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EKE 1.1.0

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EKE
This release provides workflow-based security for data within the knowledge environment.

For additional information about this project, please visit the project page.

Available downloads

Get EKE 1.1.0 for All platforms (166.2kiB)

Product Package (in bzip2-compressed tar archive)

Release Notes

Tested with Python 2.4, Plone 2.5
State Final release
License Caltech
Release Manager Sean Kelly

This release includes bug fixes to the RDF import of data as well as workflow-based security for EDRN Knowledge Environment objects.

Change log

  • 2008-12-11 21:43 kelly
  • [r4267] 1.1.0α1
  • 2008-12-11 21:43 kelly
  • [r4266] Don't assume Knowledge object will be owned by a member-role user.
  • 2008-12-10 21:00 kelly
  • [r4264] CA-203: Add a workflow for EKE objects with two simple states, Internal and Published. Start off EKE objects in the Internal state and allow view/access/ etc. permission only for Manager, Owner, and Member roles. Delete container objects when importing so they'll get the benefit of the new workflow.
  • 2008-09-24 15:09 kelly
  • [r4084] Add support for marking aliases on biomarkers.
  • 2008-09-24 13:52 kelly
  • [r4082] CA-189: use tabber only if there are 5 tabs or less.
  • 2008-09-11 12:50 kelly
  • [r4002] (Via telephone by Dan Cricthon) Make study name and abstract equally sized columns.

    (Via CA-184) Make study display larger font, move related resources below Results Outcome.
  • 2008-09-10 13:25 kelly
  • [r3998] (From Dan's phone call, 2008.9.9) Use FHCRC_ID instead of DMCC_ID when importing studies to set study ID field. In study list, make name column narrower, and abstract column wider. For abstract column, use as much text as possible from the abstract, objective, aims, and results outcome fields.
  • 2008-09-09 22:42 kelly
  • [r3995] In sites list: hide sites with no PIs (add note: "Associate members not avail at this time")
  • 2008-09-09 22:37 kelly
  • [r3994] CA-177: Remove brains from registered field. Use brains on organGroup to populate display on protocol folders. Ensure setting of organGroup from BMDB RDF.
  • 2008-09-09 22:28 kelly
  • [r3993] CA-179: adjust indexes and brains so that ID and status are available in folder listing. Show title, ID, status, and a word-boundary truncated and ellipsified abstract for each study.
  • 2008-09-09 20:48 kelly
  • [r3989] CA-175: objective, specific aims, and results outcome moved to below abstract. Further, misc details now hidden in an expandible section.
  • 2008-09-05 19:03 kelly
  • [r3976] Fold EDRNBiomarkerStudy up into EDRNProtocol and call it a Study.
  • 2008-09-05 19:03 kelly
  • [r3975] Add ingest for Resources from RDF.
  • 2008-09-05 19:02 kelly
  • [r3974] Move related resources below publications
  • 2008-09-05 19:02 kelly
  • [r3973] For pages that match, label them explicitly as "Web", not "Page".
  • 2008-09-05 19:01 kelly
  • [r3972] Show investigators at site in their own section, apart from mere staff.
  • 2008-09-05 19:01 kelly
  • [r3971] Make biomarker name stand out a bit more.
  • 2008-09-05 19:00 kelly
  • [r3970] 1. Show "body system" (aka organ) in summary search results for Biomarkers. 2. Change "Show protocols..." to "Show protcols studied by this investigator"
  • 2008-09-05 18:59 kelly
  • [r3969] Add Resources box and document actions to staff view.
  • 2008-09-05 18:59 kelly
  • [r3968] Import publications by first looking up authors already stored in Sites. Take whoever's left and add them to other authors.

    Remove creation of resources from biomarkers. Import resources from the RDF BMDB source for resources.

    Replace EDRNBiomarkerStudy with EDRNProtocol.
  • 2008-09-05 18:57 kelly
  • [r3967] Remove phase from Biomarker. Re-label as just "Biomarker". Add optional separator parameter for organ formatting.
  • 2008-09-05 18:56 kelly
  • [r3966] Remove PIs from staff members, rename method to retrieve staff members.
  • 2008-09-05 18:55 kelly
  • [r3965] Add field to hold other authors not known to EDRN.
  • 2008-09-05 18:55 kelly
  • [r3964] Set the predicate URI of the Title of a resource to http://bmdb.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#Description.

    (We'll later probably set the Description to ...#Title. ^_^)
  • 2008-08-29 16:02 kelly
  • [r3953] Change "EKE Home" to "Knowledge Base"
  • 2008-08-29 15:56 kelly
  • [r3952] Disable discussions and bumpity
  • 2008-08-29 14:21 kelly
  • [r3951] Purge all old data before importing it; BMDB is the "gold source".
  • 2008-08-29 14:19 kelly
  • [r3950] Add additional header and resources box.
  • 2008-08-28 23:17 kelly
  • [r3949] Implement last-minute BMDB exports of sites and pis and linking of related resources.
  • 2008-08-28 19:46 kelly
  • [r3942] CA-169: Added content type "Publications Folder" which contains Publication objects and provides a tabular view of their titles, journals, and pubmed IDs. Titles link to Publication objects, pubmed IDs link directly to the Pubmed Entrez. Added indexes and brains on journals and pubmed IDs.
  • 2008-08-28 19:16 kelly
  • [r3938] CA-170: Make links to member's site and details part of a bulleted list. Make member's name in a larger font.
  • 2008-08-28 18:56 kelly
  • [r3937] CA-166: Text appears if to indicate if no protocols are defined. Separate header for Staff appears above staff list.
  • 2008-08-28 17:11 kelly
  • [r3936] Bumpity
  • 2008-08-28 17:10 kelly
  • [r3935] Change "ECAS" to "Science"
  • 2008-08-28 17:10 kelly
  • [r3934] urn:oodt:Title has now become urn:edrn:Title (and it shouldn't be either!)
  • 2008-08-28 17:09 kelly
  • [r3933] Replace "ECAS" with "Science"
  • 2008-08-28 17:09 kelly
  • [r3932] Repair link to ERNE
  • 2008-08-28 17:09 kelly
  • [r3931] Replace "Phase" column with "Organ(s)" column
  • 2008-08-28 17:08 kelly
  • [r3930] Repair link to ERNE
  • 2008-08-28 17:08 kelly
  • [r3929] Repair link to ERNE
  • 2008-08-28 17:07 kelly
  • [r3928] 1. For ECAS objects, make the link go directly to ECAS instead of to the view page for the object.

    2. Hardwire the order of the Resources box.
  • 2008-08-28 17:06 kelly
  • [r3927] Add methods to get organs for the summary folder view
  • 2008-08-27 19:22 kelly
  • [r3926] Send data to its new relegated location.
  • 2008-08-27 19:04 kelly
  • [r3925] Bumpity
  • 2008-08-27 19:04 kelly
  • [r3924] Add additional fields and predicate URIs to Publications.
  • 2008-08-27 19:04 kelly
  • [r3923] get rid of bogus empty permission
  • 2008-08-27 19:04 kelly
  • [r3922] Add i18n labels for new publication fields.
  • 2008-08-27 19:03 kelly
  • [r3921] Add UI to import Publications from BMDB
  • 2008-08-27 19:02 kelly
  • [r3920] Implement import of publications. Fix import of related resources. This fixes CA-161.
  • 2008-08-22 13:56 kelly
  • [r3901] Add investigators column
  • 2008-08-20 16:22 kelly
  • [r3889] CA-151: Make resources box appear for portal search results
  • 2008-08-19 22:53 kelly
  • [r3884] Bumpity
  • 2008-08-19 22:53 kelly
  • [r3883] Add SiteFolder
  • 2008-08-19 22:53 kelly
  • [r3882] Methods to get investigators
  • 2008-08-19 22:52 kelly
  • [r3881] Add SiteFolder to initialaztion and to allowalbe child-object types
  • 2008-08-19 22:52 kelly
  • [r3880] View template for SiteFolder
  • 2008-08-19 22:52 kelly
  • [r3879] A folder to contain Site objects.
  • 2008-08-19 20:31 kelly
  • [r3878] Add documentation
  • 2008-08-19 16:06 kelly
  • [r3877] Add organ-spec biomarker data from a study to osbrs. Import organ-spec bio data from RDF.
  • 2008-08-18 23:20 kelly
  • [r3876] RDF import for biomarkers
  • 2008-08-18 22:28 kelly
  • [r3875] RDF import for studies
  • 2008-08-18 18:35 kelly
  • [r3874] bumpity
  • 2008-08-18 18:35 kelly
  • [r3873] Add i18n for addtl class
  • 2008-08-18 18:34 kelly
  • [r3872] Show a list of publications specific to each organ in a biomarker.
  • 2008-08-18 18:33 kelly
  • [r3871] Add a pubs field to OSBR
  • 2008-08-18 18:33 kelly
  • [r3870] Add access to pubs on an OSBR.
  • 2008-08-17 20:38 kelly
  • [r3868] Bumpity
  • 2008-08-17 20:38 kelly
  • [r3867] New i18n strings
  • 2008-08-17 20:38 kelly
  • [r3866] These biomarkers belong just in biomarker folders now
  • 2008-08-17 20:37 kelly
  • [r3865] FOrmatting for EKE search
  • 2008-08-17 20:37 kelly
  • [r3864] Change label: Specimens → Specimen Search. Add direct link to eCAS.
  • 2008-08-17 20:35 kelly
  • [r3863] Add biomarker folder and protocol folder
  • 2008-08-17 20:35 kelly
  • [r3862] Put search examples into a popup section. Make search more Google-like. Make sure it says it's searching just the knowledge system.
  • 2008-08-17 20:34 kelly
  • [r3861] Override so we can call it "Spotlight Search"
  • 2008-08-17 20:34 kelly
  • [r3860] Add biomarker folder and protocol folder
  • 2008-08-17 20:34 kelly
  • [r3859] Add additional contained object types
  • 2008-08-17 20:33 kelly
  • [r3858] Disable global add—these belong in protocol folders only.
  • 2008-08-17 20:33 kelly
  • [r3857] Add index on field. Add brains on index. Disable globally addable
  • 2008-08-17 20:32 kelly
  • [r3856] Add boolean field for EDRN-or-not, and disable globally addable. These belong in protocol folders only.
  • 2008-08-17 20:31 kelly
  • [r3855] Disable everywhere
  • 2008-08-17 20:31 kelly
  • [r3854] Disable everywhere
  • 2008-08-17 20:31 kelly
  • [r3853] Enable everywhere
  • 2008-08-17 20:30 kelly
  • [r3852] A folder to hold biomarkers
  • 2008-08-17 20:30 kelly
  • [r3851] A folder to hold protocols, studies, etc.
  • 2008-08-08 16:36 kelly
  • [r3807] Use urn:oodt:cas:Title if available
  • 2008-08-08 16:36 kelly
  • [r3806] Special case for ECAS data
  • 2008-08-08 16:35 kelly
  • [r3805] Get URL from Identifier, not title
  • 2008-08-08 15:14 kelly
  • [r3804] Ooops, forgot to checkin
  • 2008-03-12 16:38 kelly
  • [r3434] Fix search which was counting kinds of results as number of results instead of actual number of results.
  • 2008-03-12 15:47 kelly
  • [r3433] Add additional eCAS fields
  • 2008-03-12 14:13 kelly
  • [r3432] change class of specimens lnk
  • 2008-03-06 20:40 kelly
  • [r3420] Remove extra WS
  • 2008-02-19 19:13 kelly
  • [r3403] Send specimen search to ERNE public search interface
  • 2008-02-19 19:12 kelly
  • [r3402] Make "Data" be "Science Data".
  • 2008-01-16 17:47 kelly
  • [r3208] Blah, forgot to check in: add organ-centric view template for seeing organ-specific data, protocols studying the organ, and specimens taken from the organ.
  • 2008-01-10 16:54 kelly
  • [r3192] Update copyright boilerplate
  • 2008-01-10 16:53 kelly
  • [r3191] Workflow for the Knowledge object. This workflow has two states (private, published) and simple guards between states. It also sets the view permission for a published Knowledge object to require authenticated users.
  • 2008-01-10 16:52 kelly
  • [r3190] Install workflows associated with objects.
  • 2007-09-18 13:16 kelly
  • [r2906] Christos has '<resource id="" uri=""/>' in his XML. Filter those out.
  • 2007-09-14 19:27 kelly
  • [r2902] Make example searches show content. Fixes http://agility.jpl.nasa.gov/tracker/3
  • 2007-09-13 16:02 kelly
  • [r2901] Add link to show investigators working on a biomarker study. Add view template for investigators on study.
  • 2007-09-13 15:28 kelly
  • [r2900] Link PrincipalInvestigators to EDRNBiomarkerStudy objects. Support for http://agility.jpl.nasa.gov/tracker/4
  • 2007-09-13 15:26 kelly
  • [r2899] Move the dot.
  • 2007-09-13 14:57 kelly
  • [r2898] Add another possible view template to the Topic type, one that includes the EKE resources box and link back home. Register this template and when creating the Investigators topic set it as the selected view for the Topic.
  • 2007-09-12 15:13 kelly
  • [r2895] Don't search Organ Specific Biomarker Research objects. Fixes http://agility.jpl.nasa.gov/tracker/7
  • 2007-09-10 20:32 kelly
  • [r2894] View template for datasets
  • 2007-09-10 20:30 kelly
  • [r2893] Add a view template for datasets
  • 2007-09-10 18:41 kelly
  • [r2892] Add ECAS datasets
  • 2007-09-10 16:33 kelly
  • [r2889] Fix view template for pubs
  • 2007-09-10 16:32 kelly
  • [r2888] Ingest ECAS
  • 2007-09-07 16:55 kelly
  • [r2876] By default sort on the 'sortable_title' index. Fixes http://agility.jpl.nasa.gov/tracker/2.
  • 2007-08-20 16:51 kelly
  • [r2856] add link to pubmed on pub view
  • 2007-08-20 15:59 kelly
  • [r2855] Link from pubmed ID to publication data page
  • 2007-08-09 15:27 kelly
  • [r2826] conducting → condition
  • 2007-08-09 15:23 kelly
  • [r2825] bumpity
  • 2007-08-09 15:23 kelly
  • [r2824] delete spurious blank line for anal retentive formatting
  • 2007-08-09 15:22 kelly
  • [r2823] Add prominent section for studies. Add resources box. Fix links to related objects.
  • 2007-08-09 15:21 kelly
  • [r2822] Add tab with all results collated by relevance.
  • 2007-08-09 15:21 kelly
  • [r2821] Fix label
  • 2007-08-09 15:21 kelly
  • [r2820] Add section for studied biomarkers. Add resources box. Fix links to related objects.
  • 2007-08-09 15:20 kelly
  • [r2819] Add resources box to general EKE objects view.
  • 2007-08-09 15:20 kelly
  • [r2818] Return all results collated by relevance.
  • 2007-08-09 15:19 kelly
  • [r2817] Unify the searches.
  • 2007-07-25 19:32 kelly
  • [r2791] get rid of spurious html tag
  • 2007-07-25 19:30 kelly
  • [r2789] Add relatable for biomarker studies
  • 2007-07-25 19:29 kelly
  • [r2788] Add smart folder for list of investigators; sort by obj title.
  • 2007-07-23 14:44 kelly
  • [r2775] bumpity
  • 2007-07-23 14:44 kelly
  • [r2774] Put the resources box on every relatable obj
  • 2007-07-23 14:44 kelly
  • [r2773] Always use the knowledge obj instead of the context obj
  • 2007-07-23 14:43 kelly
  • [r2772] Update popup for plain biomarker research
  • 2007-07-21 17:15 kelly
  • [r2771] prettify the resources box, get rid of tree-widget styles
  • 2007-07-18 18:32 kelly
  • [r2766] programatically create knowledge hierarchy on installation
  • 2007-07-18 13:08 kelly
  • [r2759] add data tab
  • 2007-07-18 13:03 kelly
  • [r2758] add boilerplate
  • 2007-07-18 13:00 kelly
  • [r2757] nuke the debug logging
  • 2007-07-12 22:16 kelly
  • [r2744] Add UI for biomarker ingest. Update cardinality of fields.
  • 2007-07-12 22:11 kelly
  • [r2743] link biomarkers, studies, organs, and organ-specific biomarker research
  • 2007-07-10 19:12 kelly
  • [r2741] Add parsing of biomarker data in XML format
  • 2007-06-28 17:15 kelly
  • [r2714] Fix subclasses of Biomarker Research so they actually contain Organ-Specific Biomarker Research. Add title to resources box. Remove multiple instances of Specimens from list.
  • 2007-06-25 22:26 kelly
  • [r2703] Link to specimens
  • 2007-06-25 20:56 kelly
  • [r2701] get rid of the fieldset
  • 2007-06-25 14:14 kelly
  • [r2698] Reformat links
  • 2007-06-25 14:09 kelly
  • [r2697] Add intro text (slide #6), and links to resources and help (slide #4).
  • 2007-06-18 19:23 kelly
  • [r2686] update for scrape 1.3
  • 2007-06-13 18:51 kelly
  • [r2681] Support XML ingest.
  • 2007-06-04 21:01 kelly
  • [r2650] remove obsolete link
  • 2007-06-04 20:58 kelly
  • [r2649] define getBiomarkerInfo
  • 2007-06-04 20:56 kelly
  • [r2648] tempalte for STUDIES
  • 2007-06-04 20:26 kelly
  • [r2647] Define methods for organ-spec researches and for study data
  • 2007-06-04 16:42 kelly
  • [r2646] Add relatable folders to knowledge objects
  • 2007-06-04 14:02 kelly
  • [r2645] Add relatable folder type, view template, and styling.
  • 2007-05-24 22:17 kelly
  • [r2638] use the macro
  • 2007-05-24 22:03 kelly
  • [r2637] View for Biomarkers
  • 2007-05-24 15:07 kelly
  • [r2636] update view templates
  • 2007-05-24 15:06 kelly
  • [r2635] macro to generate home link
  • 2007-05-24 15:06 kelly
  • [r2634] css for home links
  • 2007-05-24 15:06 kelly
  • [r2633] View template for all other EKE entities
  • 2007-05-23 19:44 kelly
  • [r2632] GRRR. Some other product (probably the stupid wiki for IPDA) is conflicting. I'm implementing this to make the AttributeError from constraintypes.getImmediatelyAddableTypes go away.
  • 2007-05-23 14:16 kelly
  • [r2631] add ignores
  • 2007-05-23 14:15 kelly
  • [r2630] don't check in compiled files
  • 2007-05-23 14:14 kelly
  • [r2629] Unify biomarker db and eke
  • 2007-04-12 20:19 kelly
  • [r2570] Re-org
  • 2007-04-12 20:19 kelly
  • [r2569] Re-org
  • 2007-04-12 20:18 kelly
  • [r2568] Re-org
  • 2007-04-12 20:18 kelly
  • [r2567] Re-org
  • 2007-04-12 20:18 kelly
  • [r2566] Re-org
  • 2007-04-12 20:18 kelly
  • [r2565] Re-org
  • 2007-04-12 20:18 kelly
  • [r2564] Re-org
  • 2007-04-12 20:18 kelly
  • [r2563] Re-org
  • 2007-04-12 20:18 kelly
  • [r2562] Re-org
  • 2007-04-12 20:18 kelly
  • [r2561] Re-org
  • 2007-04-12 20:18 kelly
  • [r2560] Re-org
  • 2007-04-12 20:18 kelly
  • [r2559] Re-org
  • 2007-04-12 20:17 kelly
  • [r2558] Re-org
  • 2007-04-12 20:17 kelly
  • [r2557] Re-org
  • 2007-04-12 20:17 kelly
  • [r2556] Re-org
  • 2007-04-12 20:17 kelly
  • [r2555] Re-org
  • 2007-04-12 20:17 kelly
  • [r2554] Re-org
  • 2007-04-12 20:17 kelly
  • [r2553] Re-org
  • 2007-04-12 19:55 kelly
  • [r2497] Re-org