Last modified 3 years ago Last modified on 05/06/09 16:26:55

Extrac document status

Out of date

installation

EclipseSetup
GBrowseConfiguration
Hardware - Richard, this seems to be covered in DataLoadingPerformance. Do we need this page any more?
- It might make sense to move the information to the hardware page to make hardware recommendations easier to find.
MacInstallation
SVNCheckout
- needs to be updated to 0.9 branch
- Should be renamed subversion checkout for consistency
SubversionIntroduction
Tomcat

data integration (julie)

BioSources
- needs lots of additional info about biosources
DataIntegration
- going to be the Home Page for this section
MineProperties
- This only has mine.properties, which is already covered on WebappConfig. What is needed is the equivalent for the data integration system, eg list of config files needed for the build (priority, keys, project.xml, and mine.properties). If we don't need that, then this page should be deleted.
ModelMerging
- rns to update
PostProcessing
- needs bioseg update
PrecomputedTables
RunningABuild
SourceHowto - added make_mine script, updated project.xml examples
ant
- AntTargets - Reference
- ProjectsIntroduction
- ProjectDependencies
- ProjectProperties
- ProjectTypes
FlyMineOwnData
- updated but should test to see if it actually works. maybe.
- should rename page to be something sensible. I don't know what though.

done
- Chado - External - probably doesn't need attention
- ChadoDBSource - Data source - good document, may need update
- ChadoDBSourceImplNotes
- Ensembl - updated
- ItemsXmlFormat
- MakeMine
- MakeSource? - moved to sourcehowto
- MineExampleSources? - didn't need updating, renamed to MalariaMineData
- MirrorHowTo - updated, but need to test. maybe.
- ModelDescription - updated
- PrimaryKeys - updated
- PriorityConfig
- ProjectXMLFormat - updated

workshop (rns)

InterMineTests
- updated, need to run to make sure instructions are still accurate
GettingStarted
- Should be replaced with GettingStarted2
- workshop home page
GettingStarted2
- Should be moved to GettingStarted
InterMineWebappWorkshopFall2008.pdf
- screenshots and text need to be updated with new querybuilder
- flymine-private/doc/handouts/WebappWorkshop.doc, I think
http://www.flymine.org/download/talks/InterMineWebappWorkshopFall2008_exercises.pdf - julie
- text needs to be updated
- make sure examples still work
SuperUser - julie
WorkshopAdditionalExcercises
WorkshopCreateSourceJava
WorkshopCreateSourcePerl
WorkshopDayTwo? - julie
- renamed to GettingStartedAdvanced?
- really needs a template tutorial
WorkshopWebService
moved to GettingStarted2 by xav, we can eventually delete these pages

webapp (xav)

ClassKeys - Reference, linked from WebappConfig
ConstraintLogicEditing - Is only linked from IntegratedTemplateBuilder? - it's probably useful elsewhere too. Also, image might not be up to date. Xavier, could you do this one?
DataCategories
EnrichmentWidgets - julie
IntegratedTemplateBuilder?
- Page should be renamed to TemplateQueryTutorial or something
- All of the images are of the old QueryBuilder.
- Add link from GettingStartedAdvanced?, SuperUser when this page is done
LongDisplayers
ObjectStoreSummaryProperties
Portal?
Themes
- I think purple and modmine are the same theme.
- can be merged with WebappAppearance?
- should discuss classDescriptions.properties
UserProfile
UserProfilePorting
WebApp
WebConfigModel
WebProperties
WebappAppearance?
- can be merged with Themes
- should discuss classDescriptions.properties
WebappConfig
- Order by functionality, not by filename
Widgets

core technical (mnw21)

CoreTechnical
IQL - mnw21
PathExpressions? - new page

webservices

ClientDownloadPage? moved to WebService -xav
ItemsAPIPerl
ListWebService? moved to WebService -xav
PerlWebServiceAPI
- I'm pretty sure this hasn't been tested by anyone ever.
QueryWebService? moved to WebService -xav
TemplateWebService moved to WebService -xav
TemplateWebService0
WebService

help pages

FAQs - xav
MailingList
- needs to be updated with our new mail server (dan)
TroubleshootingTips - julie
- combine with CommonErrors

marketing

InterMineFuture
- maybe better as blog posts? rns should update otherwise.
InterMineOverview
InterMineUseCases
Talks - rns
TechnicalOverview - The diagram has a box labelled "IMStore" instead of "ObjectStore?".

no idea

BuildingTestmodelApp - Setting up - We should check that this is up to date
ContactUs - Needed no change - mnw21
- should be changed from FlyMine to be InterMine, including new intermine email addresses
FlyMine
- This page just links to FlyMine, which is fine. Unless someone wants to write an intro.
FlyMineFAQ - maybe this shouldn't be here? Seems to be something that should be in help to me.

Pages to delete

MakeSource? moved to SourceHowto - xav
ClientDownloadPage?
ListWebService?
QueryWebService?
TemplateWebService
BioModelConventions?
- Very out of date, and only linked from OldFrontPage?
- could be useful as RGD are writing converters.
BuildSystemInterMineProperties? - Only linked from InterMineBuildSystem? - what are we trying to achieve with this page?
- I think it should be deleted. The interesting bit is already on MineProperties.
DocIndex? - Old page we used to work out what docs to change
IntegratingData? - old home page, replaced by DataIntegration
InterMineBuildSystem? - old home page, replaced by DataIntegration
- Currently linked from AntIntroduction, CoreTechnical, InterMineTests, Mine (also to delete), MineHowTo?
InterMineLibraries? - this information is covered better elsewhere
- Only linked from InterMineTests
MalariaMine?
- renamed to quickstart
- Currently linked from BuildingTestmodelApp, GettingStarted2, IntegratingData?, InterMineOverview, MalariaMineData, MalariaMineProperties? (also to delete), MalariaProjectProperties? (also to delete), MineExampleSources?, MineHowTo?, MineProperties, Workshop
MalariaProjectProperties? - list of build.xml and project.properties files for malariamine. We don't need this page as these files are now created by the make_mine script instead of manually.
- Not linked to by anything.
MalariaMineProperties?
- only an include to malariamine.properties, link directly to that file instead
- Currently linked from GettingStarted2 and WebappRelease?
MalariaProjectXML? - the project XML file is covered better on ProjectXMLFormat
- Linked from MineHowTo?
MineHowTo? - replaced by Julie's QuickStart
NewFrontPage? - part of last year's redesign
OldFrontPage? - part of last year's redesign
SourceProjectProperties?
- needs to be deleted I think
- Linked to by AnatomyOfASource (also to delete), IntegratingData?
TOC? - part of last year's redesign
WebappTech? - all the information on this page is either out-of-date (eg. paged tables) or available elsewhere (eg. userprofile) or not interesting to anyone anywhere ever (eg. Struts) or some combination of the three.
- Linked to from WebApp
InterMine's layout - move to intrac
- AnatomyOfASource
  - structure of a source
  - need serious refactoring, as it doesn't work, and may be out of date
  - Currently linked from FAQs, IntegratingData?, ItemsAPIJava
- InterMineAppStructure - structure of a webapp
  - Currently linked only from InterMineBuildSystem?
- Mine - structure of a mine
  - Currently linked to from MineHowTo?

Updated for InterMine 0.9

AntIntroduction - Setting up - Linked from Prerequisites
BiosegInstallation - Setting up - mnw21
CommonErrors
DataLoadingPerformance - mnw21
ExplainPlans - mnw21
FetchingRelatedObjects - mnw21
IQLExamples - mnw21
InterMine - Redirects to InterMineOverview - That's fine. mnw21
InterMineFeatureList - Needed very little change - mnw21
InterMinePerl
ItemsAPIJava - mnw21
MaintainingAMine
- a document kmr and julie wrote for Gos for the mines4mods grant.
ORMappingTool - mnw21
OSInterMineCancellation - mnw21
OptimiserCache - mnw21
OptimiserOtherProjects - mnw21
Prerequisites - mnw21
PostgresBasics
QueryPackage - mnw21
QuickStart
ResultsPrefetching - no change
ResultsTuning - mnw21
SafeObjectStore - mnw21
SearchEngines - fixed link to properties file
SimpleObjects - mnw21
Tagging - no change
WikiStart - homepage. should be changed last

Blog posts - these never need updating

Built-in Trac pages

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