ebi-ait/hca-to-scea-tools issues and pull requests

#103 - Check species eligibility #86

Pull Request - State: closed - Opened by ami-day about 2 years ago

#102 - Check hca2scea works with multiple samples from same donor

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment
Labels: bug

#101 - Fixed issues in code associated with failure of positive test cases

Pull Request - State: closed - Opened by ami-day about 2 years ago

#100 - Removed output of old positive test cases, not in use.

Pull Request - State: closed - Opened by ami-day about 2 years ago

#99 - Removed positive tests - will create a separate branch for the positi…

Pull Request - State: closed - Opened by ami-day about 2 years ago - 1 comment

#98 - Add positive test cases to characteristic test

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment

#97 - Refactor main hca2scea code

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment
Labels: enhancement

#96 - Changed names of test files to reflect the functionality they test.

Pull Request - State: closed - Opened by ami-day about 2 years ago

#95 - Check experimental design #90

Pull Request - State: closed - Opened by ami-day about 2 years ago

#94 - Check for missing linking #91

Pull Request - State: closed - Opened by ami-day about 2 years ago - 1 comment

#93 - Enable complex experiment design #92

Pull Request - State: closed - Opened by ami-day about 2 years ago - 1 comment

#92 - Hca_to_scea: Fix protocol linking for complex experiment designs

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment

#91 - Hca_to_scea test: check for missing linking

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment

#90 - Hca_to_scea test: check experimental design

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment

#89 - Check for pooled biomaterials #88

Pull Request - State: closed - Opened by ami-day about 2 years ago

#88 - Hca_to_scea test: check for pooled biomaterials

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment

#87 - Check species eligibility #86

Pull Request - State: closed - Opened by ami-day about 2 years ago

#86 - Hca_to_scea test: eligibility of species

Issue - State: closed - Opened by ami-day about 2 years ago

#85 - Check technology eligibility #84

Pull Request - State: closed - Opened by ami-day about 2 years ago

#84 - Hca_to_scea test: eligibility of technology types

Issue - State: closed - Opened by ami-day about 2 years ago - 1 comment
Labels: enhancement

#83 - Add additional Test Cases

Issue - State: closed - Opened by ami-day about 2 years ago - 2 comments
Labels: enhancement

#82 - Fixed duplication of investigation title in the output idf file.

Pull Request - State: closed - Opened by ami-day over 2 years ago
Labels: bug

#81 - Check for floating point number and reformat it.

Pull Request - State: closed - Opened by ami-day over 2 years ago - 2 comments
Labels: bug

#80 - Duplicated Investigation title in idf file

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: bug

#79 - Correct floating point error

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: bug

#78 - dcp-69 create pypi package 2

Pull Request - State: open - Opened by ami-day over 2 years ago

#77 - dcp-151 change output file type for ui integration

Pull Request - State: closed - Opened by ami-day over 2 years ago

#76 - dcp-68 split metadata by technology type

Pull Request - State: closed - Opened by ami-day over 2 years ago - 1 comment

#75 - Enhancement: add enrichment markers to immunophenotype column in sdrf

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: enhancement

#74 - Enhancement: add Fluidigm as technology type

Issue - State: closed - Opened by ami-day over 2 years ago - 2 comments
Labels: enhancement

#73 - Enhancement: get secondary accessions from ingest

Issue - State: open - Opened by ami-day over 2 years ago - 1 comment
Labels: enhancement

#72 - Feature 69 Create pypi package

Pull Request - State: closed - Opened by ami-day over 2 years ago - 2 comments

#71 - Enhancement: Pooled samples

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: enhancement

#70 - Enhancement: organoid datasets

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: enhancement

#69 - Create PyPi package for hca-to-scea tool

Issue - State: closed - Opened by ami-day over 2 years ago - 13 comments
Labels: dev task, User Story

#68 - Bug/Enhancement: does not support more than 1 10X version in the same dataset

Issue - State: closed - Opened by ami-day over 2 years ago - 2 comments
Labels: bug, enhancement

#67 - Bug: does not support protocol type arrays of different lengths

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: bug, enhancement

#66 - Bug: does not support datasets with multiples runs/lanes linked to a single cell suspension

Issue - State: closed - Opened by ami-day over 2 years ago - 1 comment
Labels: bug, enhancement

#65 - New feature: add publication info to idf file

Pull Request - State: closed - Opened by ami-day over 2 years ago

#64 - New feature: automatically add publication information

Issue - State: closed - Opened by ami-day over 2 years ago
Labels: enhancement

#63 - Bump ajv from 6.12.0 to 6.12.6 in /hca2scea-frontend

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#62 - Bump node-sass from 4.13.1 to 7.0.0 in /hca2scea-frontend

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#61 - Feature/resolve sra file duplications

Pull Request - State: closed - Opened by ami-day over 2 years ago

#60 - SRA Object file paths are duplicated in the output sdrf file

Issue - State: closed - Opened by ami-day over 2 years ago - 3 comments
Labels: bug

#59 - Feature/hcatoscea_test_data_ami_update

Pull Request - State: closed - Opened by ami-day over 2 years ago - 4 comments

#58 - dcp-593 add test data

Pull Request - State: open - Opened by amnonkhen over 2 years ago
Labels: dev task, User Story

#57 - Feature: get sra object from ena. dcp-513

Pull Request - State: closed - Opened by ami-day almost 3 years ago

#56 - Installation of hca2scea tool on EC2

Issue - State: closed - Opened by ami-day almost 3 years ago - 1 comment

#55 - Add new deployment workflow

Pull Request - State: open - Opened by jacobwindsor almost 3 years ago
Labels: User Story, non functional, FAIRification, Submission, UX design

#54 - Update to hca2scea tool: automatically obtain fastq file paths or SRA file paths

Pull Request - State: closed - Opened by ami-day almost 3 years ago - 2 comments

#53 - Updated test_hca2scea.py

Pull Request - State: closed - Opened by ami-day almost 3 years ago - 3 comments

#52 - Updated script

Pull Request - State: closed - Opened by ami-day almost 3 years ago

#51 - Bump axios from 0.19.2 to 0.21.2 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 2 comments
Labels: dependencies

#50 - Bump color-string from 1.5.3 to 1.6.0 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 2 comments
Labels: dependencies

#49 - characteristic tests dcp-470

Pull Request - State: closed - Opened by amnonkhen almost 3 years ago

#48 - Bump path-parse from 1.0.6 to 1.0.7 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 2 comments
Labels: dependencies

#47 - Update sop

Pull Request - State: closed - Opened by ami-day about 3 years ago

#46 - Bump xlsx from 0.15.6 to 0.17.0 in /hca2scea-backend

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 2 comments
Labels: dependencies

#45 - Bump postcss from 7.0.27 to 7.0.36 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#44 - Bump glob-parent from 5.1.0 to 5.1.2 in /hca2scea-backend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#43 - Bump browserslist from 4.8.7 to 4.16.6 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#42 - Updated the readme

Pull Request - State: closed - Opened by Wkt8 over 3 years ago

#41 - Bump hosted-git-info from 2.8.5 to 2.8.9 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#40 - Bump lodash from 4.17.15 to 4.17.21 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#39 - Bump ua-parser-js from 0.7.21 to 0.7.28 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#38 - Feature/code cleanup: updates to test

Pull Request - State: closed - Opened by ami-day over 3 years ago - 2 comments
Labels: enhancement

#37 - Support spreadsheets with multiple specimen ids per donor id

Issue - State: closed - Opened by ami-day over 3 years ago - 1 comment
Labels: bug

#36 - Bump y18n from 3.2.1 to 3.2.2 in /hca2scea-frontend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#35 - Some projects give errors. Investigate these and resolve them.

Issue - State: closed - Opened by ami-day over 3 years ago - 1 comment
Labels: bug

#34 - Get sequence file paths

Pull Request - State: closed - Opened by ami-day over 3 years ago

#33 - Update name options

Pull Request - State: closed - Opened by ami-day over 3 years ago

#32 - Update UUID argument

Pull Request - State: closed - Opened by ami-day over 3 years ago

#31 - Reformatted the age range to remove '-' character

Pull Request - State: closed - Opened by ami-day over 3 years ago

#30 - Reformat technology

Pull Request - State: closed - Opened by ami-day over 3 years ago

#29 - Mismatches in fields when running from contributor spreadsheet

Issue - State: closed - Opened by mshadbolt over 3 years ago - 1 comment

#28 - Have an optional `output path` argument

Issue - State: closed - Opened by mshadbolt over 3 years ago - 1 comment
Labels: enhancement

#27 - help text for `-id` argument inconsistent

Issue - State: closed - Opened by mshadbolt over 3 years ago - 1 comment

#26 - Added new technology options

Pull Request - State: closed - Opened by ami-day over 3 years ago

#25 - added engine as openpyxl

Pull Request - State: closed - Opened by yusra-haider over 3 years ago

#24 - Hca to scea tool: add ability to curate enrichment protocol

Issue - State: closed - Opened by ami-day over 3 years ago - 1 comment
Labels: bug

#23 - Conversion hangs after clicking on 'Process' on web interface

Issue - State: closed - Opened by rays22 over 3 years ago - 29 comments
Labels: bug

#22 - Added new technology type options and edited the relevant fields

Pull Request - State: closed - Opened by ami-day over 3 years ago

#21 - Automated the updates to the project_details.json file

Pull Request - State: closed - Opened by ami-day over 3 years ago - 1 comment

#20 - Added new fields to idf

Pull Request - State: closed - Opened by ami-day over 3 years ago - 3 comments

#19 - Bump dot-prop from 4.2.0 to 4.2.1 in /hca2scea-backend

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#16 - Add ability to get all secondary accessions from the spreadsheet

Issue - State: closed - Opened by ami-day over 3 years ago - 2 comments

#15 - Ability to get full file paths for file names. Also include an initial check and exit if file paths cannot be found.

Issue - State: closed - Opened by ami-day over 3 years ago - 1 comment

#14 - Ability to check which E-HCAD-ids are in the tracker already and suggest the next id (still allowing for editing)

Issue - State: closed - Opened by ami-day over 3 years ago - 2 comments

#13 - Add ability to get hca submission id from the project in ingest prod. and also get the last update date for the project

Issue - State: closed - Opened by ami-day over 3 years ago - 1 comment

GitHub / ebi-ait/hca-to-scea-tools issues and pull requests