eke.specimens


Nameeke.specimens JSON
Version 1.1.11 PyPI version JSON
download
home_pagehttps://github.com/EDRN/eke.specimens
SummaryERNE Specimen Management for the EDRN Knowledge Environment
upload_time2016-12-06 21:47:07
maintainerNone
docs_urlNone
authorAndrew Hart
requires_pythonNone
licenseALv2
keywords web zope plone edrn cancer biomarkers eke knowledge specimen erne
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI
coveralls test coverage
            *************
eke.specimens
*************

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_.

.. References:
.. _EDRN Informatics Center: http://cancer.jpl.nasa.gov/
.. _EDRN: http://edrn.nci.nih.gov/
.. _EKE: http://cancer.jpl.nasa.gov/documents/applications/knowledge-environment
.. _JPL: http://www.jpl.nasa.gov/
.. _NCI: http://cancer.gov/
.. _Plone: http://plone.org/
.. _RDF: http://w3.org/RDF


Installation
============

Use Buildout_ with the plone.recipe.zope2instance recipe.

• Add ``eke.specimens`` to the list of eggs to install, e.g.::
 
    [buildout]
    ...
    eggs =
        ...
        eke.specimens
        
• 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.

.. References:
.. _Buildout: http://www.buildout.org/


Changelog
=========

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 https://oodt.jpl.nasa.gov/jira/browse/CA


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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