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Community Ontology Repository

esip-lab

cor's People

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graybealski ecoblockchain jonnydubowsky

cor's Issues

Handoff of GitHub repository to ESIPFed

make display names for SWEET ontology more useful

The different ontology component fragments in SWEET need more informative names. It is tricky to figure out which component to look at for a specific sub domain.

Notify ESIP management and Semantic Cluster at Initiation completion

Determine requirements for AWS instance

Working with TAMU and Technical Lead

Add Carlos and John to AWS instance alerts

Work with ESIP to enable access to a suitable AWS instance

update COR wiki on GitHub

Update the wiki content to reflect the current status of COR in ESIP.

Make modifications for ESIP branding

Add cron job to relaunch instance.

Carlos and Annie will touch bases on this.

Announce project initiated:

Announce to MMI site and other communities (EarthCube, OGC, RDA, ...)

Announce system available for testing

Announce to MMI community, others as desired

DC metadata not recognized when linking to ontology via URL

I'm registering SKOS vocabularies from the IUGS CGI; they all have dc metadata in the conceptScheme elements with dct title, date, creator, and description, and skos editorialNote and changeNote (e.g. http://resource.geosciml.org/vocabulary/cgi/2016/contacttype.rdf) , but these don't show up with the ontology metadata when I do the upload. Seems like at least the dc and dct elements should be recognized.

Initiate and troubleshoot installation

This task is to get the software running in its own AWS environment, without concern for ESIP or domain naming contexts. It should be fairly straightforward, if CentOS isn't an obstacle.

Set up automated operations monitoring of system

https access broken

I can't access COR on https://cor.esipfed.org, connection is refused.

Review the ORR instance deployment procedures to identify any concerns

Attend ESIP Summer Meeting

Provide status report

Transfer COR to new AWS AMI machine

The setup of the AWS machine itself is described at: https://github.com/ESIPFed/cor/wiki/COR-AWS-Setup

This ticket is about:

installation of the ORR software itself and all associated requirements (docker, apache...)
transfer of all the data from the previous/current AWS instance

Add ESIP badges to the readme

As I lack auth for a PR.

This will add a Testbed badge and a Semantic Web badge:

<a href="http://esipfed.org">![](http://badge.esipfed.org/testbed.svg?display=logo)</a> <a href="http://esipfed.org">![](http://badge.esipfed.org/semanticweb.svg?display=logo)</a>

Notify ESIP management and Semantic Cluster at Configuration completion

review notes from summer meeting for tickets

Review https://docs.google.com/document/d/1TwzZJ1aIlzl_Ss80ra-4YcBz6HrTR6b4Nkt9_IDcg9Q/edit to identify issues and ideas worth capturing here as tickets.

Keyword search throws error

try http://cor.esipfed.org/ont#/kw/lithology
After about 1 minute, returns:

[2018-07-24T15:06:26-07:00] An error occurred with request: GET http://cor.esipfed.org/sparql
Response from server:
 data: "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\">\n<html><head>\n<title>502 Proxy Error</title>\n</head><body>\n<h1>Proxy Error</h1>\n<p>The proxy server received an invalid\r\nresponse from an upstream server.<br />\r\nThe proxy server could not handle the request <em><a href=\"/sparql\">GET&nbsp;/sparql</a></em>.<p>\nReason: <strong>Error reading from remote server</strong></p></p>\n</body></html>\n"
 status: 502

seems like it should get some hits, e.g.
http://cor.esipfed.org/ont?iri=http://resource.geosciml.org/classifierscheme/cgi/2016.01/metamorphicgrade

Notify ESIP management and Semantic Cluster at Finalization completion

Make local customizations as necessary to run software

This task will make the software executable in the AWS and ESIP environments. It may involve some subtle changes to reflect the unique domain naming and redirection issues for the ESIP context. (Reference issue #5 for information about URLs, in particular.)

Problem registering vocab

http://resource.geosciml.org/vocabulary/cgi/2016/boreholedrillingmethod.rdf
When I try to register vocab at this URL, it doesn't load the content. Its a SKOS vocabulary, opens fine in Protege 5.0.0, and at http://vocabs.ga.gov.au/cgi/sissvoc/borehole-drilling-method/resource?uri=http://resource.geosciml.org/classifierscheme/cgi/2016.01/boreholedrillingmethod. Other GeoSciML vocabs have loaded fine. I can't figure out what the problem is.

when I try to update the metadata, an error throws:
"{
"error": "No graph writer for 'OWX'"
}"

Concept IRI doesn't resolve

http://cor.esipfed.org/ont?iri=http://resource.geosciml.org/classifier/cgi/descriptionpurpose/defining_norm returns an error:

{
  "msg": "resolveUri: error getting term",
  "error": "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\">\n<html><head>\n<title>502 Proxy Error</title>\n</head><body>\n<h1>Proxy Error</h1>\n<p>The proxy server received an invalid\r\nresponse from an upstream server.<br />\r\nThe proxy server could not handle the request <em><a href=\"/ont/api/v0/ont\">GET&nbsp;/ont/api/v0/ont</a></em>.<p>\nReason: <strong>Error reading from remote server</strong></p></p>\n</body></html>\n"
}

but
http://resource.geosciml.org/classifier/cgi/descriptionpurpose/defining_norm but defining_norm is a named individual in http://cor.esipfed.org/ont?iri=http://resource.geosciml.org/classifierscheme/cgi/2016.01/descriptionpurpose. Shouldn't it show up as a search result?

omv and omvm vocabularies should be registered in the repo

Why aren't dc and dct namespace used where appropriate? At least an omv/omvm to dc, dct, dcat mapping?

Announce System ready

Announce System ready: to ESIP Management and Semantic Web Cluster

Attend OGC Geosemantics Summit

Inform summit of ESIP deployment and evaluation planned

Notify ESIP management and Semantic Cluster at Project completion

Perform testing with multiple vocabularies

We want to install a few vocabularies, make sure the services are working and resolve terms correctly.

Cannot create requested ontology format

I tried manually uploading some RDF data and encountered the issue below. Is the following URI illegal?

file:/usr/local/ESIPDroneClusterSoftware/example/morning1.csvAirSpeed(m/s)

"org.mmisw.orr.ont.service.CannotCreateFormat: Map(uri -> http://cor.esipfed.org/ont/~lmcgibbn/morning1, version -> 20170412T000427, format -> rdf, error -> Cannot create requested ontology format: com.hp.hpl.jena.shared.InvalidPropertyURIException: file:/usr/local/ESIPDroneClusterSoftware/example/morning1.csvAirSpeed(m/s))\n\tat org.mmisw.orr.ont.service.OntService.getOntologyFile(OntService.scala:265)\n\tat org.mmisw.orr.ont.service.TripleStoreServiceAgRest.loadUriFromLocal(TripleStoreServiceAgRest.scala:109)\n\tat org.mmisw.orr.ont.app.OntController.org$mmisw$orr$ont$app$OntController$$loadOntologyInTripleStore(OntController.scala:634)\n\tat org.mmisw.orr.ont.app.OntController.org$mmisw$orr$ont$app$OntController$$createOntology(OntController.scala:399)\n\tat org.mmisw.orr.ont.app.OntController$$anonfun$7.apply(OntController.scala:123)\n\tat org.mmisw.orr.ont.app.OntController$$anonfun$7.apply(OntController.scala:99)\n\tat org.scalatra.ScalatraBase$class.org$scalatra$ScalatraBase$$liftAction(ScalatraBase.scala:270)\n\tat org.scalatra.ScalatraBase$$anonfun$invoke$1.apply(ScalatraBase.scala:265)\n\tat org.scalatra.ScalatraBase$$anonfun$invoke$1.apply(ScalatraBase.scala:265)\n\tat org.scalatra.ApiFormats$class.withRouteMultiParams(ApiFormats.scala:178)\n\tat org.mmisw.orr.ont.app.BaseController.withRouteMultiParams(BaseController.scala:11)\n\tat org.scalatra.ScalatraBase$class.invoke(ScalatraBase.scala:264)\n\tat org.mmisw.orr.ont.app.BaseController.org$scalatra$json$JsonSupport$$super$invoke(BaseController.scala:11)\n\tat org.scalatra.json.JsonSupport$$anonfun$invoke$1.apply(JsonSupport.scala:74)\n\tat org.scalatra.json.JsonSupport$$anonfun$invoke$1.apply(JsonSupport.scala:68)\n\tat org.scalatra.ApiFormats$class.withRouteMultiParams(ApiFormats.scala:178)\n\tat org.mmisw.orr.ont.app.BaseController.withRouteMultiParams(BaseController.scala:11)\n\tat org.scalatra.json.JsonSupport$class.invoke(JsonSupport.scala:68)\n\tat org.mmisw.orr.ont.app.BaseController.invoke(BaseController.scala:11)\n\tat org.scalatra.ScalatraBase$$anonfun$runRoutes$1$$anonfun$apply$8.apply(ScalatraBase.scala:240)\n\tat org.scalatra.ScalatraBase$$anonfun$runRoutes$1$$anonfun$apply$8.apply(ScalatraBase.scala:238)\n\tat scala.Option.flatMap(Option.scala:171)\n\tat org.scalatra.ScalatraBase$$anonfun$runRoutes$1.apply(ScalatraBase.scala:238)\n\tat org.scalatra.ScalatraBase$$anonfun$runRoutes$1.apply(ScalatraBase.scala:237)\n\tat scala.collection.immutable.Stream.flatMap(Stream.scala:493)\n\tat org.scalatra.ScalatraBase$class.runRoutes(ScalatraBase.scala:237)\n\tat org.scalatra.ScalatraServlet.runRoutes(ScalatraServlet.scala:49)\n\tat org.scalatra.ScalatraBase$class.runActions$1(ScalatraBase.scala:163)\n\tat org.scalatra.ScalatraBase$$anonfun$executeRoutes$1.apply$mcV$sp(ScalatraBase.scala:175)\n\tat org.scalatra.ScalatraBase$$anonfun$executeRoutes$1.apply(ScalatraBase.scala:175)\n\tat org.scalatra.ScalatraBase$$anonfun$executeRoutes$1.apply(ScalatraBase.scala:175)\n\tat org.scalatra.ScalatraBase$class.org$scalatra$ScalatraBase$$cradleHalt(ScalatraBase.scala:193)\n\tat org.scalatra.ScalatraBase$class.executeRoutes(ScalatraBase.scala:175)\n\tat org.scalatra.ScalatraServlet.executeRoutes(ScalatraServlet.scala:49)\n\tat org.scalatra.ScalatraBase$$anonfun$handle$1.apply$mcV$sp(ScalatraBase.scala:113)\n\tat org.scalatra.ScalatraBase$$anonfun$handle$1.apply(ScalatraBase.scala:113)\n\tat org.scalatra.ScalatraBase$$anonfun$handle$1.apply(ScalatraBase.scala:113)\n\tat scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)\n\tat org.scalatra.DynamicScope$class.withResponse(DynamicScope.scala:80)\n\tat org.scalatra.ScalatraServlet.withResponse(ScalatraServlet.scala:49)\n\tat org.scalatra.DynamicScope$$anonfun$withRequestResponse$1.apply(DynamicScope.scala:60)\n\tat scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)\n\tat org.scalatra.DynamicScope$class.withRequest(DynamicScope.scala:71)\n\tat org.scalatra.ScalatraServlet.withRequest(ScalatraServlet.scala:49)\n\tat org.scalatra.DynamicScope$class.withRequestResponse(DynamicScope.scala:59)\n\tat org.scalatra.ScalatraServlet.withRequestResponse(ScalatraServlet.scala:49)\n\tat org.scalatra.ScalatraBase$class.handle(ScalatraBase.scala:111)\n\tat org.scalatra.ScalatraServlet.org$scalatra$servlet$ServletBase$$super$handle(ScalatraServlet.scala:49)\n\tat org.scalatra.servlet.ServletBase$class.handle(ServletBase.scala:43)\n\tat org.mmisw.orr.ont.app.BaseController.org$scalatra$CorsSupport$$super$handle(BaseController.scala:11)\n\tat org.scalatra.CorsSupport$$anonfun$handle$1.apply$mcV$sp(CORSSupport.scala:202)\n\tat org.scalatra.CorsSupport$$anonfun$handle$1.apply(CORSSupport.scala:190)\n\tat org.scalatra.CorsSupport$$anonfun$handle$1.apply(CORSSupport.scala:190)\n\tat scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)\n\tat org.scalatra.DynamicScope$class.withResponse(DynamicScope.scala:80)\n\tat org.scalatra.ScalatraServlet.withResponse(ScalatraServlet.scala:49)\n\tat org.scalatra.DynamicScope$$anonfun$withRequestResponse$1.apply(DynamicScope.scala:60)\n\tat scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)\n\tat org.scalatra.DynamicScope$class.withRequest(DynamicScope.scala:71)\n\tat org.scalatra.ScalatraServlet.withRequest(ScalatraServlet.scala:49)\n\tat org.scalatra.DynamicScope$class.withRequestResponse(DynamicScope.scala:59)\n\tat org.scalatra.ScalatraServlet.withRequestResponse(ScalatraServlet.scala:49)\n\tat org.scalatra.CorsSupport$class.handle(CORSSupport.scala:188)\n\tat org.mmisw.orr.ont.app.OntController.org$scalatra$servlet$FileUploadSupport$$super$handle(OntController.scala:24)\n\tat org.scalatra.servlet.FileUploadSupport$class.handle(FileUploadSupport.scala:93)\n\tat org.mmisw.orr.ont.app.OntController.handle(OntController.scala:24)\n\tat org.scalatra.ScalatraServlet.service(ScalatraServlet.scala:54)\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:729)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:108)\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:522)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)\n\tat org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:349)\n\tat org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:1110)\n\tat org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)\n\tat org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:785)\n\tat org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1425)\n\tat org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\n\tat org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)\n\tat java.lang.Thread.run(Thread.java:745)\n"

Notify ESIP management and Semantic Cluster at Install/Test completion

add uptime monitoring/notification

Add a monitoring service (either StatusCake or Uptime Robot could work—I know about StatusCake a little) to keep track of when COR goes down, and sends email (and ideally text message) to interested parties. (List to be determined, but likely Annie and one or more of John, Carlos, and Lewis.)

NewRelic is another option but I think is too heavyweight.

The ideal solution would also generate an uptime report, though I predict it will very rarely add any value. But having that can help prove my claim that it 'never goes down'.

Create an ESIP fork of the appropriate mmisw code

Finalize an agreement on technical issues with ESIP

target URI paths, location of initial ESIP fork, etc

Create project description on ESIP web site

need better display for SKOS vocabulary

Since SKOS properties do not appear in the NamedIndividual descriptions in the LODE display; the properties of individuals should show up in the HTML representation. e.g. http://www.essepuntato.it/lode/owlapi/http://cor.esipfed.org/ont/api/v0/ont%3Firi=http://resource.geosciml.org/classifierscheme/cgi/2016.01/eventenvironment#d4e2185

Download ORR code to the instance to begin installation

complete the README.md

Need to add brief description of project, links to related sites, and purpose of this repository.

Install Google analytics for COR

Create a Google Analytics account that can be used for COR, and include the appropriate code in appropriate places on the site.

Initiation of Evaluation

With ESIP, begin defining evaluation goals and procedures for side-by-side comparison

Instantiate and configure the AWS instance

So the final answer (#6) is t2.medium with Amazon Linux for 1 year.

URI for omv and omvm vocabularies resolves to advertising site

goes to http://ibooked.no/onotoware.html, a Norwegian site about resorts in Greece. Bogus intro text says "The OntoWare Group provides organizational and legal support for a broad range of Semantic Web related software projects. " Looks like something has been hacked?

add Wiki

Need to add Wiki content as appropriate.

Configure ORR software for the ESIP Community Ontology Repository

This task is just to perform the basic configurations required for any new install of ORR. Getting the software running is addressed in task #12; ESIP-specific configurations and environment issues are in task #13; and branding issues are in task #14.

Issue Project Completion Report

Includes:

Resources Used
Issues,
lessons learned
“State of the Art” description on the ESIP Commons
a financial summary of expenses

SKOS rdf/xml upload error

using a remote URL:
http://resource.geosciml.org/vocabulary/cgi/2016/geneticcategory.rdf
http://resource.geosciml.org/vocabulary/cgi/2016/featureobservationmethod.rdf
http://resource.geosciml.org/vocabulary/cgi/2016/lineationtype.rdf

Get error message
"Cannot recognize ontology format
The given URL does not resolve to a recognized ontology format.", and can't continue with upload. All of these vocab files are generated by the same automated process, I'm stumped figuring out why these don't work.

They load fine from the URL using Protege 5.0.0

Create appropriate domain forwarding from ESIP to new system, and test

The principal goal here is to make sure an appropriate ESIP-level domain was where the site was hosted. As it stands, the site is at esipsw.org, which is a lovely domain name. Should ESIP decide they want it to be at, say, esip.org/cor, at least a few installation changes would have to be made and tested.

Upload new version of SWEET to COR

Hi @carueda it would be great if we could remove any previous versions of SWEET from the COR and for us to reference the development version of SWEET such that it is always up-to-date.
Can you deal with this?
Thank you in advance Carlos