Software Group Progress Report Q2 2014: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(Created page with "== Progress Report Q2 == === WebSite === * Drupal Rollout: migrated to amazon, still testing * AmiGO 2.0 released in March * AmiGO 2.1 in testing May == Authentication / Aut...")
 
 
(31 intermediate revisions by 2 users not shown)
Line 1: Line 1:
== Progress Report Q2 ==
== Progress Report Q2 ==


=== WebSite ===
=== Website ===
* Drupal Rollout: migrated to amazon, still testing
* Drupal
* AmiGO 2.0 released in March
** Drupal Content: migration complete (Moni, Seth, Rama, ...)
* AmiGO 2.1 in testing May
** Drupal Rollout: migrated to AWS, still testing (Seth, Stuart) [https://www.ebi.ac.uk/panda/jira/browse/GO-106 JIRA GO-106]
* AmiGO
** AmiGO 2.0 released in March (Seth)
** AmiGO 2.1 in testing May (Seth, Rama)
* Term Enrichment
** Panther services integrated (Anushya, Seth)


== Authentication / Auth ==
=== Authentication / Authorization ===
* Gathering GO-wide requirements
* Gathering requirements at CalTech hackathon
* Persona
* Implementing Persona authentication into Noctua
* Authentication YAML specified


== Noctua ==
=== LEGO: Noctua/Barista/Minerva ===
* CalTech hackathon
* Implemented prototype system, 3 components:
* Documentation of 3 components: Noctua, Barista and Minerva
** Noctua: client component
* Implemented LEGO->GPAD in OWLTools
** Barista: messaging/session layer
** Minerva: OWLServer
* CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua [https://github.com/kltm/go-mme/issues/51 noctua-51]
* Implemented v1 of LEGO->GPAD/GAF in OWLTools [https://www.ebi.ac.uk/panda/jira/browse/GO-288 JIRA GO-288]


== Transition to OWL ==
=== Transition to OWL and ontology support ===
* Added import catalogs to OE
 
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-222 GO-222]
 
* Berkeley OWL hackathon (with David and Tanya): gathered requirements, tested roundtripping, reasoning etc
* Added import catalogs to OE (this allowed us to add all logical defs to main ontology)
* oboeditor plugin for Protege v0.1 (Heiko, Simon J)
* oboeditor plugin for Protege v0.1 (Heiko, Simon J)
* Fixes to obo/owl converter for never_in_taxon links
* Fixes to obo/owl converter for never_in_taxon links
* TG templates (HEIKO TO ADD)
* ...


== GPAD/GPI
=== GPAD/GPI ===
* GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS)
* GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS)
* Added 2-way converters to OWLTools (Heiko)
* Added 2-way converters to OWLTools (Heiko)
* GPI exports direct from MGI (Mary)
* GPI exports direct from MGI (Mary)


This is important for future scalability but due to lack of resources we are delaying this until next quarter
=== Retire GO Mine ===
Transition to OWL
* Done? (SETH/KALPANA)
Adding
 
Berkeley OWL hackathon (with David and Tanya)
=== PAINT ===
Protege OBO metadata plugin v0.1 (Simon J and Heiko)
* Paint v1.0 release (Suzi)
* JsPAINT prototype (Mitch, Seth)


Integration of taxon constraints into editors file
MySQL retirement
awaiting developer assignment
GAF<->GPAD<->LEGO converters
Ported GAF<->GPAD to java framework (Heiko), testing required
Initial LEGO->GPAD - many details TBD (Heiko)
Migrate cron to Jenkins
ongoing
Support for groups /metrics report ontology, annotation, user (go_help), drupal, AmiGO2
todo
Retire GO Mine
??
== Priorities for Q3 ==
== Priorities for Q3 ==


=== WebSite ===
=== Website ===
* Drupal and AmiGO 2 client running in cloud?
* Attempt further virtualization/distribution of AmiGO 2 client
* AmiGO 2.3
** Image deployment at production?
** Test feasibility of AmiGO 2 client running in in hosted or PaaS?
*** PaaS may require rewrite of some high-level bits
* AmiGO [[AmiGO_2#Timeline]]
** Selenium test framework (Mary, JuanCarlos)
** AmiGO 2.2 July
** AmiGO 2.3 Oct
** Matrix improvements
 
=== LEGO ===
 
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255]
 
Milestone in github: [https://github.com/kltm/go-mme/issues?milestone=3&page=1&state=open Q3]
 
==== Noctua ====


=== Noctua ===
 
* Working prototype of Capella-Noctua integration
 
* SETH TO ADD
* Authorization
* Authentication
* Semi-permanent layout
* Undo (push to Q4?)
* Showing inference
* Improved front-end
* Species selector for new models & Filter search for appropriate genes/proteins
* Dev instance up and running at CalTech (JuanCarlos, Raymond)
* OA-type editor in Noctua (Juancarlos)
 
==== Minerva ====
 
* Import from Reactome (Chris)
* Pipeline for GAF/GPAD output (Heiko)
 
=== Paper Viewer ===
 
* Capella->Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] pushed to Q4


=== Infrastructure ===
=== Infrastructure ===
* Refactor Golr loading
 
* Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
* Refactor GOlr loading (Seth, Heiko, Chris)
* Migrate crons to Jenkins [https://www.ebi.ac.uk/panda/jira/browse/GO-99 JIRA GO-99] (Heiko, Mike)
* GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4


=== MySQL retirement ===
=== MySQL retirement ===
* Replace go-db-perl code with owltools code (Kalpana)
* Replace go-db-perl code with OWLTools code (Kalpana) [https://www.ebi.ac.uk/panda/jira/browse/GO-282 JIRA GO-282]


=== Transition to OWL ===
=== Transition to OWL ===
* oboeditor plugin v0.2
* oboeditor plugin v0.2
* prototype of solution for caching inferred links (Heiko, DavidOS)
* prototype of solution for caching inferred links (Heiko, DavidOS)
* Progress towards automation of integration with RHEA [https://www.ebi.ac.uk/panda/jira/browse/GO-190 GO-190] -- not enough resources to complete in Q3
* Progress towards automation of integration with IPR/PFAM -- not enough resources to complete in Q3


Orion Release
[[Category:Reports]]
timeline
MySQL retirement
stage 1: replace go-db-perl code [production]
Transition to OWL
timeline
        b.  Orion Release / measurable timeline
    c.  Transition to OWL / measurable timeline

Latest revision as of 10:58, 18 June 2014

Progress Report Q2

Website

  • Drupal
    • Drupal Content: migration complete (Moni, Seth, Rama, ...)
    • Drupal Rollout: migrated to AWS, still testing (Seth, Stuart) JIRA GO-106
  • AmiGO
    • AmiGO 2.0 released in March (Seth)
    • AmiGO 2.1 in testing May (Seth, Rama)
  • Term Enrichment
    • Panther services integrated (Anushya, Seth)

Authentication / Authorization

  • Gathering requirements at CalTech hackathon
  • Implementing Persona authentication into Noctua

LEGO: Noctua/Barista/Minerva

  • Implemented prototype system, 3 components:
    • Noctua: client component
    • Barista: messaging/session layer
    • Minerva: OWLServer
  • CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua noctua-51
  • Implemented v1 of LEGO->GPAD/GAF in OWLTools JIRA GO-288

Transition to OWL and ontology support

Top-level ticket: GO-222

  • Berkeley OWL hackathon (with David and Tanya): gathered requirements, tested roundtripping, reasoning etc
  • Added import catalogs to OE (this allowed us to add all logical defs to main ontology)
  • oboeditor plugin for Protege v0.1 (Heiko, Simon J)
  • Fixes to obo/owl converter for never_in_taxon links
  • TG templates (HEIKO TO ADD)
  • ...

GPAD/GPI

  • GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS)
  • Added 2-way converters to OWLTools (Heiko)
  • GPI exports direct from MGI (Mary)

Retire GO Mine

  • Done? (SETH/KALPANA)

PAINT

  • Paint v1.0 release (Suzi)
  • JsPAINT prototype (Mitch, Seth)

Priorities for Q3

Website

  • Attempt further virtualization/distribution of AmiGO 2 client
    • Image deployment at production?
    • Test feasibility of AmiGO 2 client running in in hosted or PaaS?
      • PaaS may require rewrite of some high-level bits
  • AmiGO AmiGO_2#Timeline
    • Selenium test framework (Mary, JuanCarlos)
    • AmiGO 2.2 July
    • AmiGO 2.3 Oct
    • Matrix improvements

LEGO

Top-level ticket: GO-255

Milestone in github: Q3

Noctua

  • Authorization
  • Authentication
  • Semi-permanent layout
  • Undo (push to Q4?)
  • Showing inference
  • Improved front-end
  • Species selector for new models & Filter search for appropriate genes/proteins
  • Dev instance up and running at CalTech (JuanCarlos, Raymond)
  • OA-type editor in Noctua (Juancarlos)

Minerva

  • Import from Reactome (Chris)
  • Pipeline for GAF/GPAD output (Heiko)

Paper Viewer

  • Capella->Noctua integration noctua-51 pushed to Q4

Infrastructure

  • Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
  • Refactor GOlr loading (Seth, Heiko, Chris)
  • Migrate crons to Jenkins JIRA GO-99 (Heiko, Mike)
  • GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4

MySQL retirement

  • Replace go-db-perl code with OWLTools code (Kalpana) JIRA GO-282

Transition to OWL

  • oboeditor plugin v0.2
  • prototype of solution for caching inferred links (Heiko, DavidOS)
  • Progress towards automation of integration with RHEA GO-190 -- not enough resources to complete in Q3
  • Progress towards automation of integration with IPR/PFAM -- not enough resources to complete in Q3