# 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