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ERNE Specimen Management for the EDRN Knowledge Environment

Project description

This product, eke.specimens, provides display and RDF ingest 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 any Plone compatible site.

This software is developed by the EDRN Informatics Center at JPL, operated by the California Institute of Technology, for NCI.


Use Buildout with the plone.recipe.zope2instance recipe.

  • Add eke.specimens to the list of eggs to install, e.g.:

    eggs =
  • Re-run buildout, e.g. with:

    % ./bin/buildout

You can skip the ZCML slug if you are going to explicitly include the package from another package’s configure.zcml file.


What 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 at

1.1.12 — Plone 4.3.9 Upgrade

  • CA-1592
  • CA-1593
  • CA-1594

1.1.11 — user=’kelly’

  • CA-1447: Faceted debug criteria causing test failures

1.1.10 — Bug Fixes

  • CA-1300

1.1.9 — I Had Some Chicken; Pass Me the FLOSS

  • First official release as free/libre/open source software.

1.1.8 — Like an Underling

  • Fix CA-1159: Specimens tab shows error
  • Fix CA-1114: Christopher Li Site Disappears after Specimen Ingest

1.1.7 — Like a Boss

  • Made compatible with Plone 4.3.
  • Made compatible with eea.facetednavigation 5.9
  • Work around vocabulary lookup caused by interaction of collection.vdexvocabulary-0.1.1 and Plone-4.3.
  • Use z3c.autoinclude
  • Fix content-core macros
  • Remove obsolete calls to document_relateditems
  • Remove monkey-patching and use proper technique to introduce custom faceted render pages
  • Alphabetize storage types and collection types
  • Use refactored base.cfg

1.1.6 — We’ll Never Get Specimens Right

  • Added 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 Values
  • CA-1084 - Modifications to Specimen Tab

1.1.5 — Opened

  • CA-1008 - Add an open text search to specimens

1.1.4 — Upgrades

  • Make compatible with Plone 4.1.5 and eea.facetednavigation 4.5.

1.1.3 — Third Time’s the Charm

This release addresses:

  • CA-845 - Make “Specimen Collections” compute total specimens
  • CA-844 - Combine PRoBE and Reference Sets in the “Specimens” tab
  • Numerous enhancements to the handling of specimens, including:
    • Generic specimen sets to treat PRoBE and Reference equivalently
    • File and link attachment to generic specimen sets
    • Representation of sets of specimens from inactive ERNE sites
    • Co-habitation of inactive and active ERNE sets
    • Multiple storage types for inactive ERNE sets
    • Open-ended generic reference sets
    • Separation of case and control populations into subsets
  • CA-926 - Improve Specimen Reference Sets based on feedback from Jackie Dahlgren, including:
    • Dropping the specimen count on the faceted Specimens tab for reference sets
    • Drop the specimen count on the Reference Set views
    • On 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 C
    • Moving set-specific from the Resources tab to their matching Reference Sets
    • You can mark generic sets as PRoBE sets.
  • CA-938 - Add specimen contact information to detail page of specimen sets
  • CA-937 - Add pagination to Specimen tab list of specimen sets on right

1.1.2 — Dawn’s Out, William’s In

This release handles:

  • CA-832 - Correct NYU Specimen Site, PI and Organ

1.1.1 — Thus Spake Christos

This release addresses the following:

  • CA-823 - Modify eke.specimens per Christos’s commentary
  • CA-825 - Evening telecon

1.1.0 — Strong Simplification

This release simplifies specimens so that only the common attributes between Specimen Reference Sets, PRoBE, and ERNE Specimens are represented.

1.0.1 — Upgrade Cleanup

This 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 4

This release makes eke.specimens compatible with Plone 4.

0.0.3 — NYU

This 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 Bag

This release addresses the following issue:

  • CA-698 - “Structural” objects appear in searches

0.0.1 — Goodbye, Peter Lin

This 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 search
  • CA-685 — Specimen Tab search results returns records for the same search summary more than one time (should be grouped together)

0.0.0 — Unreleased

Initial release into beta.

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