Research Object for Scholarly Communication Community Group - Activity in 2023
No matches.
Lifecycle
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1 group closed.
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The Research Object for Scholarly Communication Community Group was closed.
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GitHub
ResearchObject/ro-crate-validator-py
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1 pull request opened.
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Add validation script and Dockerfile ResearchObject/ro-crate-validator-py#8, by @johnf.
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ResearchObject/ro-crate
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1 issue received 1 new comment.
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1 pull request opened.
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Add EGI AppDB to website ResearchObject/ro-crate#280, by @stain.
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1 pull request merged.
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Add EGI AppDB to website ResearchObject/ro-crate#280.
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ResearchObject/runcrate
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1 pull request merged.
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upgrade to cwl-utils 0.30 ResearchObject/runcrate#67.
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1 pull request received 1 new comment.
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ResearchObject/runcrate#73 (1 comment by @simleo)
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GitHub
ResearchObject/workflow-run-crate
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1 issue closed.
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CQ10 - Tool wrappers ResearchObject/workflow-run-crate#18.
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3 issues received 5 new comments.
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CQ2 - Resource usage ResearchObject/workflow-run-crate#10 (3 comments by @kinow, @rsirvent, @simleo)
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Join the working group (post here to be added) ResearchObject/workflow-run-crate#1 (1 comment by @charmoniumQ)
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3 pull requests opened.
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Release 0.4 ResearchObject/workflow-run-crate#68, by @simleo.
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Add spec on software dependencies ResearchObject/workflow-run-crate#67, by @simleo.
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Add CRCC img convert crate ResearchObject/workflow-run-crate#66, by @simleo.
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3 pull requests merged.
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Release 0.4 ResearchObject/workflow-run-crate#68.
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Add spec on software dependencies ResearchObject/workflow-run-crate#67.
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Add CRCC img convert crate ResearchObject/workflow-run-crate#66.
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2 pull requests received 5 new comments.
ResearchObject/runcrate
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3 issues closed.
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Error from runcrate-analysis, scenario 2_a ResearchObject/runcrate#11.
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Error from runcrate-analysis, scenario 4_a ResearchObject/runcrate#12.
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CWLProv conversion: include creation datetime, size, checksum, format ResearchObject/runcrate#13.
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2 issues received 2 new comments.
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5 pull requests opened.
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Convert SoftwareRequirement ResearchObject/runcrate#72, by @simleo.
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Convert encoding format for output files ResearchObject/runcrate#70, by @simleo.
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More file metadata ResearchObject/runcrate#69, by @simleo.
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upgrade to cwl-utils 0.30 ResearchObject/runcrate#67, by @mr-c.
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Add ContainerImage ResearchObject/runcrate#66, by @simleo.
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4 pull requests merged.
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Convert SoftwareRequirement ResearchObject/runcrate#72.
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Convert encoding format for output files ResearchObject/runcrate#70.
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More file metadata ResearchObject/runcrate#69.
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Add ContainerImage ResearchObject/runcrate#66.
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2 pull requests received 4 new comments.
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ResearchObject/runcrate#65 (1 comment by @simleo)
ResearchObject/ro-crate
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1 issue closed.
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Use Case: compatible with BagIt ResearchObject/ro-crate#13.
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3 issues received 3 new comments.
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1 pull request opened.
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Update index.md ResearchObject/ro-crate#279, by @stain.
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ResearchObject/ro-terms
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1 pull request opened.
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workflow-run: add softwareRequirements override ResearchObject/ro-terms#19, by @simleo.
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1 pull request closed.
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workflow-run: add softwareRequirements override ResearchObject/ro-terms#19.
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1 pull request received 1 new comment.
ResearchObject/bh2023-enabling-fair-digital-objects
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1 pull request opened.
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add section on Signposting on SPAs to the chapter Results ResearchObject/bh2023-enabling-fair-digital-objects#1, by @jgrieb.
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1 pull request merged.
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add section on Signposting on SPAs to the chapter Results ResearchObject/bh2023-enabling-fair-digital-objects#1.
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GitHub
ResearchObject/workflow-run-crate
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2 issues closed.
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CQ1 - Container image ResearchObject/workflow-run-crate#9.
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Representing environment variables ResearchObject/workflow-run-crate#62.
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1 issue received 1 new comment.
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2 pull requests opened.
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0.3 Release ResearchObject/workflow-run-crate#65, by @simleo.
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Add spec to describe container images ResearchObject/workflow-run-crate#64, by @simleo.
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4 pull requests merged.
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Added initial WfExS-backend examples based on toy workflow. ResearchObject/workflow-run-crate#53.
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0.3 Release ResearchObject/workflow-run-crate#65.
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Add spec to describe container images ResearchObject/workflow-run-crate#64.
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Guidelines on representing environment variables ResearchObject/workflow-run-crate#63.
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1 pull request received 5 new comments.
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Added initial WfExS-backend examples based on toy workflow. ResearchObject/workflow-run-crate#53 (5 comments by @jmfernandez, @simleo)
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ResearchObject/ro-terms
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1 pull request opened.
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workflow-run: add terms for container images ResearchObject/ro-terms#18, by @simleo.
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2 pull requests merged.
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workflow-run: add terms for container images ResearchObject/ro-terms#18.
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workflow-run: add environment property ResearchObject/ro-terms#17.
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1 pull request received 2 new comments.
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workflow-run: add terms for container images ResearchObject/ro-terms#18 (2 comments by @kinow, @stain)
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ResearchObject/runcrate
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1 pull request opened.
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convert: add whole workflow-run context to the crate ResearchObject/runcrate#63, by @simleo.
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1 pull request merged.
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convert: add whole workflow-run context to the crate ResearchObject/runcrate#63.
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1 pull request received 1 new comment.
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ResearchObject/runcrate#64 (1 comment by @simleo)
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ResearchObject/ro-crate
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1 issue opened.
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Bug: We are not explicit enough about Data Entities -- MUST or SHOULD they exist in root directory? ResearchObject/ro-crate#277, by @ptsefton.
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2 issues received 3 new comments.
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Bug: We are not explicit enough about Data Entities -- MUST or SHOULD they exist in root directory? ResearchObject/ro-crate#277 (2 comments by @ptsefton)
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1 pull request opened.
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Tightening up wording around data entities -- we had not actual said … ResearchObject/ro-crate#278, by @ptsefton.
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1 pull request received 9 new comments.
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Tightening up wording around data entities -- we had not actual said … ResearchObject/ro-crate#278 (9 comments by @ptsefton, @simleo)
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ResearchObject/software-profiles
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1 issue opened.
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Task: Set up w3id namespace and redirect for these profiles ResearchObject/software-profiles#1, by @ptsefton.
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1 issue received 3 new comments.
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Task: Set up w3id namespace and redirect for these profiles ResearchObject/software-profiles#1 (3 comments by @dgarijo, @stain)
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ResearchObject/ro-crate-py
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1 issue opened.
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Raise an error, warning, or ignore duplicate ID's? ResearchObject/ro-crate-py#165, by @kinow.
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1 issue closed.
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Raise an error, warning, or ignore duplicate ID's? ResearchObject/ro-crate-py#165.
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1 issue received 2 new comments.
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Raise an error, warning, or ignore duplicate ID's? ResearchObject/ro-crate-py#165 (2 comments by @kinow, @simleo)
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1 pull request opened.
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Sync entity map with specific lists ResearchObject/ro-crate-py#166, by @simleo.
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1 pull request merged.
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Sync entity map with specific lists ResearchObject/ro-crate-py#166.
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ResearchObject/ro-crate-validator-py
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3 issues opened.
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Support for zip files? ResearchObject/ro-crate-validator-py#7, by @hexylena.
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feature request: cli ResearchObject/ro-crate-validator-py#6, by @hexylena.
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undeclared dependency on pytest, new release requested ResearchObject/ro-crate-validator-py#5, by @hexylena.
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2 issues received 2 new comments.
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undeclared dependency on pytest, new release requested ResearchObject/ro-crate-validator-py#5 (1 comment by @stain)
GitHub
ResearchObject/ro-crate
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2 issues opened.
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Add CodeMeta terms ResearchObject/ro-crate#275, by @stain.
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Update to schema.org 22.0, ensure schema.org is archived ResearchObject/ro-crate#274, by @stain.
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2 issues closed.
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Update to schema.org 22.0, ensure schema.org is archived ResearchObject/ro-crate#274.
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RO-Crate Tutorial ResearchObject/ro-crate#75.
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3 issues received 3 new comments.
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Update to schema.org 22.0, ensure schema.org is archived ResearchObject/ro-crate#274 (1 comment by @stain)
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2 pull requests opened.
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Add Codemeta terms ResearchObject/ro-crate#276, by @stain.
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Clarifying the dataPublished requirement ResearchObject/ro-crate#273, by @ptsefton.
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1 pull request merged.
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Clarifying the dataPublished requirement ResearchObject/ro-crate#273.
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1 pull request received 1 new comment.
ResearchObject/runcrate
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2 pull requests opened.
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report: do not expect input and output to be lists ResearchObject/runcrate#61, by @simleo.
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Set codecov-action back to v3 ResearchObject/runcrate#60, by @simleo.
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2 pull requests merged.
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report: do not expect input and output to be lists ResearchObject/runcrate#61.
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Set codecov-action back to v3 ResearchObject/runcrate#60.
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ResearchObject/ro-crate-py
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2 issues opened.
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Support tar.gz or other archive formats? ResearchObject/ro-crate-py#164, by @kinow.
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Add method to include additional contexts at the top level ResearchObject/ro-crate-py#160, by @jmfernandez.
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4 issues closed.
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BUG: Duplicate references in hasPart on root dataset cause an error on loading crate ResearchObject/ro-crate-py#159.
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hasPart property on root dataset is assumed to be an array ResearchObject/ro-crate-py#158.
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Add method to include additional contexts at the top level ResearchObject/ro-crate-py#160.
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Support indirect data entity linking from root ResearchObject/ro-crate-py#141.
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3 issues received 3 new comments.
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Add method to include additional contexts at the top level ResearchObject/ro-crate-py#160 (1 comment by @jmfernandez)
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BUG: Duplicate references in hasPart on root dataset cause an error on loading crate ResearchObject/ro-crate-py#159 (1 comment by @simleo)
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3 pull requests opened.
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Handle non-array hasPart entries ResearchObject/ro-crate-py#163, by @simleo.
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Add method to add contexts ResearchObject/ro-crate-py#162, by @simleo.
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Add indirectly linked data entities ResearchObject/ro-crate-py#161, by @simleo.
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3 pull requests merged.
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Handle non-array hasPart entries ResearchObject/ro-crate-py#163.
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Add method to add contexts ResearchObject/ro-crate-py#162.
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Add indirectly linked data entities ResearchObject/ro-crate-py#161.
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ResearchObject/workflow-run-crate
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1 issue received 1 new comment.
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Join the working group (post here to be added) ResearchObject/workflow-run-crate#1 (1 comment by @samuell)
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1 pull request received 5 new comments.
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Added initial WfExS-backend examples based on toy workflow. ResearchObject/workflow-run-crate#53 (5 comments by @jmfernandez, @simleo)
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ResearchObject/ResearchObject.github.io
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1 pull request merged.
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[ISSUE-2] Switch logo to title image instead of title ResearchObject/ResearchObject.github.io#3.
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GitHub
ResearchObject/workflow-run-crate
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2 issues received 6 new comments.
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CQ1 - Container image ResearchObject/workflow-run-crate#9 (5 comments by @ilveroluca, @rsirvent, @simleo)
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1 pull request opened.
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Guidelines on representing environment variables ResearchObject/workflow-run-crate#63, by @simleo.
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1 pull request received 1 new comment.
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Added initial WfExS-backend examples based on toy workflow. ResearchObject/workflow-run-crate#53 (1 comment by @jmfernandez)
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ResearchObject/ro-terms
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1 pull request opened.
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workflow-run: add environment property ResearchObject/ro-terms#17, by @simleo.
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ResearchObject/ro-crate-validator-py
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1 issue received 1 new comment.
ResearchObject/ro-crate-py
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2 issues opened.
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BUG: Duplicate references in hasPart on root dataset cause an error on loading crate ResearchObject/ro-crate-py#159, by @ptsefton.
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hasPart property on root dataset is assumed to be an array ResearchObject/ro-crate-py#158, by @ptsefton.
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2 issues closed.
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Add method to get entities by type ResearchObject/ro-crate-py#138.
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Export entities/models in `rocrate.model.__init__` ResearchObject/ro-crate-py#147.
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2 pull requests opened.
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Add get_by_type ResearchObject/ro-crate-py#157, by @simleo.
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Fix test skip ResearchObject/ro-crate-py#156, by @simleo.
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3 pull requests merged.
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Add get_by_type ResearchObject/ro-crate-py#157.
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Fix test skip ResearchObject/ro-crate-py#156.
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Import model ResearchObject/ro-crate-py#155.
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1 pull request received 1 new comment.
ResearchObject/ro-crate
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2 pull requests opened.
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Add Sciebo-RDS to Tools ResearchObject/ro-crate#272, by @stain.
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OR2023 presentations ResearchObject/ro-crate#271, by @stain.
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3 pull requests merged.
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Add Sciebo-RDS to Tools ResearchObject/ro-crate#272.
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Profiles for ISA and ARC ResearchObject/ro-crate#270.
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OR2023 presentations ResearchObject/ro-crate#271.
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2 pull requests received 2 new comments.
Participants
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1 participant left.
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Joseph Schulkins left.
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GitHub
ResearchObject/workflow-run-crate
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1 issue received 4 new comments.
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Representing environment variables ResearchObject/workflow-run-crate#62 (4 comments by @jmfernandez, @mr-c, @simleo)
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1 pull request merged.
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Adding RO-Crate for the Autosubmit workflow that uses mHM and their test data domains ResearchObject/workflow-run-crate#61.
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1 pull request received 28 new comments.
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Adding RO-Crate for the Autosubmit workflow that uses mHM and their test data domains ResearchObject/workflow-run-crate#61 (28 comments by @kinow, @simleo)
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ResearchObject/ro-crate-py
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1 pull request opened.
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Import model ResearchObject/ro-crate-py#155, by @simleo.
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ResearchObject/ro-crate
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2 issues opened.
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Representation of boolean values ResearchObject/ro-crate#269, by @simleo.
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Representation of property values that are defined terms ResearchObject/ro-crate#268, by @simleo.
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2 issues received 3 new comments.
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Use Case: As a profile designer I want to use WKT for geo data to avoid ambiguity ResearchObject/ro-crate#266 (2 comments by @ptsefton, @stain)
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2 pull requests opened.
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Profiles for ISA and ARC ResearchObject/ro-crate#270, by @floWetzels.
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update describo information ResearchObject/ro-crate#267, by @marcolarosa.
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1 pull request merged.
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update describo information ResearchObject/ro-crate#267.
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2 pull requests received 3 new comments.
ResearchObject/ro-terms
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1 pull request opened.
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Add sapporo terms ResearchObject/ro-terms#16, by @inutano.
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1 pull request merged.
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Add sapporo terms ResearchObject/ro-terms#16.
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1 pull request received 1 new comment.
ResearchObject/runcrate
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1 pull request received 1 new comment.
ResearchObject/ro-crate-validator-py
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1 issue received 1 new comment.
GitHub
ResearchObject/workflow-run-crate
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1 issue opened.
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Representing environment variables ResearchObject/workflow-run-crate#62, by @simleo.
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2 issues received 2 new comments.
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1 pull request opened.
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Adding RO-Crate for the Autosubmit workflow that uses mHM and their test data domains ResearchObject/workflow-run-crate#61, by @kinow.
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1 pull request received 9 new comments.
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Adding RO-Crate for the Autosubmit workflow that uses mHM and their test data domains ResearchObject/workflow-run-crate#61 (9 comments by @kinow, @rsirvent, @simleo)
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ResearchObject/runcrate
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5 issues opened.
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Basedir for data files ResearchObject/runcrate#55, by @jjkoehorst.
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Data locations using manifest file ResearchObject/runcrate#54, by @jjkoehorst.
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Error from runcrate convert ResearchObject/runcrate#53, by @HrishiDhondge.
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Run: option to download remote inputs ResearchObject/runcrate#51, by @simleo.
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AttributeError: 'CommandLineTool' object has no attribute 'rsplit' ResearchObject/runcrate#49, by @jjkoehorst.
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2 issues closed.
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Data locations using manifest file ResearchObject/runcrate#54.
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AttributeError: 'CommandLineTool' object has no attribute 'rsplit' ResearchObject/runcrate#49.
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5 issues received 7 new comments.
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Option to make data files more user friendly ResearchObject/runcrate#34 (2 comments by @jjkoehorst, @simleo)
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AttributeError: 'CommandLineTool' object has no attribute 'rsplit' ResearchObject/runcrate#49 (1 comment by @mr-c)
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6 pull requests opened.
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Get data paths from manifest ResearchObject/runcrate#57, by @simleo.
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manifest lookup for path ResearchObject/runcrate#56, by @jjkoehorst.
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Support for inline tools ResearchObject/runcrate#52, by @simleo.
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run: don't break if alternateName is same as id ResearchObject/runcrate#50, by @simleo.
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Run module: fix check_runnable ResearchObject/runcrate#48, by @simleo.
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Option to remap data entity names ResearchObject/runcrate#46, by @simleo.
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4 pull requests merged.
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Get data paths from manifest ResearchObject/runcrate#57.
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Support for inline tools ResearchObject/runcrate#52.
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run: don't break if alternateName is same as id ResearchObject/runcrate#50.
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Run module: fix check_runnable ResearchObject/runcrate#48.
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1 pull request closed.
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manifest lookup for path ResearchObject/runcrate#56.
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2 pull requests received 5 new comments.
ResearchObject/ro-crate
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1 issue opened.
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Use Case: As a profile designer I want to use WKT for geo data to avoid ambiguity ResearchObject/ro-crate#266, by @ptsefton.
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2 issues received 3 new comments.
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Use Case: As a profile designer I want to use WKT for geo data to avoid ambiguity ResearchObject/ro-crate#266 (2 comments by @marc-portier, @ptsefton)
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ResearchObject/ro-crate-py
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1 issue opened.
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dump the metadata of the RO-Crate ResearchObject/ro-crate-py#153, by @hakor.
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1 issue closed.
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dump the metadata of the RO-Crate ResearchObject/ro-crate-py#153.
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1 issue received 1 new comment.
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1 pull request opened.
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Handle CWL versions with a leading v ResearchObject/ro-crate-py#154, by @simleo.
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1 pull request merged.
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Handle CWL versions with a leading v ResearchObject/ro-crate-py#154.
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GitHub
ResearchObject/workflow-run-crate
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4 issues received 6 new comments.
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Join the working group (post here to be added) ResearchObject/workflow-run-crate#1 (1 comment by @jjkoehorst)
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3 pull requests opened.
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Resource usage example ResearchObject/workflow-run-crate#60, by @simleo.
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Add / update ER diagrams ResearchObject/workflow-run-crate#59, by @simleo.
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Updated ml-predict-pipeline-streamflow ResearchObject/workflow-run-crate#58, by @GlassOfWhiskey.
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2 pull requests merged.
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Add / update ER diagrams ResearchObject/workflow-run-crate#59.
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Updated ml-predict-pipeline-streamflow ResearchObject/workflow-run-crate#58.
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ResearchObject/runcrate
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10 issues opened.
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Filenames not in ro-crate-metadata.json ResearchObject/runcrate#42, by @jjkoehorst.
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KeyError: 'fastqc.cwl' while cwl file is in the provenance folder ResearchObject/runcrate#41, by @jjkoehorst.
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schema_salad.exceptions.ValidationException tried... ResearchObject/runcrate#39, by @jjkoehorst.
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Bug in cwltool results in packed.cwl but no individual cwl files ResearchObject/runcrate#36, by @jjkoehorst.
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Bag validation failed: data/.DS_Store exists on filesystem but is not in the manifest ResearchObject/runcrate#35, by @jjkoehorst.
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Option to make data files more user friendly ResearchObject/runcrate#34, by @jjkoehorst.
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AttributeError: 'NoneType' object has no attribute 'rsplit' ResearchObject/runcrate#33, by @jjkoehorst.
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KeyError: <cwl_utils.parser.cwl_v1_2.CommandInputEnumSchema object at 0x10aa191e0> ? ResearchObject/runcrate#32, by @jjkoehorst.
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Convert CWLProv to RO - TypeError: unhashable type: 'list' ResearchObject/runcrate#30, by @jjkoehorst.
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Handle distinct directories with same content ResearchObject/runcrate#26, by @simleo.
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12 issues closed.
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AttributeError: 'NoneType' object has no attribute 'rsplit' ResearchObject/runcrate#33.
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KeyError: 'fastqc.cwl' while cwl file is in the provenance folder ResearchObject/runcrate#41.
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Bug in cwltool results in packed.cwl but no individual cwl files ResearchObject/runcrate#36.
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Filenames not in ro-crate-metadata.json ResearchObject/runcrate#42.
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schema_salad.exceptions.ValidationException tried... ResearchObject/runcrate#39.
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Bag validation failed: data/.DS_Store exists on filesystem but is not in the manifest ResearchObject/runcrate#35.
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KeyError: <cwl_utils.parser.cwl_v1_2.CommandInputEnumSchema object at 0x10aa191e0> ? ResearchObject/runcrate#32.
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Convert CWLProv to RO - TypeError: unhashable type: 'list' ResearchObject/runcrate#30.
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CWLProv conversion: include doc, label, intent ResearchObject/runcrate#10.
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CWLProv conversion: convert basename ResearchObject/runcrate#8.
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CWLProv conversion: include primary-job.json ResearchObject/runcrate#9.
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CWLProv conversion: add profile conformance ResearchObject/runcrate#14.
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9 issues received 21 new comments.
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AttributeError: 'NoneType' object has no attribute 'rsplit' ResearchObject/runcrate#33 (6 comments by @jjkoehorst, @simleo)
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KeyError: 'fastqc.cwl' while cwl file is in the provenance folder ResearchObject/runcrate#41 (4 comments by @jjkoehorst, @mr-c)
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Bug in cwltool results in packed.cwl but no individual cwl files ResearchObject/runcrate#36 (2 comments by @jjkoehorst, @mr-c)
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schema_salad.exceptions.ValidationException tried... ResearchObject/runcrate#39 (1 comment by @jjkoehorst)
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Bag validation failed: data/.DS_Store exists on filesystem but is not in the manifest ResearchObject/runcrate#35 (1 comment by @simleo)
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9 pull requests opened.
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Fix crash related to skipped subworkflows ResearchObject/runcrate#45, by @simleo.
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Handle outputs with multiple output sources ResearchObject/runcrate#43, by @simleo.
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Unpin & upgrade cwl-utils version ResearchObject/runcrate#40, by @mr-c.
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Handle step input mappings with no source ResearchObject/runcrate#38, by @simleo.
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Fix convert_cwl_type ResearchObject/runcrate#37, by @simleo.
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Handle multi source step inputs ResearchObject/runcrate#31, by @simleo.
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Convert cwl label, doc and intent ResearchObject/runcrate#29, by @simleo.
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Add memoryRequirements to tools ResearchObject/runcrate#28, by @simleo.
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run: Support list of files/dirs in PropertyValue ResearchObject/runcrate#27, by @simleo.
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9 pull requests merged.
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Fix crash related to skipped subworkflows ResearchObject/runcrate#45.
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Unpin & upgrade cwl-utils version ResearchObject/runcrate#40.
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Handle outputs with multiple output sources ResearchObject/runcrate#43.
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Handle step input mappings with no source ResearchObject/runcrate#38.
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Fix convert_cwl_type ResearchObject/runcrate#37.
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Handle multi source step inputs ResearchObject/runcrate#31.
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Convert cwl label, doc and intent ResearchObject/runcrate#29.
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Add memoryRequirements to tools ResearchObject/runcrate#28.
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run: Support list of files/dirs in PropertyValue ResearchObject/runcrate#27.
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1 pull request received 10 new comments.
ResearchObject/ro-crate-py
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1 issue closed.
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Remove software version defaults ResearchObject/ro-crate-py#130.
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3 pull requests opened.
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Remove engine version default ResearchObject/ro-crate-py#152, by @simleo.
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Add add_tree method ResearchObject/ro-crate-py#151, by @simleo.
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Remove version from ComputerLanguage ResearchObject/ro-crate-py#150, by @simleo.
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3 pull requests merged.
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Remove engine version default ResearchObject/ro-crate-py#152.
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Add add_tree method ResearchObject/ro-crate-py#151.
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Remove version from ComputerLanguage ResearchObject/ro-crate-py#150.
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1 pull request received 2 new comments.
ResearchObject/ro-crate
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6 issues opened.
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As a repository manager I want to be able to add TEXTUAL citations to creative works and DataEntities (including whole crates) ResearchObject/ro-crate#265, by @ptsefton.
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Use Case: Use LinkML to define schemas ResearchObject/ro-crate#264, by @glyg.
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Update JSON-LD context to schema.org 15.0 ResearchObject/ro-crate#263, by @stain.
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Need to clarify what should be in profile crate for additional terms ResearchObject/ro-crate#258, by @ptsefton.
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Issue: A number of new @context terms in 1.2 that don't resolve to human readble definitions ResearchObject/ro-crate#251, by @ptsefton.
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Review Attached / Detached terminology and description ResearchObject/ro-crate#247, by @ptsefton.
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8 issues closed.
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Use Case: How to use cite-as on a crate? ResearchObject/ro-crate#202.
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Review RO-Crate 1.2-DRAFT ResearchObject/ro-crate#245.
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Update JSON-LD context to schema.org 15.0 ResearchObject/ro-crate#263.
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Requirements for every entity ResearchObject/ro-crate#225.
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BUG: Error in @context cite-as does not resolve ResearchObject/ro-crate#239.
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Task: Update publications page with FDO talks and anything else from the minutes ResearchObject/ro-crate#214.
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Issue: A number of new @context terms in 1.2 that don't resolve to human readble definitions ResearchObject/ro-crate#251.
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Review Attached / Detached terminology and description ResearchObject/ro-crate#247.
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2 issues reopened.
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Use Case: How to get the contents of a RO as a zip file? ResearchObject/ro-crate#228, by @stain.
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BUG: Error in @context cite-as does not resolve ResearchObject/ro-crate#239, by @ptsefton.
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11 issues received 24 new comments.
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As a repository manager I want to be able to add TEXTUAL citations to creative works and DataEntities (including whole crates) ResearchObject/ro-crate#265 (4 comments by @ptsefton, @stain)
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Use Case: How to get the contents of a RO as a zip file? ResearchObject/ro-crate#228 (3 comments by @dgarijo, @stain)
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Need to clarify what should be in profile crate for additional terms ResearchObject/ro-crate#258 (3 comments by @ptsefton, @stain)
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BUG: Error in @context cite-as does not resolve ResearchObject/ro-crate#239 (2 comments by @ptsefton, @stain)
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Issue: A number of new @context terms in 1.2 that don't resolve to human readble definitions ResearchObject/ro-crate#251 (2 comments by @stain)
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Task: Update publications page with FDO talks and anything else from the minutes ResearchObject/ro-crate#214 (1 comment by @stain)
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12 pull requests opened.
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Soften Profile inheritence rules ResearchObject/ro-crate#262, by @stain.
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update of changelog in progress ResearchObject/ro-crate#261, by @nsjuty.
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List required properties for entities ResearchObject/ro-crate#260, by @stain.
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contentUrl for direct download, add section on Converting to Attached RO-Crate ResearchObject/ro-crate#259, by @stain.
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Add RepositoryFile to the context ResearchObject/ro-crate#257, by @simleo.
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Add DefinedTerm for Profiles vocabulary, PCDM and cite-as ResearchObject/ro-crate#256, by @stain.
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Specify how cite-as and Signposting should be used ResearchObject/ro-crate#255, by @stain.
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Cosmetic fixes to the examples ResearchObject/ro-crate#254, by @jmfernandez.
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Minor review updates for JSON-LD appendix ResearchObject/ro-crate#252, by @a-mile.
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A few minor updates to Profiles text ResearchObject/ro-crate#250, by @ptsefton.
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Reviewed issues #178 and #182 ResearchObject/ro-crate#249, by @ptsefton.
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Terminology: "RO-Crate Metadata Document" instead of "Metadata File" ResearchObject/ro-crate#248, by @ptsefton.
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13 pull requests merged.
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update of changelog in progress ResearchObject/ro-crate#261.
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contentUrl for direct download, add section on Converting to Attached RO-Crate ResearchObject/ro-crate#259.
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List required properties for entities ResearchObject/ro-crate#260.
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Specify how cite-as and Signposting should be used ResearchObject/ro-crate#255.
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Add RepositoryFile to the context ResearchObject/ro-crate#257.
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Add DefinedTerm for Profiles vocabulary, PCDM and cite-as ResearchObject/ro-crate#256.
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Reviewed issues #178 and #182 ResearchObject/ro-crate#249.
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Terminology: "RO-Crate Metadata Document" instead of "Metadata File" ResearchObject/ro-crate#248.
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Review 1.2 draft ResearchObject/ro-crate#244.
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A few minor updates to Profiles text ResearchObject/ro-crate#250.
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Cosmetic fixes to the examples ResearchObject/ro-crate#254.
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Minor review updates for JSON-LD appendix ResearchObject/ro-crate#252.
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Update introduction.md ResearchObject/ro-crate#246.
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7 pull requests received 18 new comments.
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Terminology: "RO-Crate Metadata Document" instead of "Metadata File" ResearchObject/ro-crate#248 (6 comments by @simleo)
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contentUrl for direct download, add section on Converting to Attached RO-Crate ResearchObject/ro-crate#259 (2 comments by @ptsefton)
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Specify how cite-as and Signposting should be used ResearchObject/ro-crate#255 (1 comment by @stain)
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Add DefinedTerm for Profiles vocabulary, PCDM and cite-as ResearchObject/ro-crate#256 (1 comment by @ptsefton)
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ResearchObject/galaxy-training-material
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1 pull request opened.
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Required changes for merging ResearchObject/galaxy-training-material#1, by @hexylena.
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1 pull request merged.
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Required changes for merging ResearchObject/galaxy-training-material#1.
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1 pull request received 1 new comment.
ResearchObject/bh2022-ro-crate-galaxy-dsw
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1 pull request merged.
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Finalize report ResearchObject/bh2022-ro-crate-galaxy-dsw#6.
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GitHub
ResearchObject/ro-crate
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2 issues opened.
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Review RO-Crate 1.2-DRAFT ResearchObject/ro-crate#245, by @stain.
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Definition of RepositoryObject in ro-crate-context is wrong (#object instead of #Object) ResearchObject/ro-crate#243, by @ptsefton.
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5 issues closed.
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Use Case: Allow extra types on root dataset ResearchObject/ro-crate#182.
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Use Case: Indicate main data entity of RO-Crate ResearchObject/ro-crate#124.
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Use Case: Indicate profile of RO-Crate ResearchObject/ro-crate#153.
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Use Case: RO-Crate as collection of contextual items ResearchObject/ro-crate#122.
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Definition of RepositoryObject in ro-crate-context is wrong (#object instead of #Object) ResearchObject/ro-crate#243.
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6 issues received 11 new comments.
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BUG: Error in @context cite-as does not resolve ResearchObject/ro-crate#239 (5 comments by @hvdsomp, @ptsefton, @stain)
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Definition of RepositoryObject in ro-crate-context is wrong (#object instead of #Object) ResearchObject/ro-crate#243 (2 comments by @stain)
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Use Case: Resolve RO-Crate from persistent identifier/DOI with landing page ResearchObject/ro-crate#160 (1 comment by @stain)
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3 pull requests opened.
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Update introduction.md ResearchObject/ro-crate#246, by @nsjuty.
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Review 1.2 draft ResearchObject/ro-crate#244, by @simleo.
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Use IANA namespace for link relation cite-as ResearchObject/ro-crate#240, by @stain.
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1 pull request merged.
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Use IANA namespace for link relation cite-as ResearchObject/ro-crate#240.
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ResearchObject/bh2022-ro-crate-galaxy-dsw
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1 pull request opened.
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Finalize report ResearchObject/bh2022-ro-crate-galaxy-dsw#6, by @MarekSuchanek.
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1 pull request received 1 new comment.
ResearchObject/workflow-run-crate
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2 issues received 2 new comments.
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Join the working group (post here to be added) ResearchObject/workflow-run-crate#1 (1 comment by @RenskeW)
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1 pull request opened.
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0.2 Release ResearchObject/workflow-run-crate#57, by @simleo.
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2 pull requests merged.
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0.2 Release ResearchObject/workflow-run-crate#57.
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Update Workflow Run Crate profile ResearchObject/workflow-run-crate#55.
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ResearchObject/ro-crate-ruby
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1 issue opened.
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Try out Rubyzip 3.0.0a ResearchObject/ro-crate-ruby#30, by @fbacall.
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ResearchObject/runcrate
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1 pull request opened.
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convert: add input object document ResearchObject/runcrate#25, by @simleo.
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2 pull requests merged.
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convert: add input object document ResearchObject/runcrate#25.
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Run module ResearchObject/runcrate#24.
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3 pull requests received 4 new comments.
ResearchObject/ro-crate-validator-py
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1 issue closed.
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pytest needed as extra dependency when using ro-crate-validator-py ResearchObject/ro-crate-validator-py#4.
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2 issues received 2 new comments.
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pytest needed as extra dependency when using ro-crate-validator-py ResearchObject/ro-crate-validator-py#4 (1 comment by @stain)
ResearchObject/ro-crate-py
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1 issue received 2 new comments.
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Document how to create a Workflow Run Crate file ResearchObject/ro-crate-py#148 (2 comments by @kinow, @simleo)
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GitHub
ResearchObject/ro-crate-py
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2 issues closed.
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Allow to attach partials to a crate? ResearchObject/ro-crate-py#146.
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ro-crate profile functionality ResearchObject/ro-crate-py#142.
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4 issues received 11 new comments.
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Document how to create a Workflow Run Crate file ResearchObject/ro-crate-py#148 (7 comments by @kinow, @simleo)
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1 pull request opened.
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Add methods for adding and updating JSON-LD directly (partials for WMS) ResearchObject/ro-crate-py#149, by @kinow.
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2 pull requests merged.
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Add methods for adding and updating JSON-LD directly (partials for WMS) ResearchObject/ro-crate-py#149.
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Add Autosubmit language ResearchObject/ro-crate-py#143.
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2 pull requests received 12 new comments.
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Add methods for adding and updating JSON-LD directly (partials for WMS) ResearchObject/ro-crate-py#149 (10 comments by @kinow, @simleo)
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ResearchObject/workflow-run-crate
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2 issues received 5 new comments.
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4 pull requests opened.
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Review conformsTo in COMPSs example ResearchObject/workflow-run-crate#56, by @simleo.
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Update Workflow Run Crate profile ResearchObject/workflow-run-crate#55, by @simleo.
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Update examples generated by runcrate ResearchObject/workflow-run-crate#54, by @simleo.
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Added initial WfExS-backend examples based on toy workflow. ResearchObject/workflow-run-crate#53, by @jmfernandez.
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3 pull requests merged.
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Example Galaxy Workflowrun ro-crate ResearchObject/workflow-run-crate#44.
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Review conformsTo in COMPSs example ResearchObject/workflow-run-crate#56.
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Update examples generated by runcrate ResearchObject/workflow-run-crate#54.
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2 pull requests received 13 new comments.
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Example Galaxy Workflowrun ro-crate ResearchObject/workflow-run-crate#44 (12 comments by @pauldg, @simleo)
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Added initial WfExS-backend examples based on toy workflow. ResearchObject/workflow-run-crate#53 (1 comment by @simleo)
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ResearchObject/runcrate
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8 pull requests opened.
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Run module ResearchObject/runcrate#24, by @simleo.
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Fix context extra terms ResearchObject/runcrate#23, by @simleo.
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Set param names to those expected by CWL ResearchObject/runcrate#22, by @simleo.
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runcrate report: dump all actions ResearchObject/runcrate#21, by @simleo.
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Convert module ResearchObject/runcrate#20, by @simleo.
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Enhancements for report ResearchObject/runcrate#19, by @simleo.
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Move tools/consume_crate functionality to runcrate CLI ResearchObject/runcrate#18, by @simleo.
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WIP: ShEx validation method ResearchObject/runcrate#17, by @stain.
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6 pull requests merged.
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Set param names to those expected by CWL ResearchObject/runcrate#22.
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Fix context extra terms ResearchObject/runcrate#23.
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runcrate report: dump all actions ResearchObject/runcrate#21.
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Convert module ResearchObject/runcrate#20.
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Enhancements for report ResearchObject/runcrate#19.
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Move tools/consume_crate functionality to runcrate CLI ResearchObject/runcrate#18.
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1 pull request received 2 new comments.
ResearchObject/ro-crate
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1 issue opened.
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BUG: Error in @context cite-as does not resolve ResearchObject/ro-crate#239, by @ptsefton.
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4 issues closed.
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upcoming events on website is hopelessly out of date ResearchObject/ro-crate#206.
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Use Case: elaborate extensions to the @context want to refer to that remotely (by URI) rather than inline ResearchObject/ro-crate#150.
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encodingFormat use CWL example, mismatch with Workflow section ResearchObject/ro-crate#99.
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5 issues received 6 new comments.
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BUG: Error in @context cite-as does not resolve ResearchObject/ro-crate#239 (2 comments by @jmfernandez, @ptsefton)
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Use Case: How to get the contents of a RO as a zip file? ResearchObject/ro-crate#228 (1 comment by @stain)
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12 pull requests merged.
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Use W3C Profile vocabulary as part of Profile Crate ResearchObject/ro-crate#235.
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Indicate encoding format profile using conformsTo ResearchObject/ro-crate#231.
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Ad-hoc terms can be moved to a Profile Crate ResearchObject/ro-crate#233.
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Changed to text to allow multiple types on root - as per #182 which w… ResearchObject/ro-crate#223.
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Add concept Detached RO-Crate ResearchObject/ro-crate#189.
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Attempting to address #122 and #124 - mainEntity and mentions ResearchObject/ro-crate#211.
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Update docs on finding the root dataset ResearchObject/ro-crate#198.
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Clarify properties for data entities, avoid WebSite type ResearchObject/ro-crate#230.
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Ad-hoc terms use DefinedTerm/Class/Property ResearchObject/ro-crate#232.
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Move to latest version Just the docs + dependency update ResearchObject/ro-crate#238.
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Update FormalParameter required properties ResearchObject/ro-crate#236.
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conformsTo profile applies to root dataset, not metadata file ResearchObject/ro-crate#229.
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9 pull requests received 9 new comments.
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Use W3C Profile vocabulary as part of Profile Crate ResearchObject/ro-crate#235 (1 comment by @stain)
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Changed to text to allow multiple types on root - as per #182 which w… ResearchObject/ro-crate#223 (1 comment by @stain)
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Attempting to address #122 and #124 - mainEntity and mentions ResearchObject/ro-crate#211 (1 comment by @stain)
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Clarify properties for data entities, avoid WebSite type ResearchObject/ro-crate#230 (1 comment by @stain)
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ResearchObject/ro-crate-validator-py
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2 issues opened.
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pytest needed as extra dependency when using ro-crate-validator-py ResearchObject/ro-crate-validator-py#4, by @kinow.
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suggestion for README ResearchObject/ro-crate-validator-py#3, by @hariszaf.
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ResearchObject/bh2022-ro-crate-galaxy-dsw
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1 pull request opened.
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Add DSW-related report ResearchObject/bh2022-ro-crate-galaxy-dsw#5, by @MarekSuchanek.
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1 pull request merged.
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Add DSW-related report ResearchObject/bh2022-ro-crate-galaxy-dsw#5.
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GitHub
ResearchObject/ro-crate
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1 issue closed.
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Keep track of releases just the docs theme ResearchObject/ro-crate#141.
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1 issue received 1 new comment.
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1 pull request opened.
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Move to latest version Just the docs + dependency update ResearchObject/ro-crate#238, by @bedroesb.
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1 pull request closed.
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Move to new version Jekyll theme ResearchObject/ro-crate#221.
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2 pull requests received 3 new comments.
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Changed to text to allow multiple types on root - as per #182 which w… ResearchObject/ro-crate#223 (2 comments by @simleo, @stain)
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ResearchObject/ro-crate-py
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4 issues opened.
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Document how to create a Workflow Run Crate file ResearchObject/ro-crate-py#148, by @kinow.
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Export entities/models in `rocrate.model.__init__` ResearchObject/ro-crate-py#147, by @kinow.
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Allow to attach partials to a crate? ResearchObject/ro-crate-py#146, by @kinow.
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ro-crate profile functionality ResearchObject/ro-crate-py#142, by @bulricht.
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4 issues received 10 new comments.
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Allow to attach partials to a crate? ResearchObject/ro-crate-py#146 (4 comments by @kinow, @simleo, @stain)
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Document how to create a Workflow Run Crate file ResearchObject/ro-crate-py#148 (2 comments by @kinow, @simleo)
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3 pull requests opened.
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Fix typo on README ResearchObject/ro-crate-py#145, by @kinow.
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Fix typos in notebooks ResearchObject/ro-crate-py#144, by @kinow.
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Add Autosubmit language ResearchObject/ro-crate-py#143, by @kinow.
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2 pull requests merged.
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Fix typo on README ResearchObject/ro-crate-py#145.
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Fix typos in notebooks ResearchObject/ro-crate-py#144.
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1 pull request received 4 new comments.
ResearchObject/workflow-run-crate
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1 issue closed.
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CQ7 - Outcome ResearchObject/workflow-run-crate#15.
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5 issues received 7 new comments.
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Join the working group (post here to be added) ResearchObject/workflow-run-crate#1 (3 comments by @holubp, @kinow, @m-markovic)
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3 pull requests opened.
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Update cwltool-runcrate version of the predict pipeline crate ResearchObject/workflow-run-crate#52, by @simleo.
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0.1 Release ResearchObject/workflow-run-crate#51, by @simleo.
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Add specs on action status ResearchObject/workflow-run-crate#50, by @simleo.
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5 pull requests merged.
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Update cwltool-runcrate version of the predict pipeline crate ResearchObject/workflow-run-crate#52.
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0.1 Release ResearchObject/workflow-run-crate#51.
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COMPSs BackTrackBB WRROC example ResearchObject/workflow-run-crate#43.
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Add recommendation on adding workflow traces ResearchObject/workflow-run-crate#49.
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Add specs on action status ResearchObject/workflow-run-crate#50.
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2 pull requests received 7 new comments.
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COMPSs BackTrackBB WRROC example ResearchObject/workflow-run-crate#43 (4 comments by @rsirvent, @simleo)
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Example Galaxy Workflowrun ro-crate ResearchObject/workflow-run-crate#44 (3 comments by @simleo, @stain)
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ResearchObject/runcrate
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2 pull requests opened.
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Fix exampleOfWork duplicates ResearchObject/runcrate#16, by @simleo.
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convert: add more metadata ResearchObject/runcrate#15, by @simleo.
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2 pull requests merged.
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Fix exampleOfWork duplicates ResearchObject/runcrate#16.
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convert: add more metadata ResearchObject/runcrate#15.
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1 pull request received 1 new comment.
ResearchObject/bh2022-ro-crate-galaxy-dsw
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1 pull request merged.
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Add runcrate section ResearchObject/bh2022-ro-crate-galaxy-dsw#4.
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GitHub
ResearchObject/workflow-run-crate
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6 issues closed.
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CQ5 - Step running time ResearchObject/workflow-run-crate#13.
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CQ6 - Workflow running time ResearchObject/workflow-run-crate#14.
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CQ9 - Software version ResearchObject/workflow-run-crate#17.
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Representing secondary files ResearchObject/workflow-run-crate#36.
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CQ8 - Workflow inputs and outputs ResearchObject/workflow-run-crate#16.
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CQ3 - Configuration files ResearchObject/workflow-run-crate#11.
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8 issues received 17 new comments.
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CQ3 - Configuration files ResearchObject/workflow-run-crate#11 (5 comments by @GlassOfWhiskey, @simleo)
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Join the working group (post here to be added) ResearchObject/workflow-run-crate#1 (1 comment by @AngryMaciek)
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11 pull requests opened.
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Add recommendation on adding workflow traces ResearchObject/workflow-run-crate#49, by @simleo.
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Provenance Run Crate: clarify tool representation ResearchObject/workflow-run-crate#48, by @simleo.
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Clarify relationship with Bioschemas FormalParameter ResearchObject/workflow-run-crate#47, by @simleo.
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Remove consume_crate ResearchObject/workflow-run-crate#46, by @simleo.
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Updated ml-predict-pipeline-streamflow ResearchObject/workflow-run-crate#45, by @GlassOfWhiskey.
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Example Galaxy Workflowrun ro-crate ResearchObject/workflow-run-crate#44, by @pauldg.
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COMPSs BackTrackBB WRROC example ResearchObject/workflow-run-crate#43, by @rsirvent.
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Add recommendations for software version ResearchObject/workflow-run-crate#42, by @simleo.
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Add section on representing multi-file objects ResearchObject/workflow-run-crate#41, by @simleo.
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Add conformsTo to identify profile conformance ResearchObject/workflow-run-crate#40, by @stain.
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Profiles: specify how to represent configuration files ResearchObject/workflow-run-crate#39, by @simleo.
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9 pull requests merged.
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Provenance Run Crate: clarify tool representation ResearchObject/workflow-run-crate#48.
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Clarify relationship with Bioschemas FormalParameter ResearchObject/workflow-run-crate#47.
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Remove consume_crate ResearchObject/workflow-run-crate#46.
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Updated ml-predict-pipeline-streamflow ResearchObject/workflow-run-crate#45.
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Add recommendations for software version ResearchObject/workflow-run-crate#42.
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Add section on representing multi-file objects ResearchObject/workflow-run-crate#41.
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Add conformsTo to identify profile conformance ResearchObject/workflow-run-crate#40.
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Profiles: specify how to represent configuration files ResearchObject/workflow-run-crate#39.
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Add ML predict pipeline crate obtained with cwltool and runcrate ResearchObject/workflow-run-crate#38.
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8 pull requests received 15 new comments.
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COMPSs BackTrackBB WRROC example ResearchObject/workflow-run-crate#43 (3 comments by @rsirvent, @simleo)
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Proposed draft changes to allow for a galaxy history export to be accepted by cwlprov_to_crate.py ResearchObject/workflow-run-crate#30 (1 comment by @pauldg)
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Add conformsTo to identify profile conformance ResearchObject/workflow-run-crate#40 (1 comment by @stain)
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Add section on representing multi-file objects ResearchObject/workflow-run-crate#41 (1 comment by @simleo)
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Profiles: specify how to represent configuration files ResearchObject/workflow-run-crate#39 (1 comment by @stain)
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Add ML predict pipeline crate obtained with cwltool and runcrate ResearchObject/workflow-run-crate#38 (1 comment by @simleo)
ResearchObject/ro-crate
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1 issue opened.
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Use Case: How to get the contents of a RO as a zip file? ResearchObject/ro-crate#228, by @dgarijo.
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4 issues received 4 new comments.
-
Use Case: elaborate extensions to the @context want to refer to that remotely (by URI) rather than inline ResearchObject/ro-crate#150 (1 comment by @stain)
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encodingFormat use CWL example, mismatch with Workflow section ResearchObject/ro-crate#99 (1 comment by @stain)
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Use Case: Resolve RO-Crate from persistent identifier/DOI with landing page ResearchObject/ro-crate#160 (1 comment by @dgarijo)
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7 pull requests opened.
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Update FormalParameter required properties ResearchObject/ro-crate#236, by @simleo.
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Use W3C Profile vocabulary as part of Profile Crate ResearchObject/ro-crate#235, by @stain.
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Ad-hoc terms can be moved to a Profile Crate ResearchObject/ro-crate#233, by @stain.
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Ad-hoc terms use DefinedTerm/Class/Property ResearchObject/ro-crate#232, by @stain.
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Indicate encoding format profile using conformsTo ResearchObject/ro-crate#231, by @stain.
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Clarify properties for data entities, avoid WebSite type ResearchObject/ro-crate#230, by @stain.
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conformsTo profile applies to root dataset, not metadata file ResearchObject/ro-crate#229, by @stain.
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1 pull request merged.
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Review intro ResearchObject/ro-crate#227.
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7 pull requests received 10 new comments.
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Indicate encoding format profile using conformsTo ResearchObject/ro-crate#231 (2 comments by @stain)
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Ad-hoc terms can be moved to a Profile Crate ResearchObject/ro-crate#233 (2 comments by @simleo, @stain)
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conformsTo profile applies to root dataset, not metadata file ResearchObject/ro-crate#229 (1 comment by @stain)
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Clarify properties for data entities, avoid WebSite type ResearchObject/ro-crate#230 (1 comment by @stain)
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Use W3C Profile vocabulary as part of Profile Crate ResearchObject/ro-crate#235 (1 comment by @stain)
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ResearchObject/ro-crate-py
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1 issue opened.
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Support indirect data entity linking from root ResearchObject/ro-crate-py#141, by @simleo.
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ResearchObject/runcrate
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7 issues opened.
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CWLProv conversion: add profile conformance ResearchObject/runcrate#14, by @simleo.
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CWLProv conversion: include creation datetime, size, checksum, format ResearchObject/runcrate#13, by @simleo.
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Error from runcrate-analysis, scenario 4_a ResearchObject/runcrate#12, by @simleo.
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Error from runcrate-analysis, scenario 2_a ResearchObject/runcrate#11, by @simleo.
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CWLProv conversion: include doc, label, intent ResearchObject/runcrate#10, by @simleo.
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CWLProv conversion: include primary-job.json ResearchObject/runcrate#9, by @simleo.
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CWLProv conversion: convert basename ResearchObject/runcrate#8, by @simleo.
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ResearchObject/ro-crate-validator-py
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2 issues opened.
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Is a workflow necessary? ResearchObject/ro-crate-validator-py#2, by @bronger.
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Licence is incorrectly rejected ResearchObject/ro-crate-validator-py#1, by @bronger.
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