Owner

ebi-ait

19 indexed repositories · View on GitHub

json-converter
json-converter is a tool for translating/converting a JSON document into another JSON document with a different structure.

Python · 11 stars
hca-ebi-wrangler-central
This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.

Jupyter Notebook · 5 stars
checklist
Template repository for checklists

1 star
hca-util
CLI tool for file transfer (upload and download) to/from AWS S3.

Python · 1 star
ingest-graph-validator
HCA Ingest Service Graph Validation Suite

Python · 1 star
hca-ebi-user-value
Planning repository for the value we get out of HCA work. Other planning repos (e.g. hca-ebi-dev-team) integrate with this one

0 stars
covid-util
Tool for CLI transfer of COVID-19 data to upload areas and adminstration of those areas

0 stars
covid-excel-utils
Tools to transform and validate covid data portal metadata files.

Python · 0 stars
data-cube

JavaScript · 0 stars
submissions-workstream
A repository dedicated to the submissions workstreams - All code, materials and services go here.

Jupyter Notebook · 0 stars
sars-cov2-data-upload

HTML · 0 stars
data-catalogue-frontend

TypeScript · 0 stars
microbe-central
Central repository to store MICROBE-related issues

0 stars
dcp-ingest-central
Central point of access for the Ingestion Service of the HCA DCP

0 stars
data-catalogue-microbe

TypeScript · 0 stars
hca-to-scea-tools
Helpers and tools to assist in the conversion of HCA datasets into SCEA

Python · 0 stars
hca-dcp-to-tier1
Convert an HCA DCP spreadsheet to HCA Tier 1

Python · 0 stars
hca-ebi-dev-team
Repository for hca ebi dev team agile management. See zenhub board

Jupyter Notebook · 0 stars
hca-tier1-to-dcp
Convert HCA Tier 1, to HCA DCP spreadsheet

Python · 0 stars

Open All

835 open issues indexed

Correct errors and add (meta)data in submissions faster Open

Epic FAIRifcation-hide HCA User Story

ebi-ait/dcp-ingest-central#1 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
View all orphaned entities Open

Just Right User Story UX research

ebi-ait/dcp-ingest-central#6 · 12 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
prevent accidental export to DCP of projects that are not public Open

Small User Story

ebi-ait/dcp-ingest-central#27 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
View general summary of a submission Open

User Story

ebi-ait/dcp-ingest-central#42 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
[Broker Service ? ] Create a component which will return schema info needed for adding metadata via UI Open

non functional

ebi-ait/dcp-ingest-central#44 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Locate the part of the project to be updated Open

Just Right User Story

ebi-ait/dcp-ingest-central#76 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Delete an entire metadata entity Open

User Story

ebi-ait/dcp-ingest-central#81 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Deprecate biomaterial.projects and process.projects Open

non functional

ebi-ait/dcp-ingest-central#88 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add constraint that an entity should always be linked to the project Open

FAIRifcation-hide

ebi-ait/dcp-ingest-central#89 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create endpoint to retrieve all information about the process Open

ebi-ait/dcp-ingest-central#100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use WebSockets instead of polling Open

enhancement

ebi-ait/dcp-ingest-central#103 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Metadata table design - improvements to current views to prioritise information and actions to be taken Open

FAIRifcation-hide HCA operations should be product UX research

ebi-ait/dcp-ingest-central#107 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Design mockups for Update existing metadata/data 77 Open

FAIRifcation-hide HCA operations should be product UX design

ebi-ait/dcp-ingest-central#108 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Having to do the file transfer via the CLI Open

ebi-ait/dcp-ingest-central#114 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Elixir register integration with UI Open

bug

ebi-ait/dcp-ingest-central#115 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Individual file transfer function in hca-util Open

User Story

ebi-ait/dcp-ingest-central#116 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Project Catalogue Open

Epic FAIRifcation-hide HCA

ebi-ait/dcp-ingest-central#117 · 6 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Deprecated schemas are being returned in the latestSchemas endpoint Open

bug

ebi-ait/dcp-ingest-central#118 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Send fastq files directly from ingest prod. to SCEA Open

ebi-ait/dcp-ingest-central#120 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve automation of tracker sheet curation following addition of new datasets (rows) Open

ebi-ait/dcp-ingest-central#122 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Ability to select upload area for file transfer Open

ebi-ait/dcp-ingest-central#123 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Submission is Valid even with Draft metadata Open

bug

ebi-ait/dcp-ingest-central#132 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Protocols are being linked multiple times Open

bug

ebi-ait/dcp-ingest-central#137 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use EBI OLS ontology instead of having HCA Ontology service Open

non functional

ebi-ait/dcp-ingest-central#146 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
automatically delete an upload area Open

ebi-ait/dcp-ingest-central#149 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Archiving projects from HCA to SCEA Open

Epic FAIRifcation-hide HCA

ebi-ait/dcp-ingest-central#151 · 8 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Add constraint that files should be unique within the project Open

ebi-ait/dcp-ingest-central#162 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
[BUG] Can't remove all values from a field when editing in the UI Open

bug

ebi-ait/dcp-ingest-central#164 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Speed up submissions Open

Epic Impact

ebi-ait/dcp-ingest-central#168 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Validate schema domain Open

bug enhancement

ebi-ait/dcp-ingest-central#170 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Incorporate fastq file validation (e.g. barcode length) check into ingest Open

FAIRifcation-hide HCA

ebi-ait/dcp-ingest-central#174 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
backup for redis db of state tracker Open

ebi-ait/dcp-ingest-central#181 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Technical Debt Open

Epic

ebi-ait/dcp-ingest-central#182 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Notify Failed error in hca-util sync Open

ebi-ait/dcp-ingest-central#183 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
"Submit to project" button does not show immediately Open

bug

ebi-ait/dcp-ingest-central#184 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improving datafile transfer Open

Epic

ebi-ait/dcp-ingest-central#186 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
wild card on list for util Open

User Story

ebi-ait/dcp-ingest-central#188 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
wild card function in util Open

User Story

ebi-ait/dcp-ingest-central#189 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve CI/CD processes Open

Epic non functional

ebi-ait/dcp-ingest-central#193 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create an alert message for users when they attempt to delete a project with existing submissions. Open

User Story

ebi-ait/dcp-ingest-central#198 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Cleanup codes related to the update submission flow Open

non functional

ebi-ait/dcp-ingest-central#205 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Ability to upload a list of contributors instead of one by one Open

User Story UX design

ebi-ait/dcp-ingest-central#207 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Remove flag for supporting upload of files from nested directories in hca-util upload Open

ebi-ait/dcp-ingest-central#216 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Need to validate that all submissions have someone in the data curator role Open

Epic FAIRifcation-hide HCA

ebi-ait/dcp-ingest-central#218 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
hca-util upload progress shown on new lines Open

bug

ebi-ait/dcp-ingest-central#221 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
UI screen to run the hca-to-scea tool for valid project Open

User Story

ebi-ait/dcp-ingest-central#222 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
adding back functionality to compare_tracker_with_nxn_sheet_version2.py script Open

ebi-ait/dcp-ingest-central#227 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve error handling of move_data_from_insdc script Open

User Story

ebi-ait/dcp-ingest-central#228 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Set Expiration Policy on ingest backups Open

non functional

ebi-ait/dcp-ingest-central#229 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
message for loss of connection Open

User Story

ebi-ait/dcp-ingest-central#239 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

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