From 665dabc72cdc2623fd102038d36010ef47c35d4a Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 26 Feb 2024 12:20:27 +0100 Subject: [PATCH 01/13] missing somehow --- bin/list-recently-modified.rb | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100755 bin/list-recently-modified.rb diff --git a/bin/list-recently-modified.rb b/bin/list-recently-modified.rb new file mode 100755 index 00000000000000..dba189bb32dbc2 --- /dev/null +++ b/bin/list-recently-modified.rb @@ -0,0 +1,10 @@ +#!/usr/bin/env ruby +require './_plugins/gtn' + +months = (ARGV[1] || 6).to_i + +Gtn::PublicationTimes.init_cache +Gtn::PublicationTimes.time_cache.select do |_, v| + # Things in last 6 months + v > Time.now - (months * 30 * 24 * 60 * 60) +end.map { |k, v| puts "#{v} #{k}" } From adc0b0ebbc3ec9bd9ba7f4c65396185a8ef1c11d Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 26 Feb 2024 15:58:25 +0100 Subject: [PATCH 02/13] Implement a commit cache with only necessary metadata --- _plugins/gtn/mod.rb | 76 ++++++++++++++++++++++++++++++++++++-- bin/commit-cache-update.rb | 11 ++++++ 2 files changed, 84 insertions(+), 3 deletions(-) create mode 100644 bin/commit-cache-update.rb diff --git a/_plugins/gtn/mod.rb b/_plugins/gtn/mod.rb index fe7691293f1f71..2679aa0a5e0159 100644 --- a/_plugins/gtn/mod.rb +++ b/_plugins/gtn/mod.rb @@ -14,7 +14,7 @@ def self.init_cache @@TIME_CACHE = {} @@COMMIT_COUNT_CACHE = Hash.new(0) Jekyll.logger.info '[GTN/Time/Mod] Filling Time Cache' - `git log --name-only --pretty='GTN_GTN:%ct'` + self.cached_command .split('GTN_GTN:') .map { |x| x.split("\n\n") } .select { |x| x.length > 1 } @@ -26,6 +26,41 @@ def self.init_cache end end + def self.discover_caches + # Really there should only be one, but maybe someone's been silly so + # we'll just take the first one we find. + Dir.glob('metadata/git-mod-*.txt').first + end + + def self.generate_cache + rev = `git rev-list -n 1 main`.strip + + if discover_caches.nil? + File.write("metadata/git-mod-#{rev}.txt", self.command) + else + prev = discover_caches + File.write("metadata/git-mod-#{rev}.txt", self.cached_command) + File.delete(prev) + end + end + + def self.cached_command + if discover_caches.nil? + return self.command + end + + Jekyll.logger.info '[GTN/Time/Pub] Using cached modification times' + + previous_commit = discover_caches.split('-').last.split('.').first + previous = File.read(discover_caches) + + `git log --name-only --pretty='GTN_GTN:%ct' #{previous_commit}..main` + previous + end + + def self.command + `git log --name-only --pretty='GTN_GTN:%ct'` + end + def self.time_cache @@TIME_CACHE end @@ -80,7 +115,7 @@ def self.init_cache renames = {} Jekyll.logger.info '[GTN/Time/Pub] Filling Publication Time Cache' - `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' main` + self.command .split('GTN_GTN:') .map { |x| x.split("\n\n") } .select { |x| x.length > 1 } @@ -100,6 +135,41 @@ def self.init_cache # pp renames end + def self.discover_caches + # Really there should only be one, but maybe someone's been silly so + # we'll just take the first one we find. + Dir.glob('metadata/git-pub-*.txt').first + end + + def self.generate_cache + rev = `git rev-list -n 1 main`.strip + + if discover_caches.nil? + File.write("metadata/git-pub-#{rev}.txt", self.command) + else + prev = discover_caches + File.write("metadata/git-pub-#{rev}.txt", self.cached_command) + File.delete(prev) + end + end + + def self.cached_command + if discover_caches.nil? + return self.command + end + + Jekyll.logger.info '[GTN/Time/Pub] Using cached publication times' + + previous_commit = discover_caches.split('-').last.split('.').first + previous = File.read(discover_caches) + + `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' #{previous_commit}..main` + previous + end + + def self.command + `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' main` + end + def self.time_cache @@TIME_CACHE end @@ -125,7 +195,7 @@ def self.obtain_time(f) # Gtn::ModificationTimes.init_cache # pp Gtn::ModificationTimes.commit_count_cache - puts ' Moved tobin/list-recently-modified.rb' + puts ' Moved to bin/list-recently-modified.rb' # Gtn::PublicationTimes.init_cache # Gtn::PublicationTimes.time_cache.select do |_, v| # # Things in last 6 months diff --git a/bin/commit-cache-update.rb b/bin/commit-cache-update.rb new file mode 100644 index 00000000000000..c26217c43a6aae --- /dev/null +++ b/bin/commit-cache-update.rb @@ -0,0 +1,11 @@ +require './_plugins/gtn' + +# Write the commit log +Gtn::ModificationTimes.generate_cache +Gtn::PublicationTimes.generate_cache + +# Gziped? +# require 'zlib' +# File.write("metadata/git-mod-#{rev}.txt.gz", Zlib.gzip(Gtn::ModificationTimes.command)) +# File.write("metadata/git-pub-#{rev}.txt.gz", Zlib.gzip(Gtn::PublicationTimes.command)) +# p Gtn::ModificationTimes.discover_caches From 73d07757ee0c0b8f8a1ec194a58825bc4230ee72 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 26 Feb 2024 16:05:05 +0100 Subject: [PATCH 03/13] Regularly update this file --- .github/workflows/cron-commit-cache.yml | 62 +++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 .github/workflows/cron-commit-cache.yml diff --git a/.github/workflows/cron-commit-cache.yml b/.github/workflows/cron-commit-cache.yml new file mode 100644 index 00000000000000..53b564e5f7723b --- /dev/null +++ b/.github/workflows/cron-commit-cache.yml @@ -0,0 +1,62 @@ +name: "[Cron] Update Commit Cache" +on: + workflow_dispatch: + schedule: + - cron: '45 0 * * 1' +jobs: + runner-job: + runs-on: ubuntu-latest + # Only run on main repo on and PRs that match the main repo. + if: | + github.repository == 'galaxyproject/training-material' && + (github.event_name != 'pull_request' || + github.event.pull_request.head.repo.full_name == github.repository) + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 1000 + + # BEGIN Dependencies + - uses: ruby/setup-ruby@v1 + with: + ruby-version: "3.0" + - uses: actions/cache@v2 + with: + path: | + vendor/bundle + key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }} + restore-keys: | + ${{ runner.os }}-gems- + - name: Install dependencies + run: | + gem install bundler + bundle config path vendor/bundle + bundle install --jobs 4 --retry 3 + bundle pristine ffi + # END Dependencies + + - name: Update commit cache + id: generate + run: | + # Check if the oldest commit of the commit cache is known in this history + last_cached_commit=$(ls metadata/git-mod-*.txt | cut -d- -f 3 | cut -d. -f 1) + git show $last_cached_commit + ec=$? + if (( ec != 0 )); then + # Worst case, we need to fetch more. just fetch everything to be safe. + git fetch --unshallow + fi + + ruby bin/commit-cache-update.rb >> $GITHUB_OUTPUT + + - name: Create Pull Request + # If it's not a Pull Request then commit any changes as a new PR. + if: | + github.event_name != 'pull_request' && + steps.generate.outputs.new_ids != '' + uses: peter-evans/create-pull-request@v3 + with: + title: Update Persistent uniform resource locators + branch-suffix: commitcache + commit-message: Update Cached Commit Data + add-paths: metadata/git-*.txt From c667defd1a89a2c619358080a8eb233d71e43088 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 26 Feb 2024 16:13:23 +0100 Subject: [PATCH 04/13] no more full depth fetches --- .github/workflows/deploy.yml | 9 ++++++++- .github/workflows/matrix.yml | 2 +- .github/workflows/monthly-release.yml | 3 ++- .github/workflows/video-dry.yml | 10 +++++----- 4 files changed, 16 insertions(+), 8 deletions(-) diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 70630145ba3a66..635ff06edcd9ff 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -16,7 +16,14 @@ jobs: steps: - uses: actions/checkout@v2 with: - fetch-depth: 0 + # Avg commits between successive monday: + # Min. : 2.0 + # 1st Qu.: 25.0 + # Median : 54.5 + # Mean : 65.2 + # 3rd Qu.: 94.0 + # Max. :282.0 + fetch-depth: 400 # BEGIN Dependencies - uses: actions/setup-python@v2 diff --git a/.github/workflows/matrix.yml b/.github/workflows/matrix.yml index 1ed9efcfa40c20..c4ddb97d0a39b3 100644 --- a/.github/workflows/matrix.yml +++ b/.github/workflows/matrix.yml @@ -15,7 +15,7 @@ jobs: steps: - uses: actions/checkout@v2 with: - fetch-depth: 0 + fetch-depth: 200 # BEGIN Dependencies - uses: ruby/setup-ruby@v1 diff --git a/.github/workflows/monthly-release.yml b/.github/workflows/monthly-release.yml index ff658011cce2dd..0e299b5bfb70fc 100644 --- a/.github/workflows/monthly-release.yml +++ b/.github/workflows/monthly-release.yml @@ -32,7 +32,8 @@ jobs: - uses: actions/checkout@v2 with: - fetch-depth: 0 + # Based on logic in deploy.yml + fetch-depth: 1200 # BEGIN Dependencies - uses: actions/setup-python@v2 diff --git a/.github/workflows/video-dry.yml b/.github/workflows/video-dry.yml index 1926078310d336..dcb67d26779ac9 100644 --- a/.github/workflows/video-dry.yml +++ b/.github/workflows/video-dry.yml @@ -12,15 +12,15 @@ jobs: runs-on: ubuntu-latest services: # Label used to access the service container - mozillatts: - image: synesthesiam/mozillatts - ports: - - 5002:5002 + # mozillatts: + # image: synesthesiam/mozillatts + # ports: + # - 5002:5002 steps: # Shallow should be fine for video - uses: actions/checkout@v2 with: - fetch-depth: 0 + fetch-depth: 1 # BEGIN Dependencies - uses: actions/setup-python@v2 From 82c66b30840d79e85d508c2ca7a876ad04278c7d Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 26 Feb 2024 16:14:29 +0100 Subject: [PATCH 05/13] add commit cache --- ...0e16de5c1d2c6621c3ca488f534da270fab1e2.txt | 105993 +++++++++++++++ ...0e16de5c1d2c6621c3ca488f534da270fab1e2.txt | 18458 +++ 2 files changed, 124451 insertions(+) create mode 100644 metadata/git-mod-980e16de5c1d2c6621c3ca488f534da270fab1e2.txt create mode 100644 metadata/git-pub-980e16de5c1d2c6621c3ca488f534da270fab1e2.txt diff 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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 e48349b88d5a8f37cbe0e11b6024eee414b89ef2 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 26 Feb 2024 16:19:14 +0100 Subject: [PATCH 06/13] better text --- .github/workflows/cron-commit-cache.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cron-commit-cache.yml b/.github/workflows/cron-commit-cache.yml index 53b564e5f7723b..4d1e3d6a3b3186 100644 --- a/.github/workflows/cron-commit-cache.yml +++ b/.github/workflows/cron-commit-cache.yml @@ -56,7 +56,7 @@ jobs: steps.generate.outputs.new_ids != '' uses: peter-evans/create-pull-request@v3 with: - title: Update Persistent uniform resource locators + title: Update Cached Commit Data branch-suffix: commitcache commit-message: Update Cached Commit Data add-paths: metadata/git-*.txt From dcbb34f3fc316c4bf869588d25cfbcfe4efc6235 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 28 Feb 2024 09:54:17 +0100 Subject: [PATCH 07/13] Swap for semantic a, provide href This is only possible in recent versions of galaxy since the past year or so, we will break the tutorial mode in older ones but that is acceptable. A more useful href is provided for those outside of tutorial mode. --- _plugins/jekyll-tool-tag.rb | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/_plugins/jekyll-tool-tag.rb b/_plugins/jekyll-tool-tag.rb index a2cfdef61e56cb..f5130f50b75936 100644 --- a/_plugins/jekyll-tool-tag.rb +++ b/_plugins/jekyll-tool-tag.rb @@ -23,21 +23,24 @@ def render(context) # check if a variable was provided for the tool id tool = context[m[2].tr('{}', '')] || m[2] version = tool.split('/').last + # url encode + q = URI.encode_www_form_component("?tool_id=#{tool}") + tool_redirect = "https://my.galaxy.training/?path=#{q}" if tool.count('/').zero? - "" \ + "" \ ' ' \ "#{m[1]}" \ - '' + '' else - "" \ + "" \ ' ' \ "#{m[1]} " \ '(' \ ' ' \ "Galaxy version #{version}" \ ')' \ - '' + '' end else %(#{@text} ) From f8b90db2f8c9d5fe437487b8dd95dd06451a5bdf Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 28 Feb 2024 15:40:43 +0100 Subject: [PATCH 08/13] improve workflow display a bit --- _plugins/jekyll-topic-filter.rb | 53 +++++++++++++++++++++++++++++---- 1 file changed, 48 insertions(+), 5 deletions(-) diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 534e93d26a433c..5fda27471bb974 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -364,6 +364,14 @@ def self.collate_materials(site, pages) interesting end + def self.mermaid_safe_label(label) + (label || "") + .gsub('(', '').gsub(')', '') + .gsub('[', '').gsub(']', '') + .gsub('"', '”') # We accept that this is not perfectly correct. + .gsub("'", '’') + end + def self.mermaid(wf) # We're converting it to Mermaid.js # flowchart TD @@ -373,24 +381,59 @@ def self.mermaid(wf) # D --> B # B -- No ----> E[End] - output = "flowchart TD\n" + statements = [] wf['steps'].each_key do |id| step = wf['steps'][id] - output += " #{id}[\"#{step['name']}\"];\n" + chosen_label = mermaid_safe_label(step['label'] || step['name']) + + if step['type'] == 'data_collection_input' + statements.append "#{id}[\"ℹ️ Input Collection\\n#{chosen_label}\"];" + elsif step['type'] == 'data_input' + statements.append "#{id}[\"ℹ️ Input Dataset\\n#{chosen_label}\"];" + elsif step['type'] == 'parameter_input' + statements.append "#{id}[\"ℹ️ Input Parameter\\n#{chosen_label}\"];" + elsif step['type'] == 'subworkflow' + statements.append "#{id}[\"🛠️ Subworkflow\\n#{chosen_label}\"];" + else + statements.append "#{id}[\"#{chosen_label}\"];" + end + + if step['type'] == 'data_collection_input' or step['type'] == 'data_input' + statements.append "style #{id} stroke:#2c3143,stroke-width:4px;" + elsif step['type'] == 'parameter_input' + statements.append "style #{id} fill:#ded,stroke:#393,stroke-width:4px;" + elsif step['type'] == 'subworkflow' + statements.append "style #{id} fill:#edd,stroke:#900,stroke-width:4px;" + 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| - output += " #{v2['id']} -->|#{v2['output_name']}| #{id};\n" + statements.append "#{v2['id']} -->|#{mermaid_safe_label(v2['output_name'])}| #{id};" end else - output += " #{v['id']} -->|#{v['output_name']}| #{id};\n" + statements.append "#{v['id']} -->|#{mermaid_safe_label(v['output_name'])}| #{id};" end end + + (step['workflow_outputs'] || []) + .reject{|wo| wo['label'].nil? } + .map{|wo| + if wo['uuid'].nil? + wo['uuid'] = SecureRandom.uuid.to_s; + end + wo + } + .each do |wo| + statements.append "#{wo['uuid']}[\"Output\\n#{wo['label']}\"];" + statements.append "#{id} --> #{wo['uuid']};" + statements.append "style #{wo['uuid']} stroke:#2c3143,stroke-width:4px;" + end end - output + "flowchart TD\n" + statements.sort.map{|q| " " + q}.join("\n") end def self.resolve_material(site, material) From b9b72f43c7f08d7626e4a5eae3975740bd63ed0a Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 28 Feb 2024 15:40:43 +0100 Subject: [PATCH 09/13] improve workflow display a bit --- _plugins/jekyll-topic-filter.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 5fda27471bb974..5f24bfb9356193 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -433,7 +433,7 @@ def self.mermaid(wf) end end - "flowchart TD\n" + statements.sort.map{|q| " " + q}.join("\n") + "flowchart TD\n" + statements.map{|q| " " + q}.join("\n") end def self.resolve_material(site, material) From 3597cbd837b55397b565858cd85d09c82c49c8d7 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 29 Feb 2024 11:56:28 +0100 Subject: [PATCH 10/13] Sort by load time --- short/galaxy.html | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/short/galaxy.html b/short/galaxy.html index e0fe33d55dbd94..5c94323cdee6c5 100644 --- a/short/galaxy.html +++ b/short/galaxy.html @@ -25,10 +25,15 @@

Go!

Select your Preferred Galaxy Server

+ {% assign servers = nil | list_usegalaxy_servers_shuffle %} {% for server in servers %} - {{ server.human }} ({{ server.id | upcase }}) + + + {{ server.human }} + {% endfor %} +

@@ -70,6 +75,27 @@ let path = params.get('path') || '/'; var preferred_server = localStorage.getItem('gxy-url'); + +var startTime = new Date().getTime(); +let serverLoadTimes = {}; +function doneLoading(server) { + var loadtime = new Date().getTime() - startTime; + serverLoadTimes[server] = loadtime; + console.log(`${server} image took ${loadtime} ms to load`); + reorderServers(); +}; + +function reorderServers() { + var servers = document.querySelectorAll('.clickthrough'); + var serverArray = Array.from(servers); + serverArray.sort(function(a, b) { + return serverLoadTimes[a.id] - serverLoadTimes[b.id]; + }); + serverArray.forEach(function(el) { + document.getElementById(el.id).parentElement.appendChild(el); + }); +} + document.getElementById('path').innerHTML = path; function showPreferred(server_domain) { @@ -123,3 +149,9 @@ }); }); + + From 88e89140ff5a1bb2ab2f4d461d31a7bcded8ef47 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 29 Feb 2024 12:45:14 +0100 Subject: [PATCH 11/13] fixes --- _plugins/gtn/mod.rb | 12 +++++++----- bin/list-recently-modified.rb | 4 ++-- bin/list-recently-published.rb | 10 ++++++++++ 3 files changed, 19 insertions(+), 7 deletions(-) create mode 100644 bin/list-recently-published.rb diff --git a/_plugins/gtn/mod.rb b/_plugins/gtn/mod.rb index 2679aa0a5e0159..3fddd4bed0e630 100644 --- a/_plugins/gtn/mod.rb +++ b/_plugins/gtn/mod.rb @@ -49,12 +49,12 @@ def self.cached_command return self.command end - Jekyll.logger.info '[GTN/Time/Pub] Using cached modification times' + Jekyll.logger.info '[GTN/Time/Mod] Using cached modification times' previous_commit = discover_caches.split('-').last.split('.').first previous = File.read(discover_caches) - `git log --name-only --pretty='GTN_GTN:%ct' #{previous_commit}..main` + previous + `git log --name-only --pretty='GTN_GTN:%ct' #{previous_commit}..` + previous end def self.command @@ -86,6 +86,7 @@ def self.obtain_time(f) begin # Non git file. @@TIME_CACHE[f] = File.mtime(f) + Jekyll.logger.warning "[GTN/Time/Mod] No git cached time available for #{f}, defaulting to checkout" @@TIME_CACHE[f] rescue StandardError Time.at(0) @@ -115,7 +116,7 @@ def self.init_cache renames = {} Jekyll.logger.info '[GTN/Time/Pub] Filling Publication Time Cache' - self.command + self.cached_command .split('GTN_GTN:') .map { |x| x.split("\n\n") } .select { |x| x.length > 1 } @@ -163,11 +164,11 @@ def self.cached_command previous_commit = discover_caches.split('-').last.split('.').first previous = File.read(discover_caches) - `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' #{previous_commit}..main` + previous + `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' #{previous_commit}..` + previous end def self.command - `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' main` + `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' ` end def self.time_cache @@ -182,6 +183,7 @@ def self.obtain_time(f) begin # Non git file. @@TIME_CACHE[f] = File.mtime(f) + Jekyll.logger.warning "[GTN/Time/Pub] No git cached time available for #{f}, defaulting to checkout" @@TIME_CACHE[f] rescue StandardError Time.at(0) diff --git a/bin/list-recently-modified.rb b/bin/list-recently-modified.rb index dba189bb32dbc2..f7b7e0703873b9 100755 --- a/bin/list-recently-modified.rb +++ b/bin/list-recently-modified.rb @@ -3,8 +3,8 @@ months = (ARGV[1] || 6).to_i -Gtn::PublicationTimes.init_cache -Gtn::PublicationTimes.time_cache.select do |_, v| +Gtn::ModificationTimes.init_cache +Gtn::ModificationTimes.time_cache.select do |_, v| # Things in last 6 months v > Time.now - (months * 30 * 24 * 60 * 60) end.map { |k, v| puts "#{v} #{k}" } diff --git a/bin/list-recently-published.rb b/bin/list-recently-published.rb new file mode 100644 index 00000000000000..dba189bb32dbc2 --- /dev/null +++ b/bin/list-recently-published.rb @@ -0,0 +1,10 @@ +#!/usr/bin/env ruby +require './_plugins/gtn' + +months = (ARGV[1] || 6).to_i + +Gtn::PublicationTimes.init_cache +Gtn::PublicationTimes.time_cache.select do |_, v| + # Things in last 6 months + v > Time.now - (months * 30 * 24 * 60 * 60) +end.map { |k, v| puts "#{v} #{k}" } From d490e5c53bf1c91d8e24770108aee0c9462a92ef Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 29 Feb 2024 13:02:58 +0100 Subject: [PATCH 12/13] this is fine --- _plugins/gtn.rb | 4 ++-- _plugins/gtn/mod.rb | 20 ++++++++------------ _plugins/jekyll-topic-filter.rb | 30 +++++++++++++++--------------- bin/list-recently-published.rb | 0 4 files changed, 25 insertions(+), 29 deletions(-) mode change 100644 => 100755 bin/list-recently-published.rb diff --git a/_plugins/gtn.rb b/_plugins/gtn.rb index 78172293e42273..76a145280637c9 100644 --- a/_plugins/gtn.rb +++ b/_plugins/gtn.rb @@ -511,10 +511,10 @@ def tutorials_over_time_bar_chart(site) # https://stackoverflow.com/questions/71745593/how-to-do-a-single-line-cumulative-count-for-hash-values-in-ruby graph # Turns it into an array - .sort_by{|k, v| k} + .sort_by { |k, _v| k } # Cumulative sum .each_with_object([]) { |(k, v), a| a << [k, v + a.last&.last.to_i] }.to_h - .map{ |k, v| { 'x' => k, 'y' => v } } + .map { |k, v| { 'x' => k, 'y' => v } } .to_json end diff --git a/_plugins/gtn/mod.rb b/_plugins/gtn/mod.rb index 3fddd4bed0e630..0ce8a4d1e525af 100644 --- a/_plugins/gtn/mod.rb +++ b/_plugins/gtn/mod.rb @@ -14,7 +14,7 @@ def self.init_cache @@TIME_CACHE = {} @@COMMIT_COUNT_CACHE = Hash.new(0) Jekyll.logger.info '[GTN/Time/Mod] Filling Time Cache' - self.cached_command + cached_command .split('GTN_GTN:') .map { |x| x.split("\n\n") } .select { |x| x.length > 1 } @@ -36,18 +36,16 @@ def self.generate_cache rev = `git rev-list -n 1 main`.strip if discover_caches.nil? - File.write("metadata/git-mod-#{rev}.txt", self.command) + File.write("metadata/git-mod-#{rev}.txt", command) else prev = discover_caches - File.write("metadata/git-mod-#{rev}.txt", self.cached_command) + File.write("metadata/git-mod-#{rev}.txt", cached_command) File.delete(prev) end end def self.cached_command - if discover_caches.nil? - return self.command - end + return command if discover_caches.nil? Jekyll.logger.info '[GTN/Time/Mod] Using cached modification times' @@ -116,7 +114,7 @@ def self.init_cache renames = {} Jekyll.logger.info '[GTN/Time/Pub] Filling Publication Time Cache' - self.cached_command + cached_command .split('GTN_GTN:') .map { |x| x.split("\n\n") } .select { |x| x.length > 1 } @@ -146,18 +144,16 @@ def self.generate_cache rev = `git rev-list -n 1 main`.strip if discover_caches.nil? - File.write("metadata/git-pub-#{rev}.txt", self.command) + File.write("metadata/git-pub-#{rev}.txt", command) else prev = discover_caches - File.write("metadata/git-pub-#{rev}.txt", self.cached_command) + File.write("metadata/git-pub-#{rev}.txt", cached_command) File.delete(prev) end end def self.cached_command - if discover_caches.nil? - return self.command - end + return command if discover_caches.nil? Jekyll.logger.info '[GTN/Time/Pub] Using cached publication times' diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 5f24bfb9356193..46afe21182acf4 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -365,7 +365,7 @@ def self.collate_materials(site, pages) end def self.mermaid_safe_label(label) - (label || "") + (label || '') .gsub('(', '').gsub(')', '') .gsub('[', '').gsub(']', '') .gsub('"', '”') # We accept that this is not perfectly correct. @@ -386,23 +386,25 @@ def self.mermaid(wf) step = wf['steps'][id] chosen_label = mermaid_safe_label(step['label'] || step['name']) - if step['type'] == 'data_collection_input' + case step['type'] + when 'data_collection_input' statements.append "#{id}[\"ℹ️ Input Collection\\n#{chosen_label}\"];" - elsif step['type'] == 'data_input' + when 'data_input' statements.append "#{id}[\"ℹ️ Input Dataset\\n#{chosen_label}\"];" - elsif step['type'] == 'parameter_input' + when 'parameter_input' statements.append "#{id}[\"ℹ️ Input Parameter\\n#{chosen_label}\"];" - elsif step['type'] == 'subworkflow' + when 'subworkflow' statements.append "#{id}[\"🛠️ Subworkflow\\n#{chosen_label}\"];" else statements.append "#{id}[\"#{chosen_label}\"];" end - if step['type'] == 'data_collection_input' or step['type'] == 'data_input' + case step['type'] + when 'data_collection_input', 'data_input' statements.append "style #{id} stroke:#2c3143,stroke-width:4px;" - elsif step['type'] == 'parameter_input' + when 'parameter_input' statements.append "style #{id} fill:#ded,stroke:#393,stroke-width:4px;" - elsif step['type'] == 'subworkflow' + when 'subworkflow' statements.append "style #{id} fill:#edd,stroke:#900,stroke-width:4px;" end @@ -419,13 +421,11 @@ def self.mermaid(wf) end (step['workflow_outputs'] || []) - .reject{|wo| wo['label'].nil? } - .map{|wo| - if wo['uuid'].nil? - wo['uuid'] = SecureRandom.uuid.to_s; - end + .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 "#{wo['uuid']}[\"Output\\n#{wo['label']}\"];" statements.append "#{id} --> #{wo['uuid']};" @@ -433,7 +433,7 @@ def self.mermaid(wf) end end - "flowchart TD\n" + statements.map{|q| " " + q}.join("\n") + "flowchart TD\n" + statements.map { |q| " #{q}" }.join("\n") end def self.resolve_material(site, material) diff --git a/bin/list-recently-published.rb b/bin/list-recently-published.rb old mode 100644 new mode 100755 From c10ffe8e480ba59a7c066f47f6102599a5d88bb2 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 29 Feb 2024 13:21:40 +0100 Subject: [PATCH 13/13] add logo for alt text --- short/galaxy.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/short/galaxy.html b/short/galaxy.html index 5c94323cdee6c5..044c2f69a711fd 100644 --- a/short/galaxy.html +++ b/short/galaxy.html @@ -29,7 +29,7 @@

Go!

{% assign servers = nil | list_usegalaxy_servers_shuffle %} {% for server in servers %} - + logo {{ server.human }} {% endfor %}