https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422022-06-07T18:49:02ZArvadosArvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1042002022-06-07T18:49:02ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-1 status-1 priority-4 priority-default parent" href="/issues/18587">Bug #18587</a>: "Copy selected into collection" incorrect behavior</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1042012022-06-07T19:00:36ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/104201/diff?detail_id=100796">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1043302022-06-15T14:39:13ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-6 status-2 priority-4 priority-default behind-schedule" href="/issues/16943">Idea #16943</a>: WB2 Descriptions, project & collection operations</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1043982022-06-22T14:52:55ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-07-06</i> to <i>2022-07-20</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1046562022-07-05T21:41:41ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-07-20</i> to <i>2022-08-03 Sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1047072022-07-05T21:50:13ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Category</strong> set to <i>Workbench2</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1047132022-07-05T21:51:54ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-08-03 Sprint</i> to <i>2022-08-17 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1051192022-08-02T19:49:44ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-08-17 sprint</i> to <i>2022-09-14 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1055872022-08-12T20:55:07ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-09-14 sprint</i> to <i>2022-09-28 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1062512022-09-13T17:51:15ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-09-28 sprint</i> to <i>2022-10-12 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1067032022-09-27T18:53:17ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-10-12 sprint</i> to <i>2022-10-26 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1070192022-10-11T17:55:11ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-10-26 sprint</i> to <i>2022-11-09 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1073752022-10-26T16:05:03ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-11-09 sprint</i> to <i>2022-11-23 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1076302022-11-04T13:58:55ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-11-23 sprint</i> to <i>2022-12-07 Sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1079202022-11-09T21:01:04ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-2 status-1 priority-4 priority-default" href="/issues/16644">Feature #16644</a>: Move files into existing collection</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1079362022-11-09T21:17:50ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-2 status-1 priority-4 priority-default" href="/issues/17586">Feature #17586</a>: Merge collections</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1079462022-11-09T21:26:14ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-1 status-1 priority-4 priority-default" href="/issues/18198">Bug #18198</a>: "copy selected files into collection" function in WB2 extremely slow</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1079532022-11-09T21:33:56ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-1 status-1 priority-4 priority-default" href="/issues/19048">Bug #19048</a>: Copying a folder in collection file browser results in empty folder</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1079562022-11-09T21:39:08ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Related to</strong> <i><a class="issue tracker-1 status-1 priority-4 priority-default" href="/issues/19258">Bug #19258</a>: unexpected behaviour in "make collection from selected" in WB2</i> added</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1081392022-11-18T20:02:49ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-12-07 Sprint</i> to <i>2022-12-21 Sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1083822022-11-23T18:12:17ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2022-12-21 Sprint</i> to <i>2023-01-18 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1094552023-01-03T17:25:46ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2023-01-18 sprint</i> to <i>2023-02-01 sprint</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1094862023-01-03T17:51:09ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Tracker</strong> changed from <i>Idea</i> to <i>Feature</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1096732023-01-11T17:57:03ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Target version</strong> changed from <i>2023-02-01 sprint</i> to <i>Future</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1102522023-01-25T15:18:13ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Subject</strong> changed from <i>Workbench 2 uses replace_files API</i> to <i>Workbench 2 file operations</i></li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1102532023-01-25T15:19:47ZSarah Zaranekswz@curii.com
<ul></ul><p>List from my list of use cases --</p>
<p>Creating New Collections<br />Summary: Users want to create a new collection in WB. <br />Details: Wants to make collection in from any of the data sources:<br />From data already in an existing collection<br />From a subset of files in an existing collection<br />By combining files from different subsets of different collections<br />By Uploading files from my desktop<br />From the results of a already run workflow<br />By downloading data from another source into a collection</p>
<p>Annotating Collections<br /> Summary: User wants to annotate their collections with such details as sample<br />name, sample type, sequencing method, species, etc. <br />Details:<br />User wants to add annotations/metadata to existing collection<br />User want to verify the added metadata to the collection</p>
<p>Examining Collection Files <br />Summary: User is viewing a collection and wants to examine the files and extract the data or metadata. <br />Details:<br />User wants to find certain files within the collection <br />(visually,using search (basic and advanced search using regexp, etc)<br />User want to View or download certain files with the collection using a UI</p>
<p>Sharing Collection Files <br />Summary: User wants to share the Files in a Collection<br /> Details:<br />User wants make the collection available for downloading via ftp, s3 or other 3rd party application<br />User wants to share the collection with others (by name) in their organization, others via a defined group, to everyone in their organization, or publicly. Users want those they share the collection with to have <br />Read permission. <br />Write permissions<br />Manage permissions</p>
<p>Finding Existing Collections<br />Summary: User want to find an existing collection<br />Details: User wants to find the collection by one of the following ways:<br />By Browsing to the project that contains the collection<br />By searching the UUID of the project - and then looking through the items in the collection<br />By searching the UUID of the collection<br />By searching the collection name<br />By searching the PDH<br />By searching the collection metadata<br />By searching for the workflow that produced it<br />By a URL that can share that points to the project on WB</p>
<p>Identifying Collections<br />Summary: User needs to ID the collection for use as inputs to a workflow and/or inputs to a command using the API or CLI<br />Details: User wants to find these specific file IDs<br />User wants to get the collection UUID<br />User wants to get the collection PDH<br />User wants to get the collection metadata</p>
<p>Editing an Existing Collection <br />Summary: User wants to modify a collection for use in their new project.<br />Details: User will want to<br />Copy over an existing collection to a new project<br />Remove files in their collection to suit their needs for their new bioinformatics task. <br />Add files from either their desktop or from another collection into this new collection</p>
<p>Editing the File Structure of An Existing Collection <br />Summary: User wants to adjust the file structure of an existing collection to work better as an input to their analysis tools<br />Details: User will want to<br />Remove files from folders to have them in all in a single flat directory<br />Separate different subsets of files and place them in folders<br />Move files into folders</p>
<p>Verifying Correct Collection<br />Summary: User wants to download data from a collection, and want to make sure the collect they found is the correct collection<br />Details: User may want to check the following:<br />UUID and/or PDH<br />metadata<br />file contents<br />collection “version”<br />lineage of the collection (i.e. if the collection was generated as the result of a workflow - which workflow created this collection)</p>
<p>Creating Projects<br />Summary: User is working in the Arvados Workbench and needs a new Arvados project for a new analysis project they are working on. <br />Details: The user wants to do the following<br />Create new project<br />Create a subproject within the new project (e.g. For Testing vs Final Runs)<br />Name the project/subproject<br />Add description of the project<br />Add metadata to the project <br />Extract UUID of Project for use in workflow inputs or various command line/SDK/API functionality. <br />Copy a URL that can share to others that points to the project<br />Mark the projects as “favorites” to be able to it more easily</p>
<p>Moving or Creating Items within Project<br />Summary. A User wants to set up their project to do their work. They want to move all relevant existing data and workflows as well as upload new data and create new registered workflows. <br />Details: Users may want to:<br />Copy existing collections and register workflows into this project<br />Create new collections within the project<br />Create new registered workflows in that project<br />Run workflows in this projects having the output, logs and other created artifacts contained within this project</p>
<p>Archiving or Sharing a Project<br />Summary: Now that the work is finished and the user has the results they need. They want to get the project ready for sharing with their organization, with those outside their organization or even possible publicly in a publication. <br />Details: Users may want to<br />Clean up the project by removing old collections, logs, processes and subdirectories that are not necessary to keep. <br />Edit the name or metadata for the project<br />Freeze the project<br />Share the project with others in their organization, to everyone in their organization, publicly. These are possible configurations:<br />Others have read permission <br />Others have write permissions<br />Others have manage permissions</p>
<p>Identifying an Existing Project<br />Summary: User needs to identify the correct project in which to run their workflow. They think they found the correct project they want searching on the project name. <br />Details: The user then may want to:<br />Find the UUID of the project<br />Examine aspects of the project to double check it is the project they want to use. They might want to:<br />Check the contents of the project <br />Check the project description <br />User might want to see the history of the project (*not currently available)<br />User might want to see the metadata for the project<br />Check to see if the project is frozen</p>
<p>Finding a Project or Subproject<br />Summary: A user logs back into Arvados after a break and would like to find the project they were working on previously. <br />Details: Those users would may want to find this project by<br />Searching for UUID, metadata or the project name<br />Navigating through the project/subproject hierarchy to find the project<br />Skimming through projects marked as their “Favorites”<br />Look for projects owned or created by a specific user (* Not Currently available)</p> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1102542023-01-25T15:27:15ZSarah Zaranekswz@curii.com
<ul></ul><p>From customer interview -</p>
<p>Ability to split collections by folder<br />Merging collection (flat merge)<br />Extract files in collection by pattern<br />Rename files in collection<br />Given UUID – download listing of all files</p> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1104662023-01-31T15:06:20ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/110466/diff?detail_id=107217">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1104902023-01-31T16:35:35ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/110490/diff?detail_id=107243">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1104912023-01-31T16:45:06ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/110491/diff?detail_id=107244">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1105012023-01-31T18:00:32ZLucas Di Pentimalucas.dipentima@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/110501/diff?detail_id=107254">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1105182023-01-31T19:21:00ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/110518/diff?detail_id=107272">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1105192023-01-31T19:22:19ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/110519/diff?detail_id=107273">diff</a>)</li></ul> Arvados - Feature #19181: [tracking] Workbench 2 file operationshttps://dev.arvados.org/issues/19181?journal_id=1111012023-02-14T20:09:25ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Subject</strong> changed from <i>Workbench 2 file operations</i> to <i>[tracking] Workbench 2 file operations</i></li></ul>