{ "info": { "author": "Sean Kelly", "author_email": "sean.kelly@jpl.nasa.gov", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Web Environment", "Framework :: Plone", "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Internet :: WWW/HTTP", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "*************\neke.biomarker\n*************\n\nThis product, ``eke.biomarker``, provides display and RDF_ ingest of the\nbiomarkers being studied by the Early Detection Research Network (EDRN_).\nBiomarkers are chemical indicators for disease, and in the case of EDRN, the\ndisease being pursued is cancer. This package lets a researcher browse,\nsearch for, and discover interesting biomarkers, determine how research\nprogress is being made, find out statistical values of the biomarkers, and so\nforth. These features are integral to the EDRN Knowledge Environment (EKE_).\nEDRN uses the EKE to make it easy to discover, share, search for, and retrieve\nall of EDRN's collective knowledge, including cancers and other diseases,\nprotocols, specimens, participants, staff, and |---| as in the case of this\nproduct |---| biomarkers.\n\nAlthough intended for the EDRN public portal, it can be installed in any\nPlone_ compatible site.\n\nThis software is developed by the `EDRN Informatics Center`_ at JPL_,\noperated by the California Institute of Technology, for NCI_.\n\n.. References:\n.. _EDRN Informatics Center: http://cancer.jpl.nasa.gov/\n.. _EDRN: http://edrn.nci.nih.gov/\n.. _EKE: http://cancer.jpl.nasa.gov/documents/applications/knowledge-environment\n.. _JPL: http://www.jpl.nasa.gov/\n.. _NCI: http://cancer.gov/\n.. _Plone: http://plone.org/\n.. _RDF: http://w3.org/RDF/\n.. |---| unicode:: U+2014 .. EM DASH\n\n\nInstallation\n============\n\nUse Buildout_ with the plone.recipe.zope2instance recipe.\n\n\u2022 Add ``eke.biomarker`` to the list of eggs to install, e.g.::\n \n [buildout]\n ...\n eggs =\n ...\n eke.biomarker\n \n\u2022 Re-run buildout, e.g. with::\n \n % ./bin/buildout\n \nYou can skip the ZCML slug if you are going to explicitly include the package\nfrom another package's configure.zcml file.\n\n.. References:\n.. _Buildout: http://www.buildout.org/\n\n\nChangelog\n=========\n\nWhat follows is a history of changes from release to release. Where issue IDs\nare listed below, you can find out more about them by visiting the issue\ntracker at https://oodt.jpl.nasa.gov/jira/browse/CA.\n\n\n1.1.26 \u2014 Graphs are not funny\n-----------------------------\n\n\u2022 CA-1536: Graphs appear funny on biomarker page\n\u2022 CA-1572: biomarker ingest need to capture cancerdataexpo external resources as ast instead of json\n\u2022 CA-1592\n\n\n1.1.25 \u2014 Follow the protocols!\n------------------------------\n\n\u2022 CA-1552: 200 character truncation of protocols causes ingest issue\n\n\n1.1.24 \u2014 Fast ingestion aids digestion\n--------------------------------------\n\n\u2022 CA-1434: Id searching makes biomarker ingest take too long\n\n\n1.1.23 \u2014 You're So Vain\n-----------------------\n\n\u2022 Add a \"piUIDs\" field to Biomarker objects and set it on ingest so that\n vanity pages can quickly find Biomarkers studied by a PI.\n\n\n1.1.22 \u2014 Some Day We'll Get This Right\n--------------------------------------\n\n\u2022 CA-1454: Biomarker ingest should use the organs specified in the RDF to\n associate a biomarker with a collaborative group, not the security access\n group\n\n\n1.1.21 \u2014 By Any Other Name\n--------------------------\n\n\u2022 CA-1348: Summary source URLs should be marked as required\n\u2022 CA-1388: Pull external resource links from CancerDataExpo\n\u2022 CA-1440: Biomarker ingest should accept \"GI and Other Associated\" as well as\n \"G.I. and Other Associated\"\n\n\n1.1.20 \u2014\u00a0Protection\n-------------------\n\n\u2022 CA-1349: Summary ingest should be robust in the face of failures\n\n\n1.1.19 \u2014 Visuals\n----------------\n\n\u2022 CA-1322\n\u2022 CA-1338: Fix tests for eke.biomarker\n\n\n1.1.18 \u2014 Biomuta\n----------------\n\n\u2022 Added External Resources through simply linking with HgncName. This is a \n temporary hack, will add knowledge objects for each external resource.\n\u2022 Added Biomuta tab to a Biomarker's elemental page and also removed biomuta \n link from \"basic\" tab. Biomuta tab was not added to Panel since Biomuta entries\n reference single biomarker entities. Biomuta stats are added as an attribute \n of a Biomarker since they are characteristics associated directly with the \n biomarker. CA-1321.\n\n\n1.1.17 \u2014 Bug Fixes\n------------------\n\n\u2022 CA-1300\n\u2022 CA-1303\n\n\n1.1.16 \u2014 Broken Links\n---------------------\n\n\u2022 This release addresses an RDF ingest issue where a biomarker-bodysystem object\n refers to a biomarker that doesn't exist.\n\n\n1.1.15 \u2014 I Had Some Chicken; Pass Me the FLOSS\n----------------------------------------------\n\n\u2022 First official release as free/libre/open source software.\n\n\n1.1.14 \u2014 Download URL\n---------------------\n\nThis release specifies a full path to the download URL for this package. This\nis necessary since JPL now blocks directory listings of our distribution server,\nand previously Python would use the directory listing to find the matching\nfile by version to download.\n\n\n1.1.13 \u2014 Certified HGNNNNNNNC!\n------------------------------\n\n\u2022 CA-1235 - Make biomarkers link ID end with HGNC name\n\u2022 CA-1238 - Add free text search to Biomarkers\n\u2022 CA-1247 - Link back to BioMuta from EDRN Portal's biomarkers\n\u2022 CA-1264 - Add Clinical Certification flags\n\n\n1.1.12 \u2014\u00a0Let's Not Talk\n-----------------------\n\n\u2022 CA-1229 - Discussion re-enabled after upgrade\n\n\n1.1.11 \u2014\u00a0Bio-TASTIC!\n--------------------\n\n\u2022 Adds the PIs-by-Biomarkers report plus a menu of (future) reports\n\u2022 CA-1206 - \"No resources\" appears on a biomarker\u2013body-system when there are\n no publications, not if there are no resources\n\u2022 CA-1205 - Sort resources alphabetically on elemental- and panel-based\n biomarkers\n\u2022 CA-1156 - Show more attributes for biomarkers that are \"mostly public\"\n\u2022 CA-1163 - Make RDF ingest defensive against bad protocols from BMDB\n\u2022 CA-1182 - Recognize \"Private\" QA State of Biomarker\n\u2022 CA-1184 - Biomarker \"report\" by Organ\n\u2022 CA-1189 - Enable left+right portlets on /biomarkers\n\u2022 Drops the obsolete \"Review Listing\" type\n\n\n1.1.10 \u2014 More Upgrades\n----------------------\n\n\u2022 Compatibility with Plone 4.3.\n\u2022 Uses z3c.autoinclude.\n\n\n1.1.9 \u2014 Get Him to the Greek\n----------------------------\n\n\u2022 CA-1100 Show \"N/A\" for Prevalence, NPV and PPV\n\n\n1.1.8 \u2014 Lies, Damn Lies, and Statistics\n---------------------------------------\n\n* Made compatible with Plone 4.2.4.\n* CA-1083 - eke.biomarker RDF ingest should treat predicate\n \"hasBiomarkerStudyDatas\" as a resource-pointing predicate\n* CA-1090 - For biomarkers, show a \"-\" or \"N/A\" or SOMETHING for prevalence,\n NPV, and PPV if they're zero or not given.\n\n\n1.1.7 \u2014 Upgrades\n----------------\n\n* Made compatible with Plone 4.1.5.\n* CA-1010 - Show blank if values are 0 or 0.0\n\n\n1.1.6 \u2014 Test Support\n--------------------\n\nThis release includes:\n\n* Depending on just Plone the framework instead of Plone the application.\n\n\n1.1.5 \u2014\u00a0Dataset Linkages\n------------------------\n\nThis release includes:\n\n* CA-784: Add ability to associate eCAS datasets with Biomarker records in the\n BMDB\n* (No issue ID): Dataset links should go directly into eCAS\n\n\n1.1.4 \u2014 Resiliency: the bread and butter of PvP\n-----------------------------------------------\n\nThis release makes functional tests more resilient.\n\n\n1.1.3 \u2014 Let's Collaborate!\n--------------------------\n\nThis release includes:\n\n* A plone.app.testing layer.\n* Support for edrnsite.collaborations\n* Re-attaches biomarkers that indicate their collaborative group back to the\n \"Collaborative Group\" (from edrnsite.collaborations) objects to which they\n \"belong\".\n\n\n1.1.2 \u2014 Upgrade Cleanup\n-----------------------\n\nThis release updates the GenericSetup profile to 4, provides upgrade steps to\nthat profile, and makes the testing and development harness depend on \"trunk\"\nlevel of other eggs instead of on released versions of those eggs.\n\n\n1.1.1 \u2014 Unique IDs\n------------------\n\nThis release replaces the unique ID generation method for \"Study Statistics\"\nobjects from the \"generateUniqueId\" method (acquired from who knows where\n(possibly CacheFu?)) to UUIDs, the generation of which is part of the standard\nlibrary.\n\n\n1.1.0 \u2014 Plone 4\n---------------\n\nThis release of eke.biomarker makes it compatible with Plone 4.\n\n\n1.0.2 \u2014 A Mixed Bag\n-------------------\n\nThe following issues were addressed in this release:\n\n* CA-620 - Locks appear on biomarkers listed under a protocol incorrectly\n (test exposure)\n* CA-698 - \"Structural\" objects appear in searches\n\n\n1.0.1 \u2014 Sweeping Views\n----------------------\n\nThis release adds a number of improvements to the biomarker views to\nreflect requests made by NCI that more specific details be captured in\neach annotated biomarker.\n\nThis release addresses the following issues:\n\n* CA-674 - Add PerformanceComment to the biomarker organ tab\n* CA-675 - Portal: Change name of sensitivity/specificity and add specific assay type attribute\n* CA-676 - Portal: Add decision rule attribute to biomarker-organ-study information\n\n\n1.0.0 \u2014 Prime Time\n------------------\n\nThis release addresses a number of issues \nthat make this component (and some of its\nselected counterparts) \"prime time\" for\nthe operational NCI portal. \n\nThis release addresses the following issues:\n\n* CA-528 Automatic periodic ingest of RDF\n\nYou can find the issue tracker at https://oodt.jpl.nasa.gov/jira/browse/CA\n\n\n0.0.6 \u2014 Open Door Policy\n------------------------\n\nFor this release, we're exposing more information about biomarkers. Instead\nof making unapproved biomarkers private and requiring a log in to view them,\nyou can now view basic information about them. Full details require a login.\nFor more information, see https://oodt.jpl.nasa.gov/jira/browse/CA-650.\n\n\n0.0.5 \u2014 Eleventh Hour\n---------------------\n\nThis release includes some look-and-feel changes, specifically to support\nhttps://oodt.jpl.nasa.gov/jira/browse/CA-600.\n\n\n0.0.4 \u2014 Padlocked!\n------------------\n\nThis release addresses the following issue:\n\n* https://oodt.jpl.nasa.gov/jira/browse/CA-551 - Add lock icon to biomarkers\n and science data that are \"secure\" to protocol pages\n\n\n0.0.3 \u2014 The unnamed release\n---------------------------\n\n* http://oodt.jpl.nasa.gov/jira/browse/CA-511 - Need to index alternative\n biomarker names\n\n\n0.0.2 \u2014 Various \"CYA\" Fixes\n---------------------------\n\n* http://oodt.jpl.nasa.gov/jira/browse/CA-499 - Disclaimer needed on\n biomarker list.\n* http://oodt.jpl.nasa.gov/jira/browse/CA-500 - Show unpublished\n biomarkers in a biomarker folder.\n* http://oodt.jpl.nasa.gov/jira/browse/CA-510 - Lock box for science data and\n biomarkers should disappear if a user has access to the object\n\n\n0.0.1 \u2014 Security Ingest\n-----------------------\n\nThe sole issue addressed in this release is:\n\n* http://oodt.jpl.nasa.gov/jira/browse/CA-475 - \"Public\" should only see\n biomarkers and science data that have QAState=Accepted. 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