributors' require './_plugins/gtn/boxify' require './_plugins/gtn/mod' +require './_plugins/gtn/ro-crate' require './_plugins/gtn/images' require './_plugins/gtn/synthetic' require './_plugins/gtn/metrics' diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb new file mode 100644 index 00000000000000..91c81778ff3be1 --- /dev/null +++ b/_plugins/gtn/ro-crate.rb @@ -0,0 +1,208 @@ +# frozen_string_literal: true +require 'zip' + + +module Gtn + # Parse the git repo to get some facts + module RoCrate + GLOBAL_WORKFLOW_OFFSET = 0 + + def self.cache + @@cache ||= Jekyll::Cache.new('RoCrate') + end + + def self.name2md(site, name) + return %Q([#{Gtn::Contributors.fetch_name(site, name)}](https://training.galaxyproject.org/training-material/hall-of-fame/#{name}/)) + end + + def self.write(site, dir, associated_material, workflow, url, baseurl, time_based_version: false) + wfname = workflow['wfname'] + # {"workflow"=>"galaxy-workflow-mouse_novel_peptide_analysis.ga", + # "tests"=>false, + # "url"=> + # "http://0.0.0.0:4002/training-material/topics/.../workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga", + # "path"=> + # "topics/proteomics/tutorials/.../galaxy-workflow-mouse_novel_peptide_analysis.ga", + # "wfid"=>"proteomics-proteogenomics-novel-peptide-analysis", + # "wfname"=>"galaxy-workflow-mouse_novel_peptide_analysis", + # "trs_endpoint"=> + # "http://0.0.0.0:4002/training-material/api/.../versions/galaxy-workflow-mouse_novel_peptide_analysis", + # "license"=>nil, + # "creators"=>[], + # "name"=>"GTN Proteogemics3 Novel Peptide Analysis", + # "test_results"=>nil, + # "modified"=>2023-06-07 12:09:36.12 +0200} + + wfdir = File.join(dir, workflow['topic_id'], workflow['tutorial_id'], wfname) + FileUtils.mkdir_p(wfdir) + path = File.join(wfdir, 'ro-crate-metadata.json') + Jekyll.logger.debug "[GTN/API/WFRun] Writing #{path}" + # We have the `dot` graph code in a variable, we need to pass it to `dot -T png ` on the stdin + dot_path = File.join(wfdir, "graph.dot") + File.write(dot_path, workflow['graph_dot']) + Jekyll.logger.debug "[GTN/API/WFRun] dot -T png #{dot_path} > graph.png" + `dot -T png '#{dot_path}' > '#{File.join(wfdir, 'graph.png')}'` + + # Replace last / with # to make a valid URL + wfurlid = url + baseurl + '/' + workflow['path'].gsub(%r{/workflows/}, + '/workflows#') + + uuids = workflow['creators'].map do |c| + if c.key?('identifier') && !c['identifier'].empty? + if c['identifier'].start_with?('http') + c['identifier'] + else + "https://orcid.org/#{c['identifier']}" + end + else + "##{SecureRandom.uuid}" + end + end + author_uuids = uuids.map { |u| { '@id' => u.to_s } } + author_linked = workflow['creators'].map.with_index do |c, i| + { + '@id' => (uuids[i]).to_s, + '@type' => c['class'], + 'name' => c['name'], + } + end + wf_ga = JSON.parse(File.read(workflow['path'])) + + license = workflow['license'] ? "https://spdx.org/licenses/#{workflow['license']}" : 'https://spdx.org/licenses/CC-BY-4.0' + + version = time_based_version ? Time.now.to_i.to_s : Gtn::ModificationTimes.obtain_modification_count(workflow['path']).to_s + ".#{GLOBAL_WORKFLOW_OFFSET}" + + features = { + 'Includes [Galaxy Workflow Tests](https://training.galaxyproject.org/training-material/faqs/gtn/workflow_run_test.html)' => workflow['tests'], + # 'Test results available' => workflow['test_results'], + 'Includes a [Galaxy Workflow Report](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_report_view.html)' => wf_ga.has_key?('report'), + } + + mat_contribs = [ + ['Tutorial Author(s)', Gtn::Contributors.get_authors(associated_material).map { |n| name2md(site, n) }], + ['Tutorial Contributor(s)', Gtn::Contributors.get_non_authors(associated_material).map { |n| name2md(site, n) }], + ['Workflow Author(s)', workflow['creators'].map { |c| c['name'] }], + ['Funder(s)', Gtn::Contributors.get_funders(associated_material).map { |n| name2md(site, n) }], + ].reject { |_, v| v.empty? } + + pp mat_contribs + + description = %Q( +#{wf_ga['annotation']} + +## Associated Tutorial + +This workflows is part of the tutorial [#{workflow['name']}](#{url}#{baseurl}/topics/#{workflow['topic_id']}/tutorials/#{workflow['tutorial_id']}/tutorial.html), available in the [GTN](https://training.galaxyproject.org) + +#{"## Features" if features.values.any?} + +#{features.select { |_, v| v }.keys.map { |f| "* #{f}" }.join("\n")} + +## Thanks to... + +#{mat_contribs.map { |k, v| "**#{k}**: #{v.join(', ')}" }.join("\n\n")} + +[![gtn star logo followed by the word workflows](http://galaxy-training.s3-website.us-east-1.amazonaws.com/misc/gtn-workflows.png)](https://training.galaxyproject.org/training-material/) + ).strip + # ![gtn star logo followed by the word workflows](https://training.galaxyproject.org/training-material/assets/branding/gtn-workflows.png) + + crate = { + '@context' => ['https://w3id.org/ro/crate/1.1/context'], + '@graph' => [ + { + '@id': 'ro-crate-metadata.json', + '@type': 'CreativeWork', + about: { + '@id': wfurlid, + }, + conformsTo: { + '@id': 'https://w3id.org/ro/crate/1.1' + }, + }, + { + '@id': wfurlid, + '@type': 'Dataset', + name: workflow['name'], + description: description, + version: version, + license: license, + datePublished: workflow['modified'].strftime('%Y-%m-%dT%H:%M:%S.%L%:z'), + # hasPart: [ + # { + # '@id': '#assembly-assembly-quality-control' + # } + # ], + mainEntity: { + '@id': "#{wfname}.ga" + }, + hasPart: [ + { + '@id': "#{wfname}.ga" + }, + { + '@id': "graph.png" + }, + ] + }, + { + '@id': "#{wfname}.ga", + '@type': %w[ + File + SoftwareSourceCode + ComputationalWorkflow + ], + author: author_uuids, + name: workflow['name'], + programmingLanguage: { + '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy' + }, + image: { + '@id': 'graph.png' + } + }, + { + '@id': 'graph.png', + '@type': [ + 'File', + 'ImageObject', + 'WorkflowSketch' + ], + contentSize: File.size(File.join(wfdir, 'graph.png')), + }, + { + '@id': 'https://w3id.org/workflowhub/workflow-ro-crate#galaxy', + '@type': 'ComputerLanguage', + identifier: { + '@id': 'https://galaxyproject.org/' + }, + name: 'Galaxy', + url: { + '@id': 'https://galaxyproject.org/' + }, + version: '23.1' + } + ] + } + crate['@graph'] += author_linked + File.write(path, JSON.pretty_generate(crate)) + + wf_ga['tags'].map! { |t| t.gsub('^name:', '').capitalize } + wf_ga.delete('creator') + File.write(File.join(wfdir, 'mod.ga'), JSON.pretty_generate(wf_ga)) + # p "Writing #{File.join(wfdir, 'mod.ga')}" + + zip_path = File.join(wfdir, 'rocrate.zip') + p "[GTN/API/WFRun] Zipping #{zip_path}" + if File.exist?(zip_path) + File.delete(zip_path) + end + Zip::File.open(zip_path, create: true) do |zipfile| + # - The name of the file as it will appear in the archive + # - The original file, including the path to find it + zipfile.add('ro-crate-metadata.json', path) + zipfile.add('graph.png', File.join(wfdir, 'graph.png')) + zipfile.add("#{wfname}.ga", File.join(wfdir, 'mod.ga')) + end + end + end +end diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index bc65f8a9df3b9a..b73afa0850dbea 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -515,12 +515,9 @@ def self.graph_dot(wf) .each do |wo| statements.append "k#{wo['uuid'].gsub('-', '')}[color=lightseagreen,label=\"Output\\n#{wo['label']}\"]" statements.append "#{id} -> k#{wo['uuid'].gsub('-', '')}" - statements.append "k#{wo['uuid'].gsub('-', '')} -> logo" end end - statements.append 'logo[image="assets/branding/gtn-workflows.png", label="", color="white"];' - "digraph main {\n" + statements.map { |q| " #{q}" }.join("\n") + "\n}" end @@ -1042,6 +1039,10 @@ def fetch_tutorial_material(site, topic_name, page_name) TopicFilter.fetch_tutorial_material(site, topic_name, page_name) end + def fetch_tutorial_material_by_id(site, id) + TopicFilter.fetch_tutorial_material(site, id.split('/')[0], id.split('/')[1]) + end + def list_topics_ids(site) ['introduction'] + TopicFilter.list_topics(site).filter { |k| k != 'introduction' } end diff --git a/bin/lint.rb b/bin/lint.rb index 309345b1efafc1..93c88457317eaa 100755 --- a/bin/lint.rb +++ b/bin/lint.rb @@ -1109,11 +1109,11 @@ def self.fix_file(path) else # Load tests and run some quick checks: possible_tests.each do |test_file| - if !test_file.match(/-tests?.yml/) + if !test_file.match(/-tests.yml/) results += [ ReviewDogEmitter.file_error(path: path, - message: 'Please use the extension -test.yml ' \ - 'or -tests.yml for this test file.', + message: 'Please use the extension -tests.yml ' \ + 'for this test file.', code: 'GTN:032') ] end diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 7b70b3708ebfcb..832f59e8bde9d4 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -1,5 +1,6 @@ #!/usr/bin/env python import yaml +import json import os import sys import requests @@ -7,9 +8,12 @@ import time import multiprocessing -crates = glob.glob( - "_site/training-material/api/workflows/**/rocrate.zip", recursive=True -) +if len(sys.argv) == 2: + crates = [sys.argv[1]] +else: + crates = glob.glob( + "_site/training-material/api/workflows/**/rocrate.zip", recursive=True + ) def doUpload(crate_path): p = crate_path.split("/") @@ -19,7 +23,7 @@ def doUpload(crate_path): "ro_crate": (crate_path, open(crate_path, "rb")), "workflow[project_ids][]": (None, 63), } - headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"], 'User-Agent': 'github.com/galaxyproject/training-material@1.0'} + headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"], 'User-Agent': 'GTN (github.com/galaxyproject/training-material@1.0)'} response = requests.post( "https://dev.workflowhub.eu/workflows/submit", files=payload, headers=headers @@ -29,6 +33,8 @@ def doUpload(crate_path): print(f"Error {code} uploading {crate_path}") print(response.text) return None + else: + print(json.loads(response.text)['data']['links']['self']) data = response.json() wf_id = data["data"]["id"] diff --git a/faqs/galaxy/workflows_report_view.md b/faqs/galaxy/workflows_report_view.md index e98693762d5197..500f3ea1c216be 100644 --- a/faqs/galaxy/workflows_report_view.md +++ b/faqs/galaxy/workflows_report_view.md @@ -1,7 +1,7 @@ --- title: Viewing a workflow report area: workflows -description: When creating a workflow in Galaxy, you can also define an output report page that should be created. Here you can display certain outputs of the pipeline (e.g. output files, tables, images, etc.) and other information about the run. +description: You can find the workflow report from the workflow invocation box_type: tip layout: faq contributors: [hexylena,shiltemann] From ed422d24aa95441796ed30914e796ea1ed790fa9 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Sun, 23 Jun 2024 13:48:04 +0200 Subject: [PATCH 13/36] closer to release --- _plugins/gtn/ro-crate.rb | 7 ++++--- bin/wfh-upload.py | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb index 91c81778ff3be1..4257415f8316e9 100644 --- a/_plugins/gtn/ro-crate.rb +++ b/_plugins/gtn/ro-crate.rb @@ -85,8 +85,6 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base ['Funder(s)', Gtn::Contributors.get_funders(associated_material).map { |n| name2md(site, n) }], ].reject { |_, v| v.empty? } - pp mat_contribs - description = %Q( #{wf_ga['annotation']} @@ -187,7 +185,10 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base File.write(path, JSON.pretty_generate(crate)) wf_ga['tags'].map! { |t| t.gsub('^name:', '').capitalize } - wf_ga.delete('creator') + wf_ga['tags'].push('GTN') + wf_ga['tags'].push('Galaxy') + # wf_ga.delete('creator') + File.write(File.join(wfdir, 'mod.ga'), JSON.pretty_generate(wf_ga)) # p "Writing #{File.join(wfdir, 'mod.ga')}" diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 832f59e8bde9d4..e3071f63848ee7 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -21,7 +21,7 @@ def doUpload(crate_path): payload = { "ro_crate": (crate_path, open(crate_path, "rb")), - "workflow[project_ids][]": (None, 63), + "workflow[project_ids][]": (None, 63), # GTN's ID. } headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"], 'User-Agent': 'GTN (github.com/galaxyproject/training-material@1.0)'} From 71c484a1a800ee9fd243df7f33cc5d675a9f45d2 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Sun, 23 Jun 2024 13:52:16 +0200 Subject: [PATCH 14/36] note why --- _plugins/gtn/ro-crate.rb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb index 4257415f8316e9..d6061426e94cff 100644 --- a/_plugins/gtn/ro-crate.rb +++ b/_plugins/gtn/ro-crate.rb @@ -187,8 +187,9 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base wf_ga['tags'].map! { |t| t.gsub('^name:', '').capitalize } wf_ga['tags'].push('GTN') wf_ga['tags'].push('Galaxy') - # wf_ga.delete('creator') - + # TODO: Remove this after https://github.com/seek4science/seek/issues/1927 + wf_ga.delete('creator') + File.write(File.join(wfdir, 'mod.ga'), JSON.pretty_generate(wf_ga)) # p "Writing #{File.join(wfdir, 'mod.ga')}" From 3f90aaaa8e4170618696b3b8c582eed339c717cb Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 11:03:36 +0200 Subject: [PATCH 15/36] start permissions work --- bin/wfh-upload.py | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index e3071f63848ee7..3a8d69662c985e 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -8,6 +8,8 @@ import time import multiprocessing +GTN_PROJECT_ID = 63 + if len(sys.argv) == 2: crates = [sys.argv[1]] else: @@ -21,7 +23,7 @@ def doUpload(crate_path): payload = { "ro_crate": (crate_path, open(crate_path, "rb")), - "workflow[project_ids][]": (None, 63), # GTN's ID. + "workflow[project_ids][]": (None, GTN_PROJECT_ID), # GTN's ID. } headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"], 'User-Agent': 'GTN (github.com/galaxyproject/training-material@1.0)'} @@ -34,7 +36,30 @@ def doUpload(crate_path): print(response.text) return None else: - print(json.loads(response.text)['data']['links']['self']) + print(json.dumps(json.loads(response.text)['data'], indent=2)) + wfid = json.loads(response.text)['data']['id'] + permissions_update = { + "data": { + "id": wfid, + "type": "workflows", + "attributes": { + "policy": { + "access": "download", + "permissions": [ + { + "resource": { + "id": str(GTN_PROJECT_ID), + "type": "projects" + }, + "access": "manage" + } + ] + } + } + } + } + response = requests.put(f"https://workflowhub.eu/workflows/{wfid}", headers=headers, json=permissions_update) + print(response.text) data = response.json() wf_id = data["data"]["id"] From 73a6e8215f8ba602a4f8799b3d217f915a3e6e6b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 11:21:40 +0200 Subject: [PATCH 16/36] hmm --- _plugins/api.rb | 2 +- bin/wfh-upload.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index 1d69fece9c9871..090d9f1c8cb746 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -410,7 +410,7 @@ def generate(site) count = 0 TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material| material['workflows'].each do |workflow| - Gtn::RoCrate.write(dir, workflow, site.config['url'], site.config['baseurl']) + Gtn::RoCrate.write(site, dir, material, workflow, site.config['url'], site.config['baseurl']) count += 1 end end diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 3a8d69662c985e..2d36ecbde70379 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -58,8 +58,10 @@ def doUpload(crate_path): } } } - response = requests.put(f"https://workflowhub.eu/workflows/{wfid}", headers=headers, json=permissions_update) - print(response.text) + response2 = requests.put(f"https://dev.workflowhub.eu/workflows/{wfid}", headers=headers, json=permissions_update) + # print("curl -X PUT -d '" + json.dumps(permissions_update) + "' -H 'authorization: Token " + os.environ["DEV_WFH_TOKEN"] + "' https://workflowhub.eu/workflows/" + wfid) + print(response2.text) + sys.exit(1) data = response.json() wf_id = data["data"]["id"] From 346bced1f9154590deaed65b3fa038aa8e11e1b3 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 11:59:48 +0200 Subject: [PATCH 17/36] better handling around permissions --- bin/wfh-upload.py | 59 +++++++++++++++++++++++++---------------------- 1 file changed, 31 insertions(+), 28 deletions(-) diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 2d36ecbde70379..2e8c2a0e4120aa 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -25,7 +25,10 @@ def doUpload(crate_path): "ro_crate": (crate_path, open(crate_path, "rb")), "workflow[project_ids][]": (None, GTN_PROJECT_ID), # GTN's ID. } - headers = {"authorization": "Token " + os.environ["DEV_WFH_TOKEN"], 'User-Agent': 'GTN (github.com/galaxyproject/training-material@1.0)'} + headers = { + "authorization": "Token " + os.environ["DEV_WFH_TOKEN"], + 'User-Agent': 'GTN (github.com/galaxyproject/training-material@1.0)', + } response = requests.post( "https://dev.workflowhub.eu/workflows/submit", files=payload, headers=headers @@ -35,37 +38,37 @@ def doUpload(crate_path): print(f"Error {code} uploading {crate_path}") print(response.text) return None - else: - print(json.dumps(json.loads(response.text)['data'], indent=2)) - wfid = json.loads(response.text)['data']['id'] - permissions_update = { - "data": { - "id": wfid, - "type": "workflows", - "attributes": { - "policy": { - "access": "download", - "permissions": [ - { - "resource": { - "id": str(GTN_PROJECT_ID), - "type": "projects" - }, - "access": "manage" - } - ] + + wfid = response.json()['data']['id'] + permissions_update = { + "data": { + "id": wfid, + "type": "workflows", + "attributes": { + "policy": { + "access": "download", + "permissions": [ + { + "resource": { + "id": str(GTN_PROJECT_ID), + "type": "projects" + }, + "access": "manage" } - } + ] } } - response2 = requests.put(f"https://dev.workflowhub.eu/workflows/{wfid}", headers=headers, json=permissions_update) - # print("curl -X PUT -d '" + json.dumps(permissions_update) + "' -H 'authorization: Token " + os.environ["DEV_WFH_TOKEN"] + "' https://workflowhub.eu/workflows/" + wfid) - print(response2.text) - sys.exit(1) + } + } + headers.update({ + 'Content-type': 'application/json', + 'Accept': 'application/json', + }) + response2 = requests.put(f"https://dev.workflowhub.eu/workflows/{wfid}", headers=headers, json=permissions_update) + if response2.status_code != 200: + print(f"Error {response2.status_code} updating permissions for {wfid}: {response2.text}") - data = response.json() - wf_id = data["data"]["id"] - return (topic, tutorial, workflow, wf_id) + return (topic, tutorial, workflow, wfid) with multiprocessing.Pool(4) as p: From 5fff1ef1ec5cbf4bd7a048a4aa7303d6977e8c51 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 12:00:33 +0200 Subject: [PATCH 18/36] document why --- .github/workflows/workflowhub.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/workflowhub.yml b/.github/workflows/workflowhub.yml index b93241bf4f2b45..58693007acd5b4 100644 --- a/.github/workflows/workflowhub.yml +++ b/.github/workflows/workflowhub.yml @@ -42,6 +42,7 @@ jobs: bundle pristine ffi # END Dependencies + # Required to build the RO-Crates - name: Build Site run: | JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material From be225b42660ff16ca008f1631687c7601361583e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 12:08:32 +0200 Subject: [PATCH 19/36] add ROR ids --- ORGANISATIONS.yaml | 30 ++++++++++++++++++++++++++++-- bin/schema-organisations.yaml | 5 +++++ 2 files changed, 33 insertions(+), 2 deletions(-) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index 777f3aaf442a43..4817d2975d7121 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -19,16 +19,19 @@ avans-atgm: joined: 2020-11 url: https://avans.nl avatar: "/training-material/shared/images/logo-avans.png" + ror: "015d5s513" carpentries: name: The Carpentries joined: 2021-09 + ror: "0356fgm10" earlham: name: Earlham Institute joined: 2017-09 url: https://www.earlham.ac.uk/ avatar: "/training-material/shared/images/earlham_logo.svg" + ror: "018cxtf62" edctp: name: EDCTP @@ -36,18 +39,21 @@ edctp: url: https://www.edctp.org/ avatar: "/training-material/shared/images/edctp.jpg" github: false + ror: "031jv9v19" egi: name: EGI url: https://www.egi.eu/ avatar: https://cdn.egi.eu/app/uploads/2021/11/egi-logo.svg github: false + ror: "052jj4m32" elixir-europe: name: ELIXIR Europe joined: 2017-09 url: https://elixir-europe.org avatar: "/training-material/shared/images/elixir.png" + ror: "044rwnt51" elixir-goblet-ttt: name: ELIXIR Goblet Train the Trainers @@ -61,6 +67,7 @@ embl-ebi: url: https://www.ebi.ac.uk avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/d0fccaa9dc8dc8615eb7146d6c5e96bd36f11f3a/EMBL_EBI_Logo_black.svg github: false + ror: "02catss52" erasmusmc: name: ErasmusMC @@ -68,12 +75,14 @@ erasmusmc: url: https://www.erasmusmc.nl avatar: "/training-material/shared/images/logo-erasmusmc.png" github: false + ror: "018906e22" eu: name: The European Union url: https://european-union.europa.eu avatar: "/training-material/shared/images/EU-logo.jpg" github: false + ror: "019w4f821" find: name: FIND @@ -81,23 +90,27 @@ find: url: https://www.finddx.org/ avatar: "/training-material/shared/images/FIND.png" github: false + ror: "05tcsqz68" ifb: name: Institut Français de Bioinformatique url: https://www.france-bioinformatique.fr/ avatar: "/training-material/shared/images/ifb.png" github: false + ror: "045f7pv37" inab-certh: name: INAB|CERTH url: "https://www.inab.certh.gr/" avatar: "/training-material/shared/images/inab-certh.png" + ror: "03bndpq63" irccs: name: IRCCS Ospedale San Raffaele url: "https://www.hsr.it/" avatar: "/training-material/shared/images/irccs.jpg" github: false + ror: "039zxt351" jetstream2: name: JetStream @@ -110,6 +123,7 @@ johnshopkins: url: "https://www.jhu.edu/" avatar: "/training-material/shared/images/hopkins.png" github: false + ror: "00za53h95" linq: name: LINQ @@ -123,17 +137,20 @@ minnesotauni: url: "https://twin-cities.umn.edu/" avatar: "/training-material/shared/images/minnesotauni.png" github: false + ror: "017zqws13" MPIIE: name: Max Planck Institute of Immunology and Epigenetics url: https://www.ie-freiburg.mpg.de avatar: https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif github: false + ror: "058xzat49" ncbi: name: National Center for Biotechnology Information url: "https://www.ncbi.nlm.nih.gov/" avatar: "/training-material/shared/images/ncbi.png" + ror: "02meqm098" panacea: name: PanACEA @@ -153,6 +170,7 @@ petermac: name: Peter MacCallum Cancer Centre url: "https://www.petermac.org/" avatar: "/training-material/shared/images/petermac.png" + ror: "02a8bt934" pndb: name: Pôle National de Données de Biodiversité @@ -165,36 +183,42 @@ psu: url: http://www.psu.edu avatar: "/training-material/shared/images/psu.png" github: false + ror: "04p491231" qiime2: name: QIIME2 url: https://qiime2.org/ avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4 + sanbi: name: SANBI/UWC url: https://www.sanbi.org/ avatar: "/training-material/shared/images/sanbi.png" description: "South African National Bioinformatics Institute, University of the Western Cape" github: false + ror: "005r3tp02" san-raffaele-uni: name: Università Vita-Salute San Raffaele url: "https://www.unisr.it/" avatar: "/training-material/shared/images/uni_san_raffaele.svg" github: false + ror: "01gmqr298" sciensano: name: Sciensano url: "https://www.sciensano.be" avatar: "/training-material/shared/images/sciensano.jpg" github: false + ror: "04ejags36" swiss-tph: name: Swiss Tropical and Public Health Institute url: https://www.swisstph.ch/en/ avatar: "/training-material/shared/images/swiss-tph.png" github: false + ror: "03adhka07" tb-capt: name: TB-CAPT @@ -207,23 +231,25 @@ uga: url: https://www.univ-grenoble-alpes.fr/ avatar: /training-material/shared/images/logo-uga.svg github: false + ror: "02rx3b187" uni-freiburg: name: University of Freiburg url: https://www.uni-freiburg.de/ avatar: https://raw.githubusercontent.com/bgruening/presentations/a2e38e4b007994af798320db3a0131c4bb891c0e/shared/resources/img/logo_freiburg.jpg github: false + ror: "0245cg223" UTas: name: University of Tasmania url: https://www.utas.edu.au/ avatar: "/training-material/shared/images/UTas_logo.png" github: false + ror: "01nfmeh72" vib: name: Vlaams Instituut voor Biotechnologie url: https://vib.be/ avatar: "/training-material/shared/images/logo-vib.png" github: false - - + ror: "03xrhmk39" diff --git a/bin/schema-organisations.yaml b/bin/schema-organisations.yaml index 1f34176aacc146..a06af6d24fd72e 100644 --- a/bin/schema-organisations.yaml +++ b/bin/schema-organisations.yaml @@ -79,6 +79,11 @@ mapping: - 2020-01 avatar: type: str + ror: + type: str + description: ROR ID from https://ror.org/ + _examples: + - "019w4f821" url: type: str description: associated webpage (NOTE, funders only!) From 2067e4cab2305f55340846d7b0c90b88134db136 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 14:20:25 +0200 Subject: [PATCH 20/36] wip per-wf page --- _layouts/workflow.html | 136 ++++++++++++++++++++++++++++++++ _plugins/generator-workflows.rb | 55 +++++++++++++ _plugins/gtn/ro-crate.rb | 1 + 3 files changed, 192 insertions(+) create mode 100644 _layouts/workflow.html create mode 100644 _plugins/generator-workflows.rb diff --git a/_layouts/workflow.html b/_layouts/workflow.html new file mode 100644 index 00000000000000..fce64811904050 --- /dev/null +++ b/_layouts/workflow.html @@ -0,0 +1,136 @@ +--- +layout: base +--- + +{% assign material = page.material %} +{% assign workflow = page.workflow %} + + + + + + diff --git a/_plugins/generator-workflows.rb b/_plugins/generator-workflows.rb new file mode 100644 index 00000000000000..6789bc93fa4053 --- /dev/null +++ b/_plugins/generator-workflows.rb @@ -0,0 +1,55 @@ +# frozen_string_literal: true + +require './_plugins/gtn' + +module Jekyll + ## + # This class generates the GTN's author pags + class WorkflowPageGenerator < Generator + safe true + + ## + # This generates the recording pages, where needed. + # Params + # +site+:: The site object + def generate(site) + Jekyll.logger.info "[GTN/Workflows] Generating workflow pages" + materials = TopicFilter + .list_all_materials(site) + + # [{"workflow"=>"Calling_variants_in_non-diploid_systems.ga", + # "tests"=>true, + # "url"=>"https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/workflows/Calling_variants_in_non-diploid_systems.ga", + # "path"=>"topics/variant-analysis/tutorials/non-dip/workflows/Calling_variants_in_non-diploid_systems.ga", + # "wfid"=>"variant-analysis-non-dip", + # "wfname"=>"calling-variants-in-non-diploid-systems", + # "trs_endpoint"=>"https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-non-dip/versions/calling-variants-in-non-diploid-systems", + # "license"=>nil, + # "parent_id"=>"variant-analysis/non-dip", + # "topic_id"=>"variant-analysis", + # "tutorial_id"=>"non-dip", + # "creators"=>[], + # "name"=>"Calling variants in non-diploid systems", + # "title"=>"Calling variants in non-diploid systems", + # "test_results"=>nil, + # "modified"=>2024-03-18 12:38:46.293831071 +0100, + # "mermaid"=> + # "graph_dot"=> + # }] + # /api/workflows/#{topic_id}/#{tutorial_id}/#{wfid}/rocrate.zip + + materials.each do |material| + (material['workflows'] || []).each do |workflow| + page2 = PageWithoutAFile.new(site, '', material['dir'], "workflows/#{workflow['wfname']}.html") + page2.content = nil + page2.data['layout'] = 'workflow' + page2.data['material'] = material + page2.data['workflow'] = workflow + page2.data['js_requirements'] = {'mathjax' => false, 'mermaid' => true} + site.pages << page2 + end + end + end + end +end + diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb index d6061426e94cff..43ea618757115e 100644 --- a/_plugins/gtn/ro-crate.rb +++ b/_plugins/gtn/ro-crate.rb @@ -72,6 +72,7 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base version = time_based_version ? Time.now.to_i.to_s : Gtn::ModificationTimes.obtain_modification_count(workflow['path']).to_s + ".#{GLOBAL_WORKFLOW_OFFSET}" + # TODO: move this into jekyll-topic-filter where its discovered. features = { 'Includes [Galaxy Workflow Tests](https://training.galaxyproject.org/training-material/faqs/gtn/workflow_run_test.html)' => workflow['tests'], # 'Test results available' => workflow['test_results'], From 893a987ab92cf28dde8119fe727f0ddb2281b72e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 14:48:41 +0200 Subject: [PATCH 21/36] more annotations --- _layouts/workflow.html | 44 ++++++++++++++++++++++++--------- _plugins/gtn/ro-crate.rb | 6 ++--- _plugins/jekyll-topic-filter.rb | 8 ++++++ 3 files changed, 44 insertions(+), 14 deletions(-) diff --git a/_layouts/workflow.html b/_layouts/workflow.html index fce64811904050..2d4ccde79bef97 100644 --- a/_layouts/workflow.html +++ b/_layouts/workflow.html @@ -14,8 +14,8 @@

{{ workflow.title }}

{{ workflow.wfid }}/{{ workflow.wfname }}

- {% if workflow.description %} -

{{ workflow.description }}

+ {% if workflow.annotation %} +

{{ workflow.annotation }}

{% endif %}
@@ -51,22 +51,34 @@

{{ workflow.title }}

None Specified, defaults to CC-BY-4.0 {% endif %} - - Features + {% if workflow.tags %} + {% icon galaxy-tags %} + Tags
+ {{ workflow.tags | join: ", " }} +
+ {% endif %} + + Features + {{ workflow.features }} -
+
- {% if workflow.tags %} - {% icon galaxy-tags %} {{ workflow.tags | join: ", " }} -
- {% endif %} Tutorial
@@ -128,6 +140,16 @@

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them! {% snippet faqs/galaxy/workflows_import.md box_type="hands_on" %} + +

For Admins

+

Installing the workflow tools

+ + 
+wget {{ site.url }}{{ site.baseurl }}/{{ workflow.path }} -O workflow.ga
+workflow-to-tools -w workflow.ga -o tools.yaml
+shed-tools install -g GALAXY -a API_KEY -t tools.yaml
+workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows
+
diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb index 43ea618757115e..4450a4968f2e61 100644 --- a/_plugins/gtn/ro-crate.rb +++ b/_plugins/gtn/ro-crate.rb @@ -72,11 +72,11 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base version = time_based_version ? Time.now.to_i.to_s : Gtn::ModificationTimes.obtain_modification_count(workflow['path']).to_s + ".#{GLOBAL_WORKFLOW_OFFSET}" - # TODO: move this into jekyll-topic-filter where its discovered. features = { 'Includes [Galaxy Workflow Tests](https://training.galaxyproject.org/training-material/faqs/gtn/workflow_run_test.html)' => workflow['tests'], - # 'Test results available' => workflow['test_results'], - 'Includes a [Galaxy Workflow Report](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_report_view.html)' => wf_ga.has_key?('report'), + 'Includes a [Galaxy Workflow Report](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_report_view.html)' => workflow['features']['report'], + 'Uses [Galaxy Workflow Comments](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_comments.html)' => workflow['features']['comments'], + 'Uses [subworkflows](https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_subworkflows.html)' => workflow['features']['subworkflows'], } mat_contribs = [ diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 3f4d22309eb017..2556f46740f669 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -657,6 +657,14 @@ def self.resolve_material(site, material) 'creators' => creators, 'name' => wf_json['name'], 'title' => wftitle, + 'description' => wf_json['annotation'], + 'tags' => wf_json['tags'], + 'features' => { + 'report' => wf_json['report'], + 'subworkflows' => wf_json['steps'].map{|_, x| x['type']}.any?{|x| x == "subworkflow"}, + 'comments' => (wf_json['comments'] || []).length.positive?, + 'parameters' => wf_json['steps'].map{|_, x| x['type']}.any?{|x| x == "parameter_input"}, + }, 'test_results' => workflow_test_outputs, 'modified' => File.mtime(wf_path), 'mermaid' => mermaid(wf_json), From 533beb1ef777a1ba2eada22c35a4f6128d9e0d8f Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 16:15:08 +0200 Subject: [PATCH 22/36] add shortlinks for WFs --- _plugins/gtn.rb | 4 ++++ _plugins/gtn/shortlinks.rb | 17 +++++++++++++++++ 2 files changed, 21 insertions(+) diff --git a/_plugins/gtn.rb b/_plugins/gtn.rb index bfa0a8b45be33d..d58671865d07a5 100644 --- a/_plugins/gtn.rb +++ b/_plugins/gtn.rb @@ -711,6 +711,10 @@ def shuffle(array) array.shuffle end + def unix_time_to_date(time) + Time.at(time.to_i).strftime('%Y-%m-%d %H:%M:%S') + end + def is_date_passed(date) if date.nil? false diff --git a/_plugins/gtn/shortlinks.rb b/_plugins/gtn/shortlinks.rb index 5ece6afdc63d59..2e82c514886a62 100644 --- a/_plugins/gtn/shortlinks.rb +++ b/_plugins/gtn/shortlinks.rb @@ -9,6 +9,7 @@ module Shortlinks CATEGORY_NEWS = 'N' CATEGORY_PATHWAYS = 'P' CATEGORY_EVENTS = 'E' + CATEGORY_WORKFLOW = 'W' def self.mapped?(tutorial, current_mapping) current_mapping['id'].values.include? tutorial @@ -130,6 +131,22 @@ def self.update(current_mapping) end end + # Discover workflows + workflows = Dir.glob('topics/**/workflows/*.ga') + + workflows.each do |workflow| + html_path = "/#{workflow.gsub(/ga$/, 'html').gsub('_', '-')}" + # If it's not already mapped by a key, add it. + if !mapped?(html_path, current_mapping) + # Generate a short code + short_code_number = current_mapping['id'].select { |x| x[0] == CATEGORY_WORKFLOW }.length.to_s.rjust(5, '0') + short_code = CATEGORY_WORKFLOW + short_code_number + puts "Discovered workflow #{short_code}" + # If the target of this flavour of short code isn't already in here, then add it + current_mapping['id'][short_code] = html_path + end + end + current_mapping end end From 8e352a668eed891d345154e2e55471fda65e8cf7 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 16:15:30 +0200 Subject: [PATCH 23/36] workflow version history --- _layouts/workflow.html | 52 +++++++++++++++++++++++++-------- _plugins/jekyll-topic-filter.rb | 26 +++++++++++++++++ 2 files changed, 66 insertions(+), 12 deletions(-) diff --git a/_layouts/workflow.html b/_layouts/workflow.html index 2d4ccde79bef97..3c0749fb2d9d04 100644 --- a/_layouts/workflow.html +++ b/_layouts/workflow.html @@ -4,9 +4,11 @@ {% assign material = page.material %} {% assign workflow = page.workflow %} +
@@ -18,7 +20,7 @@

{{ workflow.title }}

{{ workflow.annotation }}

{% endif %}
-
+
{% if workflow.creators %} Author(s)
@@ -31,7 +33,7 @@

{{ workflow.title }}

{% icon version %} Version
- {{ workflow.path | get_version_number }} + {{ workflow.version }}
@@ -45,12 +47,15 @@

{{ workflow.title }}

{% icon license %} License
- {% if workflow.license %} - {{ workflow.license }} - {% else %} - None Specified, defaults to - CC-BY-4.0 - {% endif %} + + {% if workflow.license %} + {{ workflow.license }} + {% else %} + None Specified, defaults to + CC-BY-4.0 + {% endif %} +
+ {% if workflow.tags %} {% icon galaxy-tags %} Tags @@ -61,7 +66,6 @@

{{ workflow.title }}

Features - {{ workflow.features }}
    {% if workflow.features.tests %}
  • Includes Galaxy Workflow Tests
    • @@ -100,7 +104,7 @@

    {{ workflow.title }}

    - FAIR + FAIRness {% if jekyll.environment == "production" %} {% endif %} @@ -110,8 +114,6 @@

    {{ workflow.title }}

-

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

- Launch in Tutorial Mode {% icon question %}
@@ -136,11 +138,37 @@

{{ workflow.title }}

{{ workflow.mermaid }}
+

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

+ +

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them! {% snippet faqs/galaxy/workflows_import.md box_type="hands_on" %} +

Version History

+ + + + + + + + + + + {% for version in workflow.history %} + + + + + + + {% endfor %} + +
VersionCommitTimeComments
{{ version.num }}{{ version.short_hash }}{{ version.unix |unix_time_to_date }}{{ version.message }}
+ +

For Admins

Installing the workflow tools

diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 2556f46740f669..c94f169249b005 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -31,6 +31,10 @@ def self.enumerate_topics(site) list_topics_h(site).values end + def self.cache + @@cache ||= Jekyll::Cache.new('JekyllTopicFilter') + end + ## # Fill the cache with all the topics # Params: @@ -521,6 +525,26 @@ def self.graph_dot(wf) "digraph main {\n" + statements.map { |q| " #{q}" }.join("\n") + "\n}" end + def self.git_log(wf_path) + if Jekyll.env != 'production' + return [] + end + + cache.getset(wf_path) do + require 'shellwords' + + commits = %x[git log --format="%H %at %s" #{Shellwords.escape(wf_path)}] + .split("\n") + .map { |x| x.split(' ', 3) } + .map { |x| { 'hash' => x[0], 'unix' => x[1], 'message' => x[2], 'short_hash' => x[0][0..8] } } + + commits.map.with_index do |c, i| + c['num'] = commits.length - i + c + end + end + end + def self.resolve_material(site, material) # We've already # looked in every /topic/*/tutorials/* folder, and turn these disparate @@ -657,6 +681,7 @@ def self.resolve_material(site, material) 'creators' => creators, 'name' => wf_json['name'], 'title' => wftitle, + 'version' => Gtn::ModificationTimes.obtain_modification_count(wf_path), 'description' => wf_json['annotation'], 'tags' => wf_json['tags'], 'features' => { @@ -665,6 +690,7 @@ def self.resolve_material(site, material) 'comments' => (wf_json['comments'] || []).length.positive?, 'parameters' => wf_json['steps'].map{|_, x| x['type']}.any?{|x| x == "parameter_input"}, }, + 'history' => git_log(wf_path), 'test_results' => workflow_test_outputs, 'modified' => File.mtime(wf_path), 'mermaid' => mermaid(wf_json), From 0508f29bb9114f98269c28d35921b3b4ddeb7103 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 16:15:39 +0200 Subject: [PATCH 24/36] Fix admin training bug --- topics/admin/tutorials/introduction/slides.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/admin/tutorials/introduction/slides.html b/topics/admin/tutorials/introduction/slides.html index 20155804546324..f3024a9bce9b42 100644 --- a/topics/admin/tutorials/introduction/slides.html +++ b/topics/admin/tutorials/introduction/slides.html @@ -84,7 +84,7 @@ # Software Requirements Required: - - Galaxy is written in Python and depends on **Python 3.5** or newer + - Galaxy is written in Python and depends on **Python 3.8** or newer Minimal [production](https://docs.galaxyproject.org/en/master/admin/production.html) requirements: - [PostgreSQL]({% link topics/admin/tutorials/database/slides.html %}) From a769436359bd61c043f50687b01bc62de945665b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 16:30:33 +0200 Subject: [PATCH 25/36] shortlinks for wf pages --- _layouts/workflow.html | 6 ++++++ _plugins/generator-workflows.rb | 5 ++++- _plugins/gtn/shortlinks.rb | 2 +- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/_layouts/workflow.html b/_layouts/workflow.html index 3c0749fb2d9d04..c9ee73f40f80bd 100644 --- a/_layouts/workflow.html +++ b/_layouts/workflow.html @@ -37,6 +37,12 @@

{{ workflow.title }}


+ {% icon purl %} + PURL +
+ https://gxy.io/GTN:{{ page.short_id }} +
+ {% icon last_modification %} Last updated
diff --git a/_plugins/generator-workflows.rb b/_plugins/generator-workflows.rb index 6789bc93fa4053..eb60cd5f9118a9 100644 --- a/_plugins/generator-workflows.rb +++ b/_plugins/generator-workflows.rb @@ -37,15 +37,18 @@ def generate(site) # "graph_dot"=> # }] # /api/workflows/#{topic_id}/#{tutorial_id}/#{wfid}/rocrate.zip + shortlinks = site.data['shortlinks']['id'].invert materials.each do |material| (material['workflows'] || []).each do |workflow| - page2 = PageWithoutAFile.new(site, '', material['dir'], "workflows/#{workflow['wfname']}.html") + page2 = PageWithoutAFile.new(site, '', '', "#{workflow['path'].gsub(/.ga$/, '.html')}") + path = File.join('/', workflow['path'].gsub(/.ga$/, '.html')) page2.content = nil page2.data['layout'] = 'workflow' page2.data['material'] = material page2.data['workflow'] = workflow page2.data['js_requirements'] = {'mathjax' => false, 'mermaid' => true} + page2.data['short_id'] = shortlinks[path] site.pages << page2 end end diff --git a/_plugins/gtn/shortlinks.rb b/_plugins/gtn/shortlinks.rb index 2e82c514886a62..9e9460279e4205 100644 --- a/_plugins/gtn/shortlinks.rb +++ b/_plugins/gtn/shortlinks.rb @@ -135,7 +135,7 @@ def self.update(current_mapping) workflows = Dir.glob('topics/**/workflows/*.ga') workflows.each do |workflow| - html_path = "/#{workflow.gsub(/ga$/, 'html').gsub('_', '-')}" + html_path = "/#{workflow.gsub(/ga$/, 'html')}" # If it's not already mapped by a key, add it. if !mapped?(html_path, current_mapping) # Generate a short code From 8feaff6652cf96da6e9bcb583e9003467a14972b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 16:40:43 +0200 Subject: [PATCH 26/36] fix how the upload works --- bin/wfh-upload.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 2e8c2a0e4120aa..567f867720cda0 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -19,7 +19,7 @@ def doUpload(crate_path): p = crate_path.split("/") - (topic, tutorial, workflow) = p[4:7] + (topic, tutorial, workflow) = p[3:6] payload = { "ro_crate": (crate_path, open(crate_path, "rb")), @@ -78,7 +78,7 @@ def doUpload(crate_path): data = {} for (topic, tutorial, workflow, wf_id) in results: - data.setdefault(topic, {}).setdefault(tutorial, {})[workflow] = wf_id + data['/'.join([topic, tutorial, workflow])] = wf_id with open('metadata/workflowhub.yml', 'w') as handle: yaml.dump(data, handle) From cb89afdf2667fb48f86049c35e6c8b93d9ac01b5 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 16:54:41 +0200 Subject: [PATCH 27/36] add tool_dir for examples --- topics/admin/tutorials/tool-management/slides.html | 1 + 1 file changed, 1 insertion(+) diff --git a/topics/admin/tutorials/tool-management/slides.html b/topics/admin/tutorials/tool-management/slides.html index 32d3a0e3c616ff..74cf8c51eea771 100644 --- a/topics/admin/tutorials/tool-management/slides.html +++ b/topics/admin/tutorials/tool-management/slides.html @@ -127,6 +127,7 @@
+ ... ``` From 19260c0d6fc2256e07c0cb40262df55f62f353de Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 17:09:45 +0200 Subject: [PATCH 28/36] conditionally show buttons --- _layouts/workflow.html | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/_layouts/workflow.html b/_layouts/workflow.html index c9ee73f40f80bd..61f7c77852a205 100644 --- a/_layouts/workflow.html +++ b/_layouts/workflow.html @@ -113,10 +113,11 @@

{{ workflow.title }}

FAIRness {% if jekyll.environment == "production" %} + RO-Crate logo with flask Download Workflow RO-Crate + {% endif %} + {% if workflow.workflowhub_id %} + Workflowhub cloud with gears logo View on WorkflowHub {% endif %} - RO-Crate logo with flask Download Workflow RO-Crate - - Workflowhub cloud with gears logo View on WorkflowHub
From 2a25d3097091af9174fbcb43204161ffe79c266b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 17:10:04 +0200 Subject: [PATCH 29/36] finalise our IDs --- _plugins/gtn/ro-crate.rb | 7 +++---- _plugins/jekyll-topic-filter.rb | 3 +++ 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/_plugins/gtn/ro-crate.rb b/_plugins/gtn/ro-crate.rb index 4450a4968f2e61..60407464a5196d 100644 --- a/_plugins/gtn/ro-crate.rb +++ b/_plugins/gtn/ro-crate.rb @@ -43,9 +43,8 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base Jekyll.logger.debug "[GTN/API/WFRun] dot -T png #{dot_path} > graph.png" `dot -T png '#{dot_path}' > '#{File.join(wfdir, 'graph.png')}'` - # Replace last / with # to make a valid URL - wfurlid = url + baseurl + '/' + workflow['path'].gsub(%r{/workflows/}, - '/workflows#') + # Our new workflow IDs + wfurlid = url + baseurl + '/' + workflow['path'].gsub(/.ga$/, '.html') uuids = workflow['creators'].map do |c| if c.key?('identifier') && !c['identifier'].empty? @@ -195,7 +194,7 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base # p "Writing #{File.join(wfdir, 'mod.ga')}" zip_path = File.join(wfdir, 'rocrate.zip') - p "[GTN/API/WFRun] Zipping #{zip_path}" + Jekyll.logger.debug "[GTN/API/WFRun] Zipping #{zip_path}" if File.exist?(zip_path) File.delete(zip_path) end diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index c94f169249b005..23a5b43d4cb968 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -666,6 +666,8 @@ def self.resolve_material(site, material) end workflow_test_outputs = nil if workflow_test_outputs.empty? + wfhkey = [page['topic_name'], page['tutorial_name'], wfname].join('/') + { 'workflow' => wf, 'tests' => Dir.glob("#{folder}/workflows/" + wf.gsub(/.ga/, '-test*')).length.positive?, @@ -690,6 +692,7 @@ def self.resolve_material(site, material) 'comments' => (wf_json['comments'] || []).length.positive?, 'parameters' => wf_json['steps'].map{|_, x| x['type']}.any?{|x| x == "parameter_input"}, }, + 'workflowhub_id' => site.data['workflowhub'][wfhkey], 'history' => git_log(wf_path), 'test_results' => workflow_test_outputs, 'modified' => File.mtime(wf_path), From ff922055024e4efdcc70e23f91b239ce5732808f Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 17:15:44 +0200 Subject: [PATCH 30/36] would add dupes --- bin/wfh-upload.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/bin/wfh-upload.py b/bin/wfh-upload.py index 567f867720cda0..16f1202483533c 100755 --- a/bin/wfh-upload.py +++ b/bin/wfh-upload.py @@ -18,9 +18,6 @@ ) def doUpload(crate_path): - p = crate_path.split("/") - (topic, tutorial, workflow) = p[3:6] - payload = { "ro_crate": (crate_path, open(crate_path, "rb")), "workflow[project_ids][]": (None, GTN_PROJECT_ID), # GTN's ID. @@ -45,6 +42,13 @@ def doUpload(crate_path): "id": wfid, "type": "workflows", "attributes": { + # Adds duplicate links so, commented for now. No bug has been filed. + # "discussion_links": [ + # { + # "label": "Matrix", + # "url": "https://matrix.to/#/%23galaxyproject_admin:gitter.im" + # } + # ], "policy": { "access": "download", "permissions": [ @@ -68,6 +72,8 @@ def doUpload(crate_path): if response2.status_code != 200: print(f"Error {response2.status_code} updating permissions for {wfid}: {response2.text}") + p = crate_path.split("/") + (topic, tutorial, workflow) = p[3:6] return (topic, tutorial, workflow, wfid) From 59322c2c8c06d7cd619347e0dd1daca223d2f3fd Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 24 Jun 2024 17:22:38 +0200 Subject: [PATCH 31/36] Fix og:image for slides --- _layouts/base_slides.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_layouts/base_slides.html b/_layouts/base_slides.html index 8c404aebe405fc..73d5274023dc94 100644 --- a/_layouts/base_slides.html +++ b/_layouts/base_slides.html @@ -40,8 +40,8 @@ {%- elsif page.tags contains "galaxy" %}{% assign coverimage = "/assets/images/GalaxyNews.png" %} {%- elsif page.tags contains "gat" %}{% assign coverimage = "/assets/images/gat.png" %} {%- else %}{% assign coverimage = "/assets/images/GTNLogo1000.png" %}{% endif %} - {% assign og_image = page.og_image | default: coverimage | default: topic.og_image | default: "/assets/images/GTNLogo1000.png" %} - + {% assign og_image = page.og_image | default: page['cover-image'] | default: topic.og_image | default: coverimage | default: "assets/images/GTNLogo1000.png" %} +
+
+

{{ workflow.title }}

+

{{ workflow.wfid }}/{{ workflow.wfname }}

+
+ {% if workflow.description %} +

{{ workflow.description }}

+ {% endif %} +
+
+ {% if workflow.creators %} + Author(s) +
+ {% for entity in workflow.creators %} + {{ entity.name }}{% if forloop.last == false %}, {% endif %} + {% endfor %} + {% endif %} +
+ + {% icon version %} + Version +
+ {{ workflow.path | get_version_number }} + +
+ + {% icon last_modification %} + Last updated +
+ {{ workflow.path | gtn_mod_date | date: "%b %-d, %Y" }} + +
+ + {% icon license %} + License +
+ {% if workflow.license %} + {{ workflow.license }} + {% else %} + None Specified, defaults to + CC-BY-4.0 + {% endif %} + + Features +
+ + +
+ + + {% if workflow.tags %} + {% icon galaxy-tags %} {{ workflow.tags | join: ", " }} +
+ {% endif %} + + Tutorial +
+ {% icon hands_on %} {{ material.title }} +
+ + {% assign workflow_count = material.workflows | size %} + {% if workflow_count > 1 %} + {% icon workflow %} Other workflows associated with this material + {% endif %} + + +
+ Workflow Testing +
+ + Tests: {% if workflow.tests %}✅{% else %}❌{% endif %}
+ Results: {% if workflow.test_results == nil %}Not yet automated{% endif %} + +
+ + FAIR + + {% if jekyll.environment == "production" %} + {% endif %} + RO-Crate logo with flask Download Workflow RO-Crate + + Workflowhub cloud with gears logo View on WorkflowHub + +
+
+

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

+ + Launch in Tutorial Mode + {% icon question %} +
+ + + Download + + + + + + 
{{ workflow.mermaid }}
+ +

Importing into Galaxy

+ Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them! + + {% snippet faqs/galaxy/workflows_import.md box_type="hands_on" %} +
+
+