Réunion PhyloAlps #18
02/05/2019
Participants
- Frédéric Boyer
- Bruno Bzeznik
- Eric Coissac
- Anthony Hombiat
- Sébastien Lavergne
- Charles Pouchon
Latest updates
Data
- Feed the database PhyloNorway samples with adaptating PhyloAlps load samples script
- Update PhyloAlps sampling script according to Eric's XML assembling metadata file
- Collectors cleaning (1500 -> 300)
- Organizations cleaning (/2)
User interface redesign
- Box every piece of information
- Counter up on homepage
- Redesign the projects map
- Redesign navigation tabs
- Redesign breadcrumbs tab
- Responsive design
- Remove the Home module and move the registration feature to the Editor module
- Rename edit button to open button in Editor
Data model
- Add 3 kinds of annotations to Sample/Extract/Library/Sequence/Assembling/Assembly
- Automatic Assembling logs from Assembling metadata XML file
- Notes for commenting everything from Sample to Assembly with a severity level (Info/Warning/Error)
- Advices for validating everything from Sample to Assembly
New features
- Sampleset
- Add map to the sampleset template
- Add session-wide sampleset
- Add associated samplesets in samples template
- Annotations
- Add create/edit/delete annotations feature
- Add annotations badges in hero
- DNA Assembly graph
- Increase nodes and edges size
- Immediatly display tooltip on edge hovering
- Add progress indicator on loading
- Auto center project/sampleset/home maps on makers layer extent
- Display Extract/Library/Sequence/Assembling in organization template
User roles and permissions
-
ProjectMember
- Sampleset: add/change/delete
- Annotations: add/change/delete
- Sample: add/change/delete
- DNA extract: add/change/delete
- DNA library: change
-
ProjectManager
- Project: change
-
Administrator
- Project: add/delete
- Person: add/change/delete
- Organization: add/change/delete
Architecture
- Merge beta branch with master beta.phyloalps.org -> data.phyloalps.org
- Add reload metedata RESTful method with crc64 authentication
TODO
- Aggregate notices/advices from child item and display in parent template hero
- Use latest advice as the authoritative advice (which implies renaming the advices table "History of advices")
- Implement a complex quality indicator based on tables/advices
- Add the libraries number in sample tables
- Fix the sequencing status in the libraries table in the sample template
- Add play/stop toggle button to control the graph assembly rendering engine
- Fix the probing->graph->unfold->annotation order in the assembly tables of the assembling template
- Invert the wrong lon/lat geographic coordinates in some PhyloNorway samples
- Deal with samples that don't have a NCBI taxID
- Display some database stats on homepage