Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / chop-dbhi/varify issues and pull requests

#397 - Add genome version to sample and variant resources

Pull Request - State: closed - Opened by naegelyd almost 10 years ago - 1 comment

#396 - Stats model required.

Issue - State: closed - Opened by hassanNS almost 10 years ago - 6 comments
Labels: status:wontfix

#395 - Update Varify to support version 0.4.0 of vdw

Issue - State: closed - Opened by naegelyd almost 10 years ago - 1 comment
Labels: type:bug, type:refactor, version 0.1

#394 - Create new Avocado metadata migration with null translators

Issue - State: open - Opened by naegelyd almost 10 years ago
Labels: type:feature, version 0.1

#393 - Removing last surviving references to CoffeeScript

Pull Request - State: closed - Opened by naegelyd almost 10 years ago - 1 comment

#392 - Fix errata in README.md

Issue - State: open - Opened by monop almost 10 years ago

#391 - Fix case where sample modal sort direction was opposite of indicator

Pull Request - State: closed - Opened by naegelyd almost 10 years ago - 1 comment

#390 - Sample sort direction is opposite of indicator

Issue - State: closed - Opened by naegelyd almost 10 years ago
Labels: type:bug, version 0.1

#389 - Add genome version to sample and variant resources

Issue - State: closed - Opened by bruth almost 10 years ago - 3 comments
Labels: status:needinfo, type:feature, version 0.1

#388 - Headless tests need to be reworked for latest version of varify

Issue - State: open - Opened by hassanNS almost 10 years ago - 1 comment
Labels: version 0.1, type:test

#387 - Performance problem due to redundant queries

Issue - State: open - Opened by murphyke almost 10 years ago - 1 comment
Labels: type:refactor, version 0.1

#386 - Set sample from context when absent in workspace

Pull Request - State: closed - Opened by naegelyd almost 10 years ago - 1 comment

#385 - Workspace doesn't refresh when navigated to from another page

Issue - State: closed - Opened by naegelyd almost 10 years ago
Labels: type:bug, version 0.1

#384 - Embed a SolveBio variant-detail dashboard

Pull Request - State: closed - Opened by davecap almost 10 years ago - 7 comments

#383 - Wait until samples sync to set sample label in results workflow

Pull Request - State: closed - Opened by naegelyd almost 10 years ago

#382 - Limit cohort formatter to cohorts from projects user has permision for

Pull Request - State: closed - Opened by naegelyd almost 10 years ago

#381 - Update samplesInContext utility method to handle bare sample IDs

Pull Request - State: closed - Opened by naegelyd almost 10 years ago

#380 - Sample label shows "undefined" in results toolbar for single sample

Issue - State: closed - Opened by naegelyd almost 10 years ago
Labels: type:bug, version 0.1

#379 - Fix issue where cohort popover lost scrolling on overflow

Pull Request - State: closed - Opened by naegelyd almost 10 years ago

#378 - Allow users to select multiple samples

Pull Request - State: closed - Opened by naegelyd almost 10 years ago - 1 comment

#377 - Cohort sample popover no longer has constrained height and scrolling

Issue - State: closed - Opened by naegelyd almost 10 years ago
Labels: type:bug, version 0.1

#376 - Cohort formatter does not restrict cohort list when request user is present

Issue - State: closed - Opened by naegelyd about 10 years ago
Labels: type:bug, version 0.1

#375 - Add cancel button to sample modal

Pull Request - State: closed - Opened by naegelyd about 10 years ago

#374 - Add multi-sample selection to the sample chooser modal

Issue - State: closed - Opened by naegelyd about 10 years ago
Labels: type:feature, version 0.1

#373 - Use explicit comparison when parsing result genes

Pull Request - State: closed - Opened by naegelyd about 10 years ago - 1 comment

#372 - All gene symbols appear as "Unknown" in results table

Issue - State: closed - Opened by naegelyd about 10 years ago
Labels: type:bug, version 0.1

#371 - Add cancel button to sample selection modal

Issue - State: closed - Opened by naegelyd about 10 years ago
Labels: type:feature, version 0.1

#370 - Limit frequencies to cohorts in projects users have permissions on

Pull Request - State: closed - Opened by naegelyd about 10 years ago - 1 comment

#369 - Restrict cohorts to those for projects user has access to

Issue - State: closed - Opened by naegelyd about 10 years ago
Labels: type:feature, version 0.1

#367 - Move bench/ to vdw

Issue - State: closed - Opened by naegelyd about 10 years ago - 1 comment

#366 - Add new SolveBio "Dashboard" to variant detail view

Pull Request - State: closed - Opened by davecap about 10 years ago - 11 comments

#365 - Resource tests required

Issue - State: closed - Opened by hassanNS about 10 years ago

#364 - Added resource test cases

Pull Request - State: closed - Opened by hassanNS about 10 years ago - 10 comments

#363 - Provide local CSS when external CDN fails

Pull Request - State: closed - Opened by ryanjohara about 10 years ago - 5 comments

#362 - Provide local CSS when external CDN fails

Pull Request - State: closed - Opened by ryanjohara about 10 years ago - 5 comments

#361 - Don't hide loading overlay until variant data is returned

Pull Request - State: closed - Opened by naegelyd about 10 years ago - 2 comments

#360 - Disable Alamut button if nothing is running on port 10000

Issue - State: open - Opened by ryanjohara about 10 years ago
Labels: type:bug, version 0.1

#359 - Update Docs to include varify-data-warehouse and instructions of use.

Issue - State: closed - Opened by hassanNS about 10 years ago - 1 comment

#358 - Loading indicator on results page is cleared before results are displayed

Issue - State: closed - Opened by naegelyd about 10 years ago
Labels: type:bug, version 0.1

#357 - Update templates and tests to comply with schema changes

Pull Request - State: closed - Opened by awenocur about 10 years ago

#356 - Integrate JBrowse into Varify

Pull Request - State: closed - Opened by ryanjohara about 10 years ago - 12 comments

#355 - Genotypes are shown as numbers instead of text

Issue - State: closed - Opened by hassanNS about 10 years ago - 1 comment

#354 - handler issue while loading samples and using queue command

Issue - State: closed - Opened by hassanNS about 10 years ago - 2 comments

#353 - Update varify to leverage varify-data-warehouse

Pull Request - State: closed - Opened by naegelyd about 10 years ago - 7 comments

#352 - Add fallback code for libraries loaded via CDN

Issue - State: open - Opened by naegelyd about 10 years ago - 1 comment
Labels: version:future, type:feature

#351 - Resolving Test Case Clashes

Issue - State: closed - Opened by awenocur about 10 years ago - 2 comments
Labels: status:deferred, type:community

#350 - Add support for regions in gene sets

Issue - State: open - Opened by naegelyd about 10 years ago - 1 comment
Labels: type:feature, version 0.1

#349 - Add support for result/variant sets

Pull Request - State: closed - Opened by naegelyd about 10 years ago - 8 comments

#348 - Added create_db management command

Pull Request - State: closed - Opened by hassanNS about 10 years ago

#347 - Changes to Travis file and settings

Pull Request - State: closed - Opened by hassanNS about 10 years ago

#346 - Duplicate display of genotypes for heterozygous alternate calls on variant-sets

Issue - State: closed - Opened by awenocur about 10 years ago - 2 comments
Labels: type:bug, version 0.1

#344 - Remove unused variants management commands

Pull Request - State: closed - Opened by naegelyd about 10 years ago - 1 comment

#343 - Replace variant resource SolveBio queries with JS dashboard code

Pull Request - State: closed - Opened by davecap about 10 years ago - 7 comments

#341 - Issue 322

Pull Request - State: closed - Opened by awenocur about 10 years ago - 2 comments

#338 - Integrate JBrowse into Varify as Alamut replacement

Issue - State: open - Opened by ryanjohara over 10 years ago - 3 comments

#336 - Reduce result template to include only data used by client

Pull Request - State: closed - Opened by ryanjohara over 10 years ago - 3 comments

#333 - RQ Workers fail to load samples due to get_cache failure

Issue - State: closed - Opened by hassanNS over 10 years ago - 6 comments
Labels: status:needinfo, version 0.1

#328 - Headless Test Needed to Verify Issue 286

Issue - State: open - Opened by lcdavidson over 10 years ago
Labels: type:test

#327 - second attempt to add the VCF exporter

Pull Request - State: closed - Opened by awenocur over 10 years ago - 20 comments

#325 - Position sorting broken

Issue - State: closed - Opened by leipzig over 10 years ago - 1 comment
Labels: type:bug, version 0.1

#322 - add workaround to readme: LLVM 5.1 interferes with installation of requirements

Issue - State: closed - Opened by awenocur over 10 years ago - 2 comments
Labels: type:docs, version 0.1

#318 - Headless Test for Varify Issue 224

Issue - State: open - Opened by lcdavidson over 10 years ago
Labels: type:test

#310 - Loader does not support single number AD fields

Issue - State: closed - Opened by naegelyd over 10 years ago - 2 comments
Labels: type:bug, version 0.1

#302 - Updated Phenotype modal

Pull Request - State: closed - Opened by hassanNS over 10 years ago - 16 comments

#299 - Update dependencies

Issue - State: open - Opened by naegelyd over 10 years ago
Labels: type:refactor, version 0.1

#297 - Progress for Variant importer from spreadsheet

Pull Request - State: closed - Opened by hassanNS over 10 years ago - 6 comments

#295 - Split Varify into multiple apps

Issue - State: closed - Opened by naegelyd over 10 years ago - 1 comment
Labels: type:idea, version 0.1

#290 - Remove system_site_packages flag in travis config

Pull Request - State: closed - Opened by naegelyd over 10 years ago

#289 - Convert cohort_variant and result primary key types to bigint

Pull Request - State: closed - Opened by ryanjohara over 10 years ago - 17 comments

#282 - Exclude null values when filtering using range control

Issue - State: closed - Opened by naegelyd over 10 years ago - 6 comments
Labels: type:bug, version 0.1

#277 - Implement SampleDialog for new method of selecting a sample

Pull Request - State: closed - Opened by bruth over 10 years ago - 1 comment

#274 - 0/1 1/1 genotypes are a VCF abstract, we should store nucleotides

Issue - State: closed - Opened by leipzig over 10 years ago - 4 comments
Labels: version:1.0, type:refactor

#273 - Move contents of global_settings to settings

Pull Request - State: closed - Opened by bruth over 10 years ago

#249 - Changed tests to use fixtures, added gene testcase and fixed bug w/ gene resources

Pull Request - State: closed - Opened by hassanNS over 10 years ago - 4 comments

#239 - Reduce result template to include only the data used by the client

Issue - State: closed - Opened by naegelyd over 10 years ago - 1 comment
Labels: version:1.0, status:needinfo, type:refactor

#237 - Excel and CSV formatters should use same column order and column set

Issue - State: closed - Opened by naegelyd over 10 years ago - 2 comments
Labels: type:refactor, version 0.1

#234 - Change non-loader tests to use fixture

Issue - State: closed - Opened by naegelyd over 10 years ago - 3 comments
Labels: type:refactor, version 0.1

#223 - Reset cohort_variant when updating allele frequencies

Pull Request - State: closed - Opened by ryanjohara over 10 years ago - 3 comments

#211 - Increase test performance

Issue - State: closed - Opened by naegelyd over 10 years ago - 1 comment
Labels: version:1.0, type:idea

#210 - Correct close button height in results modal

Pull Request - State: closed - Opened by ryanjohara over 10 years ago

#174 - Port utils to JavaScript

Pull Request - State: closed - Opened by naegelyd over 10 years ago - 1 comment

#171 - Glacial query performance with gene sets

Issue - State: closed - Opened by mitalia over 10 years ago - 3 comments
Labels: status:needinfo, version 0.1

#146 - Removing load off the database during VCF processing

Issue - State: closed - Opened by bruth over 10 years ago - 6 comments
Labels: version:future, type:refactor

#140 - Add additional information to distinguish samples

Issue - State: closed - Opened by mitalia over 10 years ago - 1 comment
Labels: version:future, status:needinfo

#137 - Fix problems reading data from PyVCF call objects

Pull Request - State: closed - Opened by naegelyd over 10 years ago

#135 - "The Loader" needs improved tests to fully cover all cases

Issue - State: closed - Opened by naegelyd over 10 years ago - 1 comment
Labels: version:1.0, type:refactor

#134 - Update API resources to use Serrano's base resource class

Pull Request - State: closed - Opened by bruth over 10 years ago

#112 - Force user to select a sample

Pull Request - State: closed - Opened by naegelyd over 10 years ago

#98 - Remove Project field from Sample concept

Pull Request - State: closed - Opened by naegelyd over 10 years ago

#91 - Ability to display QC Data is missing

Issue - State: open - Opened by mitalia over 10 years ago - 1 comment
Labels: version:1.0, type:feature

#78 - Add result id field and variant result id concept to fixture

Pull Request - State: closed - Opened by naegelyd over 10 years ago - 1 comment

#54 - Consolidate avocado metadata migrations into single one

Pull Request - State: closed - Opened by naegelyd over 10 years ago - 1 comment

#37 - Show the sample name in the results toolbar when it is available

Pull Request - State: closed - Opened by naegelyd over 10 years ago - 1 comment

#23 - Implement custom results workflow, remove analysis workflow

Pull Request - State: closed - Opened by naegelyd over 10 years ago - 4 comments

#13 - Add support for Django 1.5

Issue - State: closed - Opened by naegelyd almost 11 years ago - 4 comments
Labels: type:refactor, version 0.1

#9 - Add ability to (re)queue particular stages in the pipeline

Issue - State: closed - Opened by naegelyd almost 11 years ago - 2 comments
Labels: version:future, type:feature

#4 - Add support for pipeline webhooks

Issue - State: closed - Opened by bruth almost 11 years ago - 1 comment
Labels: version:future, type:feature