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TDOC-326
Q1-2021 Biobank Progress on pathology workflow and hosting plan (with Van Andel)
Biobank: 2. Tracking system(s) (with Brenda) finalized (used to generate monthly report section)
Q1-2021 Biobank: 1 Biobank section in monthly reports finalized and included in reports 2. Tracking system(s) (with Brenda) finalized (used to generate monthly report section) 3. Progress on pathology workflow and hosting plan (with Van Andel)
Q1-2021 APOLLO: Progress on APOLLO-2 Pathology collection and hosting
Q1-2021 APOLLO: 1. Progress on GYN-COE APOLLO-5 DICOM workflow
Discuss optical imaging at defacing meeting with UAMS & NCI: Colposcopy & other optical-imaging large-dataset issues One-page summary for AI
Remove analysis result entries from the wordpress table for DOIs that aren't actually analysis results
Collection wiki page clean up: Propose and implement a solution to clarify when we’re linking to “External Resources” that are websites out of our control such as PDC, GDC, & NCTN Archive that host non-image data related to our collections
Satellite curation teams: Submit a request for HJF - UAMS agreement for Betty
Satellite curation teams: Finish getting IROC staff on to UAMS IRB to reduce duplicative steps
Satellite curation teams: Document an SOP similar to https://wiki.cancerimagingarchive.net/display/Private/New+Collections+SOP which details *only* the steps that occur at UAMS to certify release of datasets curated at satellite curation locations
Implement the plan you developed last quarter to leverage RelationType for Citations and References in Datacite using information from https://www.cancerimagingarchive.net/endnote/Pubs_basedon_TCIA.xml
Add Aspera download stats to monthly reports. This will include the number of full downloads and the number of partial downloads. For partial downloads we won't be able to discern how much data was actually downloaded
Document how to create Faspex packages and train at least one other staff member to back up Larry (Natasha - pathology, Tracy’s team-NLST)
Deploy Keycloak for TCIA (After PRISM development and implementation)
POSDA Work with VA on acceptance of Posda 0.8.x Work with VA on using Posda on server
POSDA: Deliver transfer method IROC-Posda to TCIA-Posda
POSDA for APOLLO-VA: Make required adaptations to Posda for completion of APOLLO VA installation
POSDA: Deploy new version of POSDA that boosts scalability by shifting background processes into worker nodes
Collections: RSNA COVID - Develop workflow for collection of 10,000 cases from RSNA in Sept.2020
Collections: DBT data from Duke for SPIE/AAPM challenge
Collections: IDC derived data steps -- Update SOP for analysis results datasets to get IDC feedback early (e.g. to avoid duplication of curation we had after Andrey identified problems with ProstateX segmentations recently)
Collections Implement some of the feedback the curation teams provided in https://nih.app.box.com/file/714887545659?s=nylkp9zmqdm4q8th1wamddmbpvkhiob9 on collection tracking process/system (JIRA Service Desk)
Defacing TCIA images: Modify https://wiki.cancerimagingarchive.net/display/Public/Data+Usage+Policies+and+Restrictions to reflect guidance from Nathan on de-facing
NBIA: Review proposed documentation changes to https://wiki.cancerimagingarchive.net/x/NIIiAQ to include additional NBIA API endpoints. Documentation/proposal will be prepared by the NBIA team. TCIA team will review/approve.
NBIA: Update MariaDB
NBIA: Roll out new replication solution
NBIA Test and deploy any new releases
Hardware maintenance: Develop a plan for migrating the NAS storage to the new Storage system
Expand the Pathology Curation SOP at https://wiki.cancerimagingarchive.net/display/Private/Curation+Workflow to include curation steps for: Loading of pathology into Datascope and caMicroscope
Expand the Pathology Curation SOP at https://wiki.cancerimagingarchive.net/display/Private/Curation+Workflow to include curation steps for: Creating Aspera/Faspex downloads
3) Create Fastpex package following prioritized list of collections (published CPTAC discory cohart (Pathology) (Justin to circulate prioritized list of additional pathology/NIFTI collectons for discussion
Support one site uploading data with Aspera faspex package
Adoption of PRISM tools: Notify us of any newly available PRISM tools see description
Deploy Keycloak for TCIA (After PRISM development and implementation)
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data-simple-status=\"{"id":"10202","name":"Backlog","description":"","iconUrl":"/images/icons/subtask.gif","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Backlog</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/subtask.gif\" value=\"10203\" title=\"Selected for Development\" data-simple-status=\"{"id":"10203","name":"Selected for Development","description":"","iconUrl":"/images/icons/subtask.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Selected for Development</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10302\" title=\"Waiting for Support\" data-simple-status=\"{"id":"10302","name":"Waiting for Support","description":"This was auto-generated by JIRA Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Waiting for Support</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10303\" title=\"Waiting for Customer\" data-simple-status=\"{"id":"10303","name":"Waiting for Customer","description":"This was auto-generated by JIRA Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Waiting for Customer</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10304\" title=\"Waiting for Triage\" data-simple-status=\"{"id":"10304","name":"Waiting for Triage","description":"This was auto-generated by JIRA Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Waiting for Triage</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/information.png\" value=\"10305\" title=\"In Review\" data-simple-status=\"{"id":"10305","name":"In Review","description":"","iconUrl":"/images/icons/statuses/information.png","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">In Review</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10306\" title=\"Under Review\" data-simple-status=\"{"id":"10306","name":"Under Review","description":"","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Under Review</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10307\" title=\"Released\" data-simple-status=\"{"id":"10307","name":"Released","description":"Subtasks include:\\nConfirm all images are \\"Visible\\"\\nUpdate Private Wiki\\nClose TCS issue\\nTest with non-admin login\\nSocial Media: Facebook, LinkedIn, Twitter\\nupdate landing page with \\"Public\\"\\nConfirm public-facing wiki page is accurate\\nConfirm DOI links work","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Released</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10308\" title=\"Cancelled\" data-simple-status=\"{"id":"10308","name":"Cancelled","description":"","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Cancelled</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10309\" title=\"Rejected\" data-simple-status=\"{"id":"10309","name":"Rejected","description":"","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Rejected</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10406\" title=\"Declined\" data-simple-status=\"{"id":"10406","name":"Declined","description":"This was auto-generated by JIRA Service Desk during workflow import","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Declined</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10407\" title=\"Awaiting approval\" data-simple-status=\"{"id":"10407","name":"Awaiting approval","description":"This was auto-generated by JIRA Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":1,"key":"undefined","colorName":"default"}}\">Awaiting approval</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10408\" title=\"Awaiting implementation\" data-simple-status=\"{"id":"10408","name":"Awaiting implementation","description":"This was auto-generated by JIRA Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":1,"key":"undefined","colorName":"default"}}\">Awaiting implementation</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10409\" title=\"Review/Test\" data-simple-status=\"{"id":"10409","name":"Review/Test","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Review/Test</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10410\" title=\"Requirements\" data-simple-status=\"{"id":"10410","name":"Requirements","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Requirements</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10411\" title=\"Archive\" data-simple-status=\"{"id":"10411","name":"Archive","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Archive</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10507\" title=\"Refinement\" data-simple-status=\"{"id":"10507","name":"Refinement","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Refinement</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10508\" title=\"Next\" data-simple-status=\"{"id":"10508","name":"Next","description":"Highest Priority work items that are understood well enough for work to beging","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Next</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10509\" title=\"Testing\" data-simple-status=\"{"id":"10509","name":"Testing","description":"","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Testing</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10510\" title=\"Review\" data-simple-status=\"{"id":"10510","name":"Review","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Review</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10606\" title=\"Approved\" data-simple-status=\"{"id":"10606","name":"Approved","description":"","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Approved</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10607\" title=\"Green Light\" data-simple-status=\"{"id":"10607","name":"Green Light","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Green Light</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10706\" title=\"Change Control\" data-simple-status=\"{"id":"10706","name":"Change Control","description":"This status is managed internally by JIRA Software","iconUrl":"/","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Change Control</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10806\" title=\"Pending\" data-simple-status=\"{"id":"10806","name":"Pending","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Pending</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10807\" title=\"Canceled\" data-simple-status=\"{"id":"10807","name":"Canceled","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Canceled</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10808\" title=\"Escalated\" data-simple-status=\"{"id":"10808","name":"Escalated","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Escalated</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10809\" title=\"Waiting for approval\" data-simple-status=\"{"id":"10809","name":"Waiting for approval","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Waiting for approval</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10810\" title=\"Awaiting CAB approval\" data-simple-status=\"{"id":"10810","name":"Awaiting CAB approval","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Awaiting CAB approval</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10811\" title=\"Planning\" data-simple-status=\"{"id":"10811","name":"Planning","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Planning</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10812\" title=\"Implementing\" data-simple-status=\"{"id":"10812","name":"Implementing","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Implementing</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10813\" title=\"Peer review / change manager approval\" data-simple-status=\"{"id":"10813","name":"Peer review / change manager approval","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":2,"key":"new","colorName":"default"}}\">Peer review / change manager approval</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10814\" title=\"Work in progress\" data-simple-status=\"{"id":"10814","name":"Work in progress","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Work in progress</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10815\" title=\"Completed\" data-simple-status=\"{"id":"10815","name":"Completed","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Completed</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/status_generic.gif\" value=\"10816\" title=\"Under investigation\" data-simple-status=\"{"id":"10816","name":"Under investigation","description":"This was auto-generated by Jira Service Desk during workflow import","iconUrl":"/images/icons/status_generic.gif","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Under investigation</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10907\" title=\"Waiting for Release\" data-simple-status=\"{"id":"10907","name":"Waiting for Release","description":"","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":3,"key":"done","colorName":"success"}}\">Waiting for Release</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"10908\" title=\"Stuck\" data-simple-status=\"{"id":"10908","name":"Stuck","description":"This status is managed internally by Jira Software","iconUrl":"/","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Stuck</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"11006\" title=\"On Hold\" data-simple-status=\"{"id":"11006","name":"On Hold","description":"","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">On Hold</option>\n <option class=\"imagebacked\" data-icon=\"/\" value=\"11106\" title=\"Ready For Prod\" data-simple-status=\"{"id":"11106","name":"Ready For Prod","description":"This status is managed internally by Jira Software","iconUrl":"/","statusCategory":{"id":4,"key":"indeterminate","colorName":"inprogress"}}\">Ready For Prod</option>\n </optgroup>\n</select>\n </div>\n \n","validSearcher":true,"isShown":true},"labels":{"name":"Label","viewHtml":" <div class=\"searcherValue\">\n \n <label class=\"fieldLabel\" for=\"fieldlabels\">Label:</label><span id=\"fieldlabels\" class=\"fieldValue\">\n \n Q1-2021\n</span></div>\n","editHtml":"\n <div class=\"field-group aui-field-labels\" >\n <label for=\"searcher-labels\">Labels</label> <select class=\"js-label-checkboxmultiselect\" multiple=\"multiple\" id=\"searcher-labels\" name=\"labels\" data-placeholder-text=\"Find Labels...\">\n <option value=\"Q1-2021\" title=\"Q1-2021\" selected=\"selected\">Q1-2021</option>\n </select>\n </div>\n \n","jql":"labels = Q1-2021","validSearcher":true,"isShown":true}}}
[{"id":-1,"name":"My open issues","jql":"assignee = currentUser() AND resolution = Unresolved order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":true},{"id":-2,"name":"Reported by me","jql":"reporter = currentUser() order by created DESC","isSystem":true,"sharePermissions":[],"requiresLogin":true},{"id":-4,"name":"All issues","jql":"order by created DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-5,"name":"Open issues","jql":"resolution = Unresolved order by priority DESC,updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-9,"name":"Done issues","jql":"statusCategory = Done order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-3,"name":"Viewed recently","jql":"issuekey in issueHistory() order by lastViewed DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-6,"name":"Created recently","jql":"created >= -1w order by created DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-7,"name":"Resolved recently","jql":"resolutiondate >= -1w order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false},{"id":-8,"name":"Updated recently","jql":"updated >= -1w order by updated DESC","isSystem":true,"sharePermissions":[],"requiresLogin":false}]
0.3
0