Ecosyste.ms: Issues

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

GitHub / usegalaxy-eu/ena-upload-cli issues and pull requests

#103 - Bugfix paired end reads throwing type error

Pull Request - State: closed - Opened by bedroesb about 1 month ago

#102 - Allow for custom attributes and read type description of fastq

Pull Request - State: open - Opened by cgirardot about 1 month ago - 18 comments

#101 - Improved use of GitHub Actions + pandas warning fix

Pull Request - State: closed - Opened by bedroesb 2 months ago - 4 comments

#97 - pyyaml 5.4.* is giving problems upon installation

Pull Request - State: closed - Opened by bedroesb 4 months ago - 6 comments

#96 - Submitting paired reads plus their indices

Issue - State: closed - Opened by mobilegenome 8 months ago - 2 comments

#95 - Submitting new project to ENA

Issue - State: closed - Opened by Najatamk 8 months ago - 5 comments

#94 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] 9 months ago
Labels: automatic PR

#93 - Increase timeouts and improve handling of high-latency connections

Pull Request - State: closed - Opened by nuwang 9 months ago

#92 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago
Labels: automatic PR

#91 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago
Labels: automatic PR

#90 - Bugfix: isa-json not working when tool is not launched in the ENA-upload-cli directory

Pull Request - State: closed - Opened by bedroesb 11 months ago
Labels: bug

#89 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] 12 months ago
Labels: automatic PR

#88 - Adding ISA-JSON support as input file.

Pull Request - State: closed - Opened by bedroesb about 1 year ago - 2 comments

#87 - Add support for the submission of analysis objects

Issue - State: open - Opened by bedroesb over 1 year ago
Labels: enhancement

#86 - Add support for custom attributes

Issue - State: open - Opened by bedroesb over 1 year ago
Labels: enhancement

#85 - The license_file parameter is deprecated, use license_files instead.

Issue - State: closed - Opened by FernandoDuarteF over 1 year ago - 3 comments

#84 - Add support for pandas 2.0 support + lock versions

Pull Request - State: closed - Opened by bedroesb over 1 year ago - 1 comment

#83 - Name: experiment_alias, dtype: object has no member named "iteritems"

Issue - State: closed - Opened by FernandoDuarteF over 1 year ago - 2 comments

#82 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: automatic PR

#81 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: automatic PR

#80 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: automatic PR

#79 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago
Labels: automatic PR

#78 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago
Labels: automatic PR

#77 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago
Labels: automatic PR

#76 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago
Labels: automatic PR

#75 - The read operation timed out

Issue - State: closed - Opened by mthang about 2 years ago - 13 comments

#74 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: automatic PR

#73 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: automatic PR

#72 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago
Labels: automatic PR

#71 - Bug fix: mandatory fields are handled better when not filled in

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

#70 - Include script used to generate tabular metadata templates

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

#69 - Bug fix for the remote check

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

#68 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] almost 3 years ago - 2 comments
Labels: automatic PR

#67 - Adding units to templates

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

#66 - Correct criteria for a successful submission

Issue - State: closed - Opened by wna-se almost 3 years ago - 2 comments

#65 - Added units where requires by ERC000033

Pull Request - State: closed - Opened by wna-se almost 3 years ago - 10 comments

#64 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] almost 3 years ago
Labels: automatic PR

#63 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] almost 3 years ago
Labels: automatic PR

#62 - nan is filled in when column is mandatory and cell is empty

Issue - State: closed - Opened by bedroesb almost 3 years ago - 1 comment
Labels: bug

#61 - Fixing float giving error when parsed in the xml

Pull Request - State: closed - Opened by bedroesb about 3 years ago
Labels: bug

#60 - Automatic check if an object already exists on ENA

Pull Request - State: closed - Opened by bedroesb about 3 years ago - 4 comments
Labels: enhancement

#59 - Hotfix

Pull Request - State: closed - Opened by bedroesb about 3 years ago - 2 comments

#57 - Hotfix for release/cancel to not require files

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

#56 - XLSX support

Pull Request - State: closed - Opened by bedroesb about 3 years ago - 3 comments
Labels: enhancement

#55 - FTPS stability and speed improvements

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

#54 - Drop empty rows

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

#52 - Empty rows give error

Issue - State: closed - Opened by bedroesb about 3 years ago

#51 - Updating introduction

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

#50 - Adding TLS to the ftp connection

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

#49 - Create CITATION.cff

Pull Request - State: closed - Opened by bedroesb about 3 years ago - 3 comments

#48 - Support FTPS connection to protect account credidentials

Issue - State: closed - Opened by wna-se about 3 years ago - 7 comments

#47 - [WIP] add module to parse xlsx to tsv/pandas

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

#46 - Correct use of optional attributes in run/experiment and study tables

Pull Request - State: closed - Opened by bedroesb about 3 years ago - 4 comments

#45 - Handling tables that have no actions in the status column

Pull Request - State: closed - Opened by bedroesb over 3 years ago - 2 comments

#44 - Adding draft flag to not perform a submission

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

#43 - Adding flag to not do a submission but just to generate the XMLs

Issue - State: closed - Opened by bedroesb over 3 years ago
Labels: enhancement

#42 - Automatic update of ENA Sample Checklists

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago - 2 comments
Labels: automatic PR

#41 - Adding release and cancel as an action

Pull Request - State: closed - Opened by bedroesb over 3 years ago - 2 comments

#40 - Adding controlled vocabulary to the sample checklists

Issue - State: open - Opened by bedroesb over 3 years ago
Labels: enhancement

#39 - Adding back tool name to sample metadata

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

#38 - Catching errors better + more clear error messages

Issue - State: open - Opened by bedroesb over 3 years ago
Labels: enhancement

#37 - Supporting all optional fields in the run/experiment and study xml

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

#36 - Changing release date through API

Issue - State: closed - Opened by bedroesb over 3 years ago - 3 comments
Labels: enhancement

#35 - Generating md5 hash when not given with -no_upload flag

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

#34 - If table is given without action values, an error is thrown

Issue - State: closed - Opened by bedroesb over 3 years ago
Labels: enhancement

#33 - --no_upload parameter not working

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

#32 - Updating documentation about modify

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

#31 - Fixing template to allow no filled in optional fields

Pull Request - State: closed - Opened by bedroesb over 3 years ago - 2 comments

#30 - Possible values for file_format are not clear

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

#29 - Most minimal example not working

Issue - State: closed - Opened by bedroesb over 3 years ago
Labels: bug

#28 - Fixing bug if empty cell for file_checksum column

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

#27 - Taxon ID parsing improvements

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

#26 - Adding support for all official sample checklists on ENA

Pull Request - State: closed - Opened by bedroesb over 3 years ago - 7 comments

#25 - Taking away the need to give columns that are automatically filled in by the tool

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

#24 - Allow to skip file upload and provide a file of filenames as source for data files

Pull Request - State: closed - Opened by mobilegenome over 3 years ago - 4 comments

#23 - Library name generation

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

#22 - Using the labels from ENA in the tsv table headers instead of the underscore version

Issue - State: closed - Opened by bedroesb over 3 years ago
Labels: enhancement, question

#21 - Dropping unnecessary columns

Issue - State: closed - Opened by bedroesb over 3 years ago
Labels: enhancement

#20 - Adding support for all official ENA checklists

Issue - State: closed - Opened by bedroesb over 3 years ago - 2 comments
Labels: enhancement

#19 - Adding support for multiple checklists

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

#18 - Read md5sum from table, and only generate if missing

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

#17 - Add ENA_template_ERC000011_sample.xml

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

#16 - Small fixes based on #15

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

#15 - Adding all optional and recommended fields to the viral template

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

#14 - Add GitHub Action to check if new xsd templates are added to ENA

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

#13 - Updating the templates to 1.6

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

#12 - Replace calling "curl" by using Python's "request" module

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

#11 - Missing / Wrong sequencer identifiers in templates

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

#10 - test optional field

Pull Request - State: closed - Opened by tpall almost 4 years ago - 5 comments

#9 - Possibility to upload non-mandatory (virus) metadata

Issue - State: closed - Opened by tpall almost 4 years ago - 2 comments

#8 - Support for viral sample template

Pull Request - State: closed - Opened by bedroesb over 4 years ago

#7 - Support for ERC000033 checklist

Issue - State: closed - Opened by bedroesb over 4 years ago - 1 comment
Labels: enhancement

#6 - Possibility to give the taxon_id through the table

Issue - State: closed - Opened by bedroesb over 4 years ago - 1 comment
Labels: enhancement

#5 - FTPS instead of FTP

Issue - State: closed - Opened by bedroesb over 4 years ago
Labels: enhancement

#4 - pip install fix

Pull Request - State: closed - Opened by bedroesb over 4 years ago