Software Group Progress Report Q2 2014: Difference between revisions

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** Panther services integrated (Anushya, Seth)
** Panther services integrated (Anushya, Seth)


=== Authentication / Auth ===
=== Authentication / Authorization ===
* Gathering requirements at CalTech hackathon
* Gathering requirements at CalTech hackathon
* Implementing Persona authentication into Noctua
* Implementing Persona authentication into Noctua


=== Noctua ===
=== LEGO: Noctua/Barista/Minerva ===
* Implemented Prototype system, 3 components
* Implemented prototype system, 3 components:
** Noctua: client component
** Noctua: client component
** Barista: middleware layer
** Barista: messaging/session layer
** Minerva: OWLServer
** Minerva: OWLServer
* CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua [https://github.com/kltm/go-mme/issues/51 noctua-51]
* CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua [https://github.com/kltm/go-mme/issues/51 noctua-51]
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== Priorities for Q3 ==
== Priorities for Q3 ==


=== WebSite ===
=== Website ===
* Drupal and AmiGO 2 client running in cloud?
* 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]]
* AmiGO [[AmiGO_2#Timeline]]
** Selenium test framework (Mary, JuanCarlos)
** Selenium test framework (Mary, JuanCarlos)
** AmiGO 2.2 July
** AmiGO 2.2 July
** AmiGO 2.3 Oct
** AmiGO 2.3 Oct
** Matrix improvements


=== Noctua ===
=== LEGO ===


Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255]
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]
Milestone in github: [https://github.com/kltm/go-mme/issues?milestone=3&page=1&state=open Q3]
==== Noctua ====


* Authorization
* Authorization
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* Showing inference
* Showing inference
* Improved front-end
* Improved front-end
* species selector for new models & Filter search for appropriate genes/proteins
* Species selector for new models & Filter search for appropriate genes/proteins
 
* import from Reactome (Chris)
* Dev instance up and running at CalTech (JuanCarlos, Raymond)
* Dev instance up and running at CalTech (JuanCarlos, Raymond)
* OA-type editor in Noctua (Juancarlos)
* OA-type editor in Noctua (Juancarlos)
==== Minerva ====
* Import from Reactome (Chris)
* Pipeline for GAF/GPAD output (Heiko)
* Pipeline for GAF/GPAD output (Heiko)


=== Paper Viewer ===
=== Paper Viewer ===
* Capella-Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] pushed to Q4
 
* Capella->Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] pushed to Q4


=== Infrastructure ===
=== Infrastructure ===
* Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
* Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
* Refactor Golr loading (Seth, Heiko, Chris)
* 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)
* 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
* GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4


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

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
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