(Apologies if this is addressed already)

Describe the bug
There is a problem with the ontology ns redirection.
https://www.opmw.org/ontology/executionStatus works, but
https://www.opmw.org/ontology/ does not work (404), and neither does
https://www.opmw.org/ontology

To Reproduce
N/A

Expected behavior
The redirection of the ontology should work. @sirspock where is the htaccess?

Suggestion from @varunratnakar

Describe the bug

Wings tried to obtain the individual, and it does not exist https://www.opmw.org/export/resource/DataVariable/ClimComp_Precipi-5dc4dde3-c4c9-478e-9207-d072b63bc25e_v1_weather

Individual concreteTemplateVariable = concreteTemplateExport.getOpmwModel().getIndividual(concreteTemplateVariableURI);

Execution does not exist! Publishing new execution
Execution expanded template http://localhost:8080/export/users/mint/MINT-production/executions/ClimComp_Precipi-5dc4dde3-c4c9-478e-9207-d072b63bc25e.owl# loaded successfully
WINGS Template hash: 12bc10fd707baeac3e6d68c3aee34e10
Template ClimComp_Precipi-5dc4dde3-c4c9-478e-9207-d072b63bc25e has already been published as https://www.opmw.org/export/resource/WorkflowTemplate/ClimComp_Precipi-5dc4dde3-c4c9-478e-9207-d072b63bc25e_v1
https://www.opmw.org/export/resource/WorkflowTemplate/ClimComp_Precipi-5dc4dde3-c4c9-478e-9207-d072b63bc25e_v1
java.lang.NullPointerException
        at org.apache.jena.rdf.model.impl.ModelCom.add(ModelCom.java:1202)
        at org.apache.jena.rdf.model.impl.ResourceImpl.addProperty(ResourceImpl.java:299)
        at edu.isi.wings.opmm.WorkflowExecutionExport.convertExecutionToOPMW(WorkflowExecutionExport.java:262)

To Reproduce
Steps to reproduce the behavior:

1. Export any cycles execution of mint production domain

No, this one we need to add the right redirect. We need to discuss a
methodology. And the pending conversation is the link back to
ontosoft/model catalog.

El mié., 27 feb. 2019 12:16 p. m., Maximiliano Osorio <
[email protected]> escribió:

Assigned #9
#9
to @dgarijo https://github.com/dgarijo.

—
You are receiving this because you were assigned.
Reply to this email directly, view it on GitHub
#9 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/ABc0GtioyiHJfuCidPKdntIxP79udxspks5vRuemgaJpZM4bVXc3
.

Originally posted by @dgarijo in #9 (comment)

Right now we have 2, one for expanded templates and one for templates. Since they are both templates, it should be possible to conflate it into one function

Describe the bug
Prefixes are super confusing

To Reproduce
N/A

Expected behavior
https://www.opmw.org/ontology/WorkflowTemplateProcess should be opmw:WorkflowTemplateProcess.

wings:export/MINT-production/Component#cycles_v2Class_V1 should be mint:cycles_v2Class_V1

etc.

Is your feature request related to a problem? Please describe.
The source used for a component (i.e., the model catalog URI of the model config) is not exported. It should.

Describe the solution you'd like
That when I export an activity of a component, in the software configuration associated to it we can find the source (model catalog URI)

In another graph. This will facilitate querying

For example:

     @prefix j.3:   <http://www.opmw.org/ontology/> .
<http://www.opmw.org/export/resource/WorkflowExecutionArtifact/Caesar_Cypher-1f-f788bcd8-75d9-4996-974d-ef6a442a36da_EncryptedDocument>
        a                   j.3:WorkflowExecutionArtifact ;

Thus, the type of resource is:
http://www.opmw.org/ontology/WorkflowExecutionArtifact
However, http://www.opmw.org/model/OPMW/WorkflowExecutionArtifact doesn't exist.

http://www.opmw.org/model/OPMW#WorkflowExecutionArtifact exist.

Do you except replace / to # or is an error?

I would like the label to reflect the date when it was created, on a readable manner.
Right now they say something like : Execution account created on 1461051226867.
Instead, it should be something like: Execution of template on 7/16/2017:2:37PM PT

Otherwise you cannot invoke the mapper object twice

Using LODI to browse the things in the endpoint

Describe the bug

The code generates many null exceptions

        if(rs.hasNext()){
            //variables to extract: ?doc ?contrib ?time ?license
            QuerySolution qs = rs.next();
            try{
                Literal docContent = qs.getLiteral("?doc");
                wtInstance.addLiteral(opmwModel.createProperty(Constants.OPMW_DATA_PROP_HAS_DOCUMENTATION), docContent);
            }catch(Exception e){}
            try{
                Literal contrib = qs.getLiteral("?contrib");
                OntClass agentClass = opmwModel.createClass(Constants.OPM_AGENT);
                Individual contributor = agentClass.createIndividual(Constants.PREFIX_EXPORT_RESOURCE+
                        Constants.CONCEPT_AGENT+"/"+URLEncoder.encode(""+contrib, "UTF-8"));
                contributor.addLabel(contrib);
                wtInstance.addProperty(opmwModel.createProperty(Constants.PROP_HAS_CONTRIBUTOR), contributor);
            }catch(Exception e){}
            try{
                Literal timeLastModified = qs.getLiteral("?time");
                wtInstance.addLiteral(opmwModel.createProperty(Constants.DATA_PROP_MODIFIED), timeLastModified);
            }catch(Exception e){}
            try{
                Literal userVersion = qs.getLiteral("?version");
                wtInstance.addLiteral(opmwModel.createProperty(Constants.OPMW_DATA_PROP_RELEASE_VERSION), userVersion);
            }catch(Exception e){}
            try{
                Literal license = qs.getLiteral("?license");
                wtInstance.addLiteral(opmwModel.createProperty(Constants.DATA_PROP_RIGHTS), license);
            }catch(Exception e){//no license declared, add license by default
                opmwModel.add(wtInstance,opmwModel.createProperty(Constants.DC_LICENSE),"http://creativecommons.org/licenses/by/3.0/",
                        XSDDatatype.XSDanyURI);
            }
        }

To Reproduce
Steps to reproduce the behavior:

1. Export a execution

Expected behavior
Check if the literals are null

Describe the bug
https://w3id.org/wings/export/MINT-production/resource/CanonicalInstance/cycles_v2_V1 leads to a 404. It should be redirected to where the file is published. But I don't know where is it published yet! This is the "domain" file @sirspock. Is it published anywhere?

To Reproduce
N/A

Expected behavior
https://w3id.org/wings/export/MINT-production/resource/CanonicalInstance/cycles_v2_V1 should redirect to the canonical instance file

Is your feature request related to a problem? Please describe.
Test must be start clean

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Is this URI correct? Is it deprecated?
https://w3id.org/wings/export/CaesarCypher/extension#uses_as_Param1key

Describe the bug
The domain for https://www.opmw.org/export/resource/WorkflowTemplate/cycles_v2_standa-a1eac1b5-3eb5-4d86-9fe5-f13b28e0f9e1_v1 should not be cycles_v2_standa-a1eac1b5-3eb5-4d86-9fe5-f13b28e0f9e1.owl#

To Reproduce
Go to https://www.opmw.org/export/resource/WorkflowTemplate/cycles_v2_standa-a1eac1b5-3eb5-4d86-9fe5-f13b28e0f9e1_v1 and check property hasDomain

Expected behavior
The domain should be "mint". There is a wrong assumption on where to extract it from the URL of the template. It should be a parameter.

Is your feature request related to a problem? Please describe.

      Mapper.main(domain, exportPrefix, exportUrl, catalogRepositoryDirectory, componentLibraryFilePath, planFilePath,
          endpointQueryURI, endpointPostURI, executionFilePath, expandedTemplateFilePath, abstractFilePath,
          filePublisher, serialization);

The following parameters can be group in the TriplesPublisher

• endpointQueryURI
• endpointPostURI
• exportUrl
• exportPrefix
• serialization

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Is your feature request related to a problem? Please describe.
Metadata fields used for data in executions are not exported in the provenance export. This means that any custom metadata added in a file, such as the data catalog dataset id, will not not be exported.

Describe the solution you'd like
I would like the custom metadata to be exported.

Describe the bug
When the template exported is concrete, the abstract template does not seem to be exported correctly.

To Reproduce
See https://www.opmw.org/export/resource/WorkflowTemplate/ClimComp_Precipitation_v1

Expected behavior
There should be a template in the above URL. Instead there is nothing.

Is your feature request related to a problem? Please describe.
Export the Documentation of the component

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context

That way files would not have to be uploaded separately

Describe the bug

If the WorkflowExecution is published, then WorkflowExpandedTemplate fails.

To Reproduce
Steps to reproduce the behavior:

1. Run the tests twice

• The config has a node blank
  https://www.opmw.org/page/export/resource/SoftwareConfiguration/SingleProteomicS-7eca5052-f1de-4ef5-a0b8-b383fa805293_myrimatchNode_config

• The ontology does not have information about the property https://www.opmw.org/model/OPMW/#hasMainScript

Describe the bug
See https://www.opmw.org/page/export/resource/WorkflowExecutionArtifact/ClimComp_Precipi-90455b3a-0079-4a54-a444-a39fd1959e2b_weather

To Reproduce
Go to https://www.opmw.org/page/export/resource/WorkflowExecutionArtifact/ClimComp_Precipi-90455b3a-0079-4a54-a444-a39fd1959e2b_weather and check the hasLocation property

Expected behavior
Should have a path to the uploader URL, or the WINGS URL if the file is too big (server, not local path)

Example: opmw:hasNativeSystemTemplate
http://localhost:8080/export/users/mosorio/MINT-production/executions/ClimComp_Precipi-894eb652-60be-497e-974a-d64c5ffdad86.owl#ClimComp_Precipi-894eb652-60be-497e-974a-d64c5ffdad86

After talking with @sirspock, we have agreed that these local links should be uploaded as well, as the user could delete them in the future.

Describe the bug
https://w3id.org/wings/export/MINT-production/Component#cycles_v2Class_V1 leads to a 404. It should be redirected to where the file is published. But I don't know where is it published yet! This is the "domain" file @sirspock. Is it published anywhere?

To Reproduce
N/A

Expected behavior
https://w3id.org/wings/export/MINT-production/Component#cycles_v2Class_V1 should redirect to the description file

The export RDF explorer has multiple locations.
Maybe, the hashing is the problem

In http://www.opmw.org/page/export/resource/WorkflowTemplate/ClimComp_Precipi-894eb652-60be-497e-974a-d64c5ffdad86_v1
It says
opmw:hasDomain ClimComp_Precipi-894eb652-60be-497e-974a-d64c5ffdad86.owl#
Which is not correct. The domain probably is "MINT-Production".

Check whether this is an error in the mapper code or when doing the merging in WINGS.