Package: eke.specimens
This product,eke.specimens, provides display andRDFingest of
ERNE (EDRN Resource Network Exchange) specimens for the Early Detection
Research Network (EDRN) Knowledge Environment (EKE).  EDRN uses the EKE to
make it easy to discover, share, search for, and retrieve all of EDRN’s
collective knowledge, including cancers and other diseases, biomarkers,
publications, investigators, participants, studies, protocols, and, as in the
case of this product, specimens.Although intended for the EDRN public portal, it can be installed in anyPlonecompatible site.This software is developed by theEDRN Informatics CenteratJPL,
operated by the California Institute of Technology, forNCI.InstallationUseBuildoutwith the plone.recipe.zope2instance recipe.Addeke.specimensto the list of eggs to install, e.g.:[buildout]
...
eggs =
    ...
    eke.specimensRe-run buildout, e.g. with:% ./bin/buildoutYou can skip the ZCML slug if you are going to explicitly include the package
from another package’s configure.zcml file.ChangelogWhat follows is a history of changes from release to release.  Within each
description, you can find more details about cited issue numbers by visiting
the issue tracker athttps://oodt.jpl.nasa.gov/jira/browse/CA1.1.12 — Plone 4.3.9 UpgradeCA-1592CA-1593CA-15941.1.11 — user=’kelly’CA-1447: Faceted debug criteria causing test failures1.1.10 — Bug FixesCA-13001.1.9 — I Had Some Chicken; Pass Me the FLOSSFirst official release as free/libre/open source software.1.1.8 — Like an UnderlingFix CA-1159: Specimens tab shows errorFix CA-1114: Christopher Li Site Disappears after Specimen Ingest1.1.7 — Like a BossMade compatible with Plone 4.3.Made compatible with eea.facetednavigation 5.9Work around vocabulary lookup caused by interaction of
collection.vdexvocabulary-0.1.1 and Plone-4.3.Use z3c.autoincludeFix content-core macrosRemove obsolete calls to document_relateditemsRemove monkey-patching and use proper technique to introduce custom faceted
render pagesAlphabetize storage types and collection typesUse refactored base.cfg1.1.6 — We’ll Never Get Specimens RightAdded site 593 (CERC at FHCRC with PI Christopher Li)Compatible with Plone 4.2.4 and eea.facetednavigation 5.3.CA-1087 - Additional Specimen_Stored_Code Permissible ValuesCA-1084 - Modifications to Specimen Tab1.1.5 — OpenedCA-1008 - Add an open text search to specimens1.1.4 — UpgradesMake compatible with Plone 4.1.5 and eea.facetednavigation 4.5.1.1.3 — Third Time’s the CharmThis release addresses:CA-845 - Make “Specimen Collections” compute total specimensCA-844 - Combine PRoBE and Reference Sets in the “Specimens” tabNumerous enhancements to the handling of specimens, including:Generic specimen sets to treat PRoBE and Reference equivalentlyFile and link attachment to generic specimen setsRepresentation of sets of specimens from inactive ERNE sitesCo-habitation of inactive and active ERNE setsMultiple storage types for inactive ERNE setsOpen-ended generic reference setsSeparation of case and control populations into subsetsCA-926 - Improve Specimen Reference Sets based on feedback from Jackie
Dahlgren, including:Dropping the specimen count on the faceted Specimens tab for reference setsDrop the specimen count on the Reference Set viewsOn the faceted Specimens tab, sort reference sets specially:
alphabetically, except for Lung, which should be in the order: Set A
Rapid, Set A Panel Pre-Validation, Set A Phase II Validation, Set B,
Set CMoving set-specific from the Resources tab to their matching Reference
SetsYou can mark generic sets as PRoBE sets.CA-938 - Add specimen contact information to detail page of specimen setsCA-937 - Add pagination to Specimen tab list of specimen sets on right1.1.2 — Dawn’s Out, William’s InThis release handles:CA-832 - Correct NYU Specimen Site, PI and Organ1.1.1 — Thus Spake ChristosThis release addresses the following:CA-823 - Modify eke.specimens per Christos’s commentaryCA-825 - Evening telecon1.1.0 — Strong SimplificationThis release simplifies specimens so that only the common attributes between
Specimen Reference Sets, PRoBE, and ERNE Specimens are represented.1.0.1 — Upgrade CleanupThis release updates the GenericSetup profile to 4, provides upgrade steps to
that profile, and makes the testing and development harness depend on “trunk”
level of other eggs instead of on released versions of those eggs.  It also
takes advantage of factored out common testing setup.1.0.0 — Plone 4This release makes eke.specimens compatible with Plone 4.0.0.3 — NYUThis release tackles the following:If an ERNE site is down and the ERNE cache returns an HTTP 500 error, don’t
abort the entire ingest.  Just skip that site and go forward.  “Keep calm
and carry on.”0.0.2 — A Mixed BagThis release addresses the following issue:CA-698 - “Structural” objects appear in searches0.0.1 — Goodbye, Peter LinThis time around, the EKE specimen package provides direct display of ERNE
specimen data without having to delegate to the ERNE UI web application.
(There is no corresponding issue in the issue tracker for this new feature; or
if there is, the issue tracker is down as I write this and can’t confirm.)This release also addresses the following issues:CA-683 — Counts are off on specimen searchCA-685 — Specimen Tab search results returns records for the same search
summary more than one time (should be grouped together)0.0.0 — UnreleasedInitial release into beta.