Metadata from JWS archives is not read

[matthiaskoenig]

I added an example of the JWS archives to the tests
#21

Currently, the metadata from this archives cannot be read with libCombine which gives

********************************************************************************
Print archive: testdata/zhao2013_fig3a-user.sedx
********************************************************************************
  no metadata for '.'
Num Entries: 3
 0: location: metadata.rdf format: http://identifiers.org/combine.specifications/omex-metadata
  no metadata for 'metadata.rdf'
 1: location: sedml/zhao2013_fig3a-user.sedml format: http://identifiers.org/combine.specifications/sed-ml.level-1.version-3
  no metadata for 'sedml/zhao2013_fig3a-user.sedml'
 2: location: models/zhao1.sbml format: http://identifiers.org/combine.specifications/sbml.level-3.version-1
  no metadata for 'models/zhao1.sbml'

Despite metadata in the metadata.rdf (see below listed).
This could be related to #18, i.e. that you only check for metadata.xml and not for metadata.rdf other tools use to write the metadata.

metadata.rdf:

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:vCard="http://www.w3.org/2006/vcard/ns#"><rdf:Description rdf:about="."><dcterms:description>Build by JWS Online.</dcterms:description><dcterms:created><dcterms:W3CDTF>2017-07-11T09:20:34Z</dcterms:W3CDTF></dcterms:created></rdf:Description><rdf:Description rdf:about="sedml/zhao2013_fig3a-user.sedml"><dcterms:description>Exported by JWS Online from:
https://jjj.bio.vu.nl/models/experiments/zhao2013_fig3a-user/</dcterms:description><dcterms:created><dcterms:W3CDTF>2017-07-11T09:20:34Z</dcterms:W3CDTF></dcterms:created></rdf:Description><rdf:Description rdf:about="sedml/zhao2013_fig3a-user.sedml"><dcterms:description>Mathematical insights in evaluating state dependent effectiveness of HIV prevention interventions.
  Bull. Math. Biol. 2013; 75 (4): 649-675

PubMed ID: 23435680
DOI: 10.1007/s11538-013-9824-7
PubMed Central: 4642742
ISSN: 1522-9602

Abstract
--------
Mathematical models have been used to simulate HIV transmission and to study the use of preexposure prophylaxis (PrEP) for HIV prevention. Often a single intervention outcome over 10 years has been used to evaluate the effectiveness of PrEP interventions. However, different metrics express a wide variation over time and often disagree in their forecast on the success of the intervention. We develop a deterministic mathematical model of HIV transmission and use it to evaluate the public-health impact of oral PrEP interventions. We study PrEP effectiveness with respect to different evaluation methods and analyze its dynamics over time. We compare four traditional indicators, based on cumulative number or fractions of infections prevented, on reduction in HIV prevalence or incidence and propose two additional methods, which estimate the burden of the epidemic to the public-health system. We investigate the short and long term behavior of these indicators and the effects of key parameters on the expected benefits from PrEP use. Our findings suggest that public-health officials considering adopting PrEP in HIV prevention programs can make better informed decisions by employing a set of complementing quantitative metrics.</dcterms:description><dcterms:created><dcterms:W3CDTF>2013-01-01T00:00:00Z</dcterms:W3CDTF></dcterms:created><dcterms:creator rdf:parseType="Resource"><vCard:hasName rdf:parseType="Resource"><vCard:family-name>Kuang</vCard:family-name><vCard:given-name>Yang</vCard:given-name></vCard:hasName></dcterms:creator></rdf:Description><rdf:Description rdf:about="models/zhao1.sbml"><dcterms:description>Exported by JWS Online from:
https://jjj.bio.vu.nl/models/zhao1/</dcterms:description><dcterms:created><dcterms:W3CDTF>2017-07-11T09:20:34Z</dcterms:W3CDTF></dcterms:created></rdf:Description><rdf:Description rdf:about="models/zhao1.sbml"><dcterms:description>Mathematical insights in evaluating state dependent effectiveness of HIV prevention interventions.
  Bull. Math. Biol. 2013; 75 (4): 649-675

PubMed ID: 23435680
DOI: 10.1007/s11538-013-9824-7
PubMed Central: 4642742
ISSN: 1522-9602

Abstract
--------
Mathematical models have been used to simulate HIV transmission and to study the use of preexposure prophylaxis (PrEP) for HIV prevention. Often a single intervention outcome over 10 years has been used to evaluate the effectiveness of PrEP interventions. However, different metrics express a wide variation over time and often disagree in their forecast on the success of the intervention. We develop a deterministic mathematical model of HIV transmission and use it to evaluate the public-health impact of oral PrEP interventions. We study PrEP effectiveness with respect to different evaluation methods and analyze its dynamics over time. We compare four traditional indicators, based on cumulative number or fractions of infections prevented, on reduction in HIV prevalence or incidence and propose two additional methods, which estimate the burden of the epidemic to the public-health system. We investigate the short and long term behavior of these indicators and the effects of key parameters on the expected benefits from PrEP use. Our findings suggest that public-health officials considering adopting PrEP in HIV prevention programs can make better informed decisions by employing a set of complementing quantitative metrics.</dcterms:description><dcterms:created><dcterms:W3CDTF>2013-01-01T00:00:00Z</dcterms:W3CDTF></dcterms:created><dcterms:creator rdf:parseType="Resource"><vCard:hasName rdf:parseType="Resource"><vCard:family-name>Kuang</vCard:family-name><vCard:given-name>Yang</vCard:given-name></vCard:hasName></dcterms:creator></rdf:Description></rdf:RDF>

[fbergmann]

Indeed, the library so far only reads meta data information precisely as given in the specification. For several reasons this fails for the file given in the archive. The main reason, since it does not have an xml declaration, the stream is invalid and rejected. But even if i were to allow for it, then we would still have the problem, that each entry has 2 metadata segments. And in that case you get only one of them:

<rdf:Description rdf:about="sedml/zhao2013_fig3a-user.sedml"><dcterms:description>Exported by JWS Online from:
https://jjj.bio.vu.nl/models/experiments/zhao2013_fig3a-user/</dcterms:description><dcterms:created><dcterms:W3CDTF>2017-07-11T09:20:34Z</dcterms:W3CDTF></dcterms:created></rdf:Description>
<rdf:Description rdf:about="sedml/zhao2013_fig3a-user.sedml"><dcterms:description>Mathematical insights in evaluating state dependent effectiveness of HIV prevention interventions.
  Bull. Math. Biol. 2013; 75 (4): 649-675

PubMed ID: 23435680
DOI: 10.1007/s11538-013-9824-7
PubMed Central: 4642742
ISSN: 1522-9602

Abstract
--------
Mathematical models have been used to simulate HIV transmission and to study the use of preexposure prophylaxis (PrEP) for HIV prevention. Often a single intervention outcome over 10 years has been used to evaluate the effectiveness of PrEP interventions. However, different metrics express a wide variation over time and often disagree in their forecast on the success of the intervention. We develop a deterministic mathematical model of HIV transmission and use it to evaluate the public-health impact of oral PrEP interventions. We study PrEP effectiveness with respect to different evaluation methods and analyze its dynamics over time. We compare four traditional indicators, based on cumulative number or fractions of infections prevented, on reduction in HIV prevalence or incidence and propose two additional methods, which estimate the burden of the epidemic to the public-health system. We investigate the short and long term behavior of these indicators and the effects of key parameters on the expected benefits from PrEP use. Our findings suggest that public-health officials considering adopting PrEP in HIV prevention programs can make better informed decisions by employing a set of complementing quantitative metrics.</dcterms:description><dcterms:created><dcterms:W3CDTF>2013-01-01T00:00:00Z</dcterms:W3CDTF></dcterms:created><dcterms:creator rdf:parseType="Resource"><vCard:hasName rdf:parseType="Resource"><vCard:family-name>Kuang</vCard:family-name><vCard:given-name>Yang</vCard:given-name></vCard:hasName></dcterms:creator></rdf:Description>

instead of the other:

<rdf:Description rdf:about="sedml/zhao2013_fig3a-user.sedml"><dcterms:description>Exported by JWS Online from:
https://jjj.bio.vu.nl/models/experiments/zhao2013_fig3a-user/</dcterms:description><dcterms:created><dcterms:W3CDTF>2017-07-11T09:20:34Z</dcterms:W3CDTF></dcterms:created></rdf:Description>

Additionally i so far only consider descriptions as valid, that contain:

• a description
• and at least a non-empty creator

By the way, since I only have limited support for rdf metadata, you should be able to do any advanced processing on it yourself. You should be able to get the full metadata document using:

[matthiaskoenig]

I reported the issue to JWS. Is clearly a problem of their metadata.

You should be able to get the full metadata document using:

Something is missing here. How can I get the full metadata?

So for clarification: I could store additional things like for instance cvterms for entries inside of <rdf:Description rdf:about=".">, e.g., if I would store a chemical formula

<rdf:Description rdf:about="./images/formula1.png">
<bqbiol:is> 
         <rdf:Bag> 
           <rdf:li rdf:resource="#metaid_M_329_inchi"/> 
           <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI:24636"/> 
         </rdf:Bag> 
       </bqbiol:is>
...
</rdf:Description>

But I would have to parse such things myself. Is this correct?

[fbergmann]

correct. the omex description elements are very limited. But you could always just not use the description object that I provide and just upload your own rdf files and add them to the archive. Similarly you ought to be able to extract them as well. and parse them.