EDRN RDF Server
Project description
Server for the Early Detection Research Network (EDRN) that provides descriptions of EDRN’s knowledge using the Resource Description Format (RDF).
edrn.rdf Installation
Use zc.buildout and the plone.recipe.zope2instance recipe to manage your project, and do the following:
Add edrn.rdf to the list of eggs to install, e.g.:
[buildout] ... eggs = ... edrn.rdfRe-run buildout, e.g. with:
$ ./bin/buildout
You don’t need a ZCML slug because it uses z3c.autoinclude.plugin with the Plone target.
Changelog
What follows is a log of changes from release to release. Where issue identifiers appear, you can find more about them by visiting this project’s issue tracker at https://oodt.jpl.nasa.gov/jira/browse/CA.
1.3.7 — LabCAS
This release provides an RDF format of LabCAS data from Solr
1.3.6 — Involved Logs
CA-1492 - Involved investigator sites not appearing on protocols
Fixed biomuta default data source to point to new location.
CA-1525: RDF Server needs to provide current employment status on person feed
CA-1526: Provide site ID in publications RDF
CA-1547: Have EDRN RDF server log unused slots
1.3.5 — Upgrades
Added an upgrade step to enable Biomuta RDF ingestion.
1.3.4 — Biomuta
Added Biomuta RDF ingestion system and source.
1.3.3 — Predicates and Packaging
Fix predicate URIs for EDRN title and account name.
Obey PyPI’s new restrictions on package hosting, PEP-470.
Added Biomuta RDF generator and source.
Upgrade for Travis-CI container & caching mechanisms.
1.3.2 — Ontology 1.8
This release sets up additional predicate handlers and is compatible with the SOAP Ontology API 1.8.
1.3.1 — I Had Some Chicken; Pass the FLOSS
This package is now free, open source software under the Apache License v2.
1.3.0 — Texas-Sized
Compatible with RDFLib 4.0.1
Compatible with Plone 4.3.2
Compatible with zc.buildout 2.2.1
Compatible with EDRN Ontology 1.8
Compatible with DMCC Web Services (test tier) as of 20140401
1.2.3 — Protocols Without Publications
The DMCC’s SOAP service always lists a slot for publications even when a protocol has no publications. But in RDF, we don’t want make any statement about publications when there aren’t any. This release addresses that.
1.2.2 — Upgrades
This release addresses the following:
Compatible with RDFLib 3.2.3
Compatible with Plone 4.2.2
1.2.1 — Links
This release addresses the following:
CA-1031 - New RDF server fails to link protocols correctly
1.2.0 — Webbed
This release drops the SQL Server access and uses the DMCC’s SOAP services instead.
1.1.3 — Ahoy Skipper
This release updates the tunnel to contact the DMCC’s SQL Server database on its new home, skipper.fhcrc.org.
CA-957 - DMCC SQL Server for dbEKE password is no longer valid
1.1.2 — Release Early, Release Often
This release fixes the default password for the EKE database. (We should really just make this a parameter on a control panel, except we’re supposed to switch over to the ws_newcompass webservice anyway.)
1.1.1 — Default Database Deliberation
This release uses the database on localhost by default, since that’s the point of combining the RDF server with the tunneled backend deployment.
1.1.0 — Upgrade Containerize
This release makes edrn.rdf compatible with:
Zope 2.13
Plone 4.1
plone.testing 4.0.2
It also prepares the RDF server for decommissioning on ginger.fhcrc.org and relocating at the EDRN Informatics Center.
1.0.0 - Committees
The following are addressed in this release:
Physical, mailing, and shipping addresses are no longer provided for each EDRN site. The DMCC removed all of them from the EKE database. However, they did add a single address to registered people. As a result, this release drops addresses from sites and adds them to people.
Committees. RDF feeds for the list of committees, their types, and their members are now available.
0.0.10 - PyMSSQL Lockdown
This package depends on the Python Microsoft SQL Server library known as “pymssql”, but never specified a version of the library to use. The latest version available was just fine for quite some time.
Until today.
Today, pymssql 1.9.905.1 was suddenly available, and it doesn’t build. So, we’re locking ourselves down to pymssql version 1.0.2, which does build and works just fine for what we need.
0.0.9 - Account Names
The DMCC now provides user account names for registered people. This release supports that by providing a place to specify the URI to the RDF predicate, and the RDF export uses that URI to state the account names of people who have accounts.
0.0.8 - Official EKE Database
This release updates the database server changing it from pongo to compass1. The new server, compass1, hosts the official RDF source information and contains no funky testing data like “Greg’s Cool Protocol”.
0.0.7 - Protocol Types and Eligibility Criteria
Greg Warnick has added additional data to the DMCC RDF database, comprising the two following new slots:
Elibility_critera describing eligibility criteria of a protocol
Protocol_type, what we thought was once long lost, is back!
This release of the RDF Server provides these two additional fields. Additionally, it updates its test data and function test battery.
0.0.6 - Investigators and Staff Strike Back
The “Site” view within the DMCC RDF database has gotten tons of action recently. It’s changed as follows:
Site_Specialty_Description is now called Site_Program_Description
New field: IDs_for_Investigators
New field: IDs_for_CoInvestigators
New field: IDs_for_CoPrincipalInvestigator
In addition, the Registered_Person view gained four new fields:
Fax
Specialty
Photo
EDRN_Title
Therefore, this release of the EDRN RDF Server accommodates these updates. In addition, it also updates its battery of tests and test data.
0.0.5 - Investigators and Staff
The “Site” view within the DMCC RDF database now provides primary investigators, co-investigators, and other staff members at each site. This release updates the Site RDF generation to include such details.
0.0.4 - Database Correction
Release 0.0.3 got away with a test database setting still set. This release corrects that and uses the correct source of RDF data.
0.0.3 - Registered People
This release of EDRN RDF Server provides a new data source: registered people. Registered people are people known to EDRN. This data source provides RDF descriptions of EDRN people. In addition, it also fixes the following issues:
CA-296: Site-Specific URI Prefix missing on Protocol control panel. Added it in r4905.
CA-285: Numeric fields of research replaced with actual names; r4906.
CA-264: Export registered people; r4907.
In addition, we’ve reduced the amount of test data and made the unit tests run a lot faster.
0.0.2 - New DB Structure
This release of the EDRN RDF Server accommodates the new DMCC database structure, particularly for diseases and protocols. Specifically, it addresses these issues:
CA-252: http://ginger.fhcrc.org/dmcc/rdf-data/diseases/rdf produces error
CA-253: http://ginger.fhcrc.org/dmcc/rdf-data/protocols/rdf produces error
In addition, it updates the functional tests’ test database.
0.0.1 - Protocols
This release of the EDRN RDF Server includes implementation of RDF service for EDRN Protocols and Studies as tracked by the Data Management and Coordinating Center (DMCC).
In addition, this release contains:
Fixes to the layout of control panel pages for Body Systems, Diseases, Publications, and Site RDF sources.
Addition of a download URL to the PyPI package data.
Updates to the functional tests’ test database.
0.0.0 - Unreleased
Initial release
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