From e01df4ac597f812f16106c7c809ad1b00165faa7 Mon Sep 17 00:00:00 2001 From: Jasmine Baker Date: Thu, 10 Oct 2024 12:27:01 -0500 Subject: [PATCH 01/12] Update issue templates --- .github/ISSUE_TEMPLATE/feature_request.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 00000000..bbcbbe7d --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. From 93cbd15f0a6c24f268646ecb6acd6b2b362ea590 Mon Sep 17 00:00:00 2001 From: Kyle Moad Date: Mon, 28 Oct 2024 14:21:17 -0400 Subject: [PATCH 02/12] Delete release_note.txt --- release_note.txt | 54 ------------------------------------------------ 1 file changed, 54 deletions(-) delete mode 100644 release_note.txt diff --git a/release_note.txt b/release_note.txt deleted file mode 100644 index 4cf441fa..00000000 --- a/release_note.txt +++ /dev/null @@ -1,54 +0,0 @@ -##1.3.2 -January 31, 2019 -Updates on Interactive Result Viewer (cravat-view): -* Data loading indicator -* Local filter select box -* Show-all and hide-all buttons for widgets -* Load filter of cravat-view now has two modes, simple and advanced, and it shows only the filter operators relevant to the type of the filtered data. -* Widgets can be hidden by default and its show/hide status can be saved and loaded. -Updates on cravat web GUI (wcravat): -* Store now has a Front Page with Most Downloaded and Newest modules. -* Store shows annotator modules' source data version for provenance. -* Store can sort modules by their name, size, and date of post. -Updates on cravat: -* cravat detects input files’ encoding and reads them correctly and writes output files always in UTF-8. -Others: -* Module updates have been concurrently released. -* Fixed various bugs. - -##1.3.1 -January 10, 2019 -Patch release for bugs: -* Fixed bug that prevented excel spreadsheet download in the wcravat jobs page. -* Handle summary widget issues so that results will still be presented (filters on some jobs locking up results). -* wcravat server stops cleanly with cntrl-C. -* Updated Mac and Linux install instructions. -* Fixed favicon.ico error on Chrome. - *cravat detects and reads input files according to their encoding and always writes in UTF-8 across platforms. - -## 1.3.0 -December 12, 2018 -* Categorical data type has been added. -* aggregator is now a part of the open-cravat pip package for better coherence. -* Three new optional column attributes have been added, column type "category", column width, and column description. -* wcravat improvements: -** Log file can be viewed from the job list. -* Result Viewer improvements: -** Can filter with multiple-selection boxes with pre-filled options for data fields of categorical type. -** Improved the speed by removing asynchronous calls. -** More stable widget layout (do not change widget width according to long text content) -** New gradient bar widget component which can do both forward and backward gradients. -* Fixed various minor bugs - -## 0.0.140 -December 5, 2018 -* Annotators run in parallel for faster analysis (# cores - 1 by default) -* 'New' Icon when updates available for installed modules in CRAVAT Store -* Protein Change column (base information) -* Sequence Ontology - Codes translated to full terms (e.g. missense rather than MIS) -* Selected Row Highlighted -* New 'QuickSave" button on top right saves current filter and layout for when results are next opened. -* Fix so applying filter does not remove loaded IGV tracks -* Filter panel fixes. -* Consolidated Error Log - From f87a911fc75eacdfbaa7d96a40e87bce0566c498 Mon Sep 17 00:00:00 2001 From: Kyle Anderson Date: Mon, 28 Oct 2024 16:10:02 -0400 Subject: [PATCH 03/12] Add clingen example input file --- .../websubmit/input-examples/clingen.hg38.txt | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 cravat/websubmit/input-examples/clingen.hg38.txt diff --git a/cravat/websubmit/input-examples/clingen.hg38.txt b/cravat/websubmit/input-examples/clingen.hg38.txt new file mode 100644 index 00000000..a59263c0 --- /dev/null +++ b/cravat/websubmit/input-examples/clingen.hg38.txt @@ -0,0 +1,46 @@ +CA10578967 s0 +CA399017172 s0 +CA175996 s0 +CA16602420 s0 +CA130471 s0 +CA16602411 s0 +CA337714 s0 +CA351756203 s0 +CA16602916 s0 +CA000276 s0 +CA008815 s0 +CA135775 s0 +CA16602491 s1 +CA000359 s1 +CA2330856 s1 +CA351756398 s1 +CA295247 s1 +CA16603005 s1 +CA127263 s1 +CA397842854 s1 +CA16602774 s1 +CA10586089 s1 +CA280203 s1 +CA645557562 s1 +CA149708 s2 +CA510466634 s2 +CA5339658 s2 +CA446206656 s2 +CA8673081 s2 +CA1899284 s2 +CA048107 s2 +CA000646 s2 +CA250582 s2 +CA645576717 s2 +CA557558 s2 +CA9604922 s3 +CA144753 s3 +CA122528 s3 +CA338870 s3 +CA333572 s3 +CA384902497 s3 +CA16602487 s3 +CA248610 s3 +CA10579920 s3 +CA134595 s3 +CA279999 s3 From fde01af0c2f73f72f2fcd5d1529e673ff2c9bda3 Mon Sep 17 00:00:00 2001 From: Kyle Anderson Date: Tue, 29 Oct 2024 09:45:05 -0400 Subject: [PATCH 04/12] Add ClinGen Allele registry example input to GUI --- cravat/websubmit/nocache/index.html | 1 + cravat/websubmit/nocache/websubmit.js | 27 +++++++++++++++++++-------- 2 files changed, 20 insertions(+), 8 deletions(-) diff --git a/cravat/websubmit/nocache/index.html b/cravat/websubmit/nocache/index.html index da3485c2..c29fff65 100644 --- a/cravat/websubmit/nocache/index.html +++ b/cravat/websubmit/nocache/index.html @@ -106,6 +106,7 @@ + diff --git a/cravat/websubmit/nocache/websubmit.js b/cravat/websubmit/nocache/websubmit.js index ce778ed5..e6f12781 100644 --- a/cravat/websubmit/nocache/websubmit.js +++ b/cravat/websubmit/nocache/websubmit.js @@ -2040,18 +2040,28 @@ function addListeners () { }); } -function checkDbSNPInput() { - if ('dbsnp-converter' in OC.localModuleInfo) { - document.getElementById('dbsnp-input').classList.remove('disabled'); - document.getElementById('dbsnp-input').removeAttribute('title'); - document.getElementById('dbsnp-input').removeAttribute('disabled'); +function checkConverterInstalled(name) { + const converterName = `${name}-converter`; + const inputName = `${name}-input`; + if (converterName in OC.localModuleInfo) { + document.getElementById(inputName).classList.remove('disabled'); + document.getElementById(inputName).removeAttribute('title'); + document.getElementById(inputName).removeAttribute('disabled'); } else { - document.getElementById('dbsnp-input').title = 'Install dbsnp-converter to use'; - document.getElementById('dbsnp-input').disabled = 'true'; - document.getElementById('dbsnp-input').classList.add('disabled'); + document.getElementById(inputName).title = `Install ${converterName} to use`; + document.getElementById(inputName).disabled = 'true'; + document.getElementById(inputName).classList.add('disabled'); } } +function checkDbSNPInput() { + checkConverterInstalled('dbsnp'); +} + +function checkClingenInput() { + checkConverterInstalled('clingen'); +} + function addMediatorListeners() { OC.mediator.subscribe('navigate', changePage); OC.mediator.subscribe('populateJobs', populateJobs); @@ -2059,6 +2069,7 @@ function addMediatorListeners() { OC.mediator.subscribe('setupJobs', handleSetupJobsTab); OC.mediator.subscribe('moduleinfo.local', setVariantReportURL) OC.mediator.subscribe('moduleinfo.local', checkDbSNPInput); + OC.mediator.subscribe('moduleinfo.local', checkClingenInput); } function requestUserEmail() { From 9f6994933dabc1f6081658a59783ccb469832cb9 Mon Sep 17 00:00:00 2001 From: Kyle Anderson Date: Tue, 29 Oct 2024 10:35:17 -0400 Subject: [PATCH 05/12] Add clingen allele registry example input to CLI --- cravat/admin_util.py | 2 ++ cravat/constants.py | 1 + cravat/cravat_admin.py | 3 +++ 3 files changed, 6 insertions(+) diff --git a/cravat/admin_util.py b/cravat/admin_util.py index 43768068..216f4348 100644 --- a/cravat/admin_util.py +++ b/cravat/admin_util.py @@ -1344,6 +1344,8 @@ def make_example_input(out_directory, type='cravat'): out_fn = 'example_input.hgvs.txt' elif type == 'dbsnp': out_fn = 'example_input.rsid.txt' + elif type == 'clingen': + out_fn = 'example_input.clingen.txt' else: raise ValueError(f'Invalid example input type: {type}') out_path = Path(out_directory)/out_fn diff --git a/cravat/constants.py b/cravat/constants.py index 0dad662b..ae8f189d 100644 --- a/cravat/constants.py +++ b/cravat/constants.py @@ -88,6 +88,7 @@ 'vcf': Path(packagedir)/'websubmit'/'input-examples'/'vcf.hg38.txt', 'hgvs': Path(packagedir)/'websubmit'/'input-examples'/'hgvs.hg38.txt', 'dbsnp': Path(packagedir)/'websubmit'/'input-examples'/'dbsnp.hg38.txt', + 'clingen': Path(packagedir) / 'websubmit' / 'input-examples' / 'clingen.hg38.txt', } # Base modules diff --git a/cravat/cravat_admin.py b/cravat/cravat_admin.py index 6521e672..3bb076bb 100644 --- a/cravat/cravat_admin.py +++ b/cravat/cravat_admin.py @@ -445,6 +445,9 @@ def make_example_input (args): if args.type == 'dbsnp' and au.get_local_module_info('dbsnp-converter') is None: print('Must install dbsnp-converter.') exit(1) + if args.type == 'clingen' and au.get_local_module_info('clingen-converter') is None: + print('Must install clingen-converter.') + exit(1) out_path = au.make_example_input(args.directory, type=args.type) print(out_path) From cb040f5986f18a386cc05add7f33f570f38e10c8 Mon Sep 17 00:00:00 2001 From: Kyle Moad Date: Tue, 29 Oct 2024 14:05:42 -0400 Subject: [PATCH 06/12] add clingen-converter to base modules --- cravat/constants.py | 1 + 1 file changed, 1 insertion(+) diff --git a/cravat/constants.py b/cravat/constants.py index ae8f189d..dd3f0326 100644 --- a/cravat/constants.py +++ b/cravat/constants.py @@ -97,6 +97,7 @@ 'vcf-converter', 'oldcravat-converter', 'hgvs-converter', + 'clingen-converter', 'textreporter', 'excelreporter', 'tagsampler', From 239e7fc88f092e48a422d822056fb81e1f655e73 Mon Sep 17 00:00:00 2001 From: Kyle Anderson Date: Thu, 14 Nov 2024 10:51:01 -0500 Subject: [PATCH 07/12] Add new OpenCRAVAT logo to store, submit, and results pages --- cravat/webresult/index.html | 2 +- cravat/webresult/nocache/variant.html | 2 +- cravat/websubmit/OC_COLOR.svg | 1 + cravat/websubmit/OC_LOGO_ONLY.svg | 84 ++++++++++++++++++++++++++ cravat/websubmit/nocache/index.html | 2 +- cravat/websubmit/nocache/websubmit.css | 3 +- 6 files changed, 89 insertions(+), 5 deletions(-) create mode 100644 cravat/websubmit/OC_COLOR.svg create mode 100644 cravat/websubmit/OC_LOGO_ONLY.svg diff --git a/cravat/webresult/index.html b/cravat/webresult/index.html index dc477161..e051f1d6 100644 --- a/cravat/webresult/index.html +++ b/cravat/webresult/index.html @@ -60,7 +60,7 @@
- +