User:Andreas Plank/Import issues with CETAF identifiers

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Screenshot of the Firefox RESTED plugin (steps to retrieve an RDF data source)

Note: Unresolved or pending issues are on top and issues that are done get to the end. To check for RDF in your browser you can (1) use the CETAF Specimen URI Tester (http://herbal.rbge.info) or use a plugin in your browser, e.g. RESTED Client and then adding Header Accept: application/rdf+xml (see example aside)

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coldb.mnhn.fr (MNHN)

Pending unicode/XML issues:

• http://coldb.mnhn.fr/catalognumber/mnhn/f/dac98.2 see ? <dwc:municipality>Szirdokpisp?Ki</dwc:municipality>
rdfparse found: [line: …, col: 34] An invalid XML character (Unicode: 0x19) was found in the element content of the document
• http://coldb.mnhn.fr/catalognumber/mnhn/ic/1966-0058 see ? <dwc:occurrenceRemarks>LOC.: TRAPEANG-REPOU, ROUTE VEAL-RENG, KAMP?T</dwc:occurrenceRemarks>
rdfparse found: [line: …, col: 71] An invalid XML character (Unicode: 0x5) was found in the element content of the document.
• http://coldb.mnhn.fr/catalognumber/mnhn/ic/1986-0545 see ? <dwc:occurrenceRemarks>1986-545 A 547 DANS LE M?ME BOCAL</dwc:occurrenceRemarks>
rdfparse found: [line: …, col: 52] An invalid XML character (Unicode: 0x14) was found in the element content of the document
  AP: probably »DANS LE MÊME BOCAL«
• http://coldb.mnhn.fr/catalognumber/mnhn/ic/1963-0398 see ? <dwc:occurrenceRemarks>1963-398 A 400 DANS LE M?ME BOCAL</dwc:occurrenceRemarks>
rdfparse found: [line: …, col: 52] An invalid XML character (Unicode: 0x14) was found in the element content of the document
  AP: probably »DANS LE MÊME BOCAL«
• http://coldb.mnhn.fr/catalognumber/mnhn/ic/1980-1259 see ? <dwc:occurrenceRemarks>M?ME BOCAL QUE 1980-1260</dwc:occurrenceRemarks>
rdfparse found: [line: …, col: 29] An invalid XML character (Unicode: 0x14) was found in the element content of the document
  AP: probably »MÊME BOCAL QUE 1980-1260«
• http://coldb.mnhn.fr/catalognumber/mnhn/ic/1995-0897 see ? <dwc:occurrenceRemarks>don du northern territory museum extrait du n°13530-003. Proc. Biol. Soc. Wash. v. 109 (no. 2). B?ocal a cote de la 230-0-0-1.</dwc:occurrenceRemarks>
rdfparse found: [line: …, col: 125] An invalid XML character (Unicode: 0x16) was found in the element content of the document
• http://coldb.mnhn.fr/catalognumber/mnhn/ic/b-2510 see ? <dwc:occurrenceRemarks>PARALECTOTYPE DESIGNE PAR SPRINGER, 1962 IN COPEIA No 2? 2 : 4321 EX. EXTRAIT DE A.2024 / D.XII-23 , A.II-23 / VOIR SMITH. CONTR. TO ZOOL., No 73,</dwc:occurrenceRemarks>
rdfparse found: [line: …, col: 83] An invalid XML character (Unicode: 0x1b) was found in the element content of the document

Notes for a general work around during harvest/import: invalid unicode characters break rdfparse and subsequent import, so the harvested RDF must be fixed first manually at this point --Andreas Plank (talk) 12:33, 8 June 2020 (CEST)

data.rbge.org.uk (RBGE)

( Pending) the RDF embedded XML contains pure “&” which is not properly escaped in the XML realm (the propper escape is &). Many RDF files e.g. http://data.rbge.org.uk/herb/E00011206, seems a generic problem --Andreas Plank (talk) 16:33, 16 March 2020 (CET)

• it will be fixed during harvesting routine, but provided XML should be valid including escaped ampersand & --Andreas Plank (talk) 16:33, 16 March 2020 (CET)

data.nhm.ac.uk (NHM)

( Pending (minor issue does not block)) Requesting “Content-Type: application/rdf+xml” results in 404 (not found) instead of getting RDF (see https://github.com/NaturalHistoryMuseum/ckanext-nhm/issues/458) --Andreas Plank (talk) 14:06, 18 February 2020 (CET)

• minor issue not relevant because header “Content-Type: application/rdf+xml” is meant for the (returned) resource, not the request --Andreas Plank (talk) 10:40, 20 February 2020 (CET)

No or mixed up RDF description of CETAF-ID

See perhaps the example of CETAF Specimen Preview Profile (CSPP) in general.

id.luomus.fi (LUOMUS)

( Pending) The requested RDF does not describe the requested CETAF-ID http://id.luomus.fi/GL.749 itself, the ID “hangs somewhat in the air” (from a descriptive point of view):

1. http://id.luomus.fi/GL.749 gets redirected to http://id.luomus.fi/GL.749?format=RDFXML and
2. by analysing the RDF via Apache Jena’s rdfparse it reveals that it describes <http://id.luomus.fi/GL.749?format=RDFXML> <http://purl.org/dc/terms/subject> <http://id.luomus.fi/GL.749> just to be related, but
3. http://id.luomus.fi/GL.749 itself has no related description (rdf:Description) but there are two descriptions http://tun.fi/MY.275076 and http://tun.fi/MY.881682 which do not relate to http://id.luomus.fi/GL.749. So CETAF-ID http://id.luomus.fi/GL.749 “hangs somewhat in the air” because it is not described.

--Andreas Plank (talk) 12:10, 20 February 2020 (CET)

id.zfmk.de (ZFMK)

( Pending) The requested RDF does not describe the requested CETAF-ID http://id.zfmk.de/collection_ZFMK/1650/733377/90217 itself, the ID “hangs somewhat in the air” (from a descriptive point of view):

1. http://id.zfmk.de/collection_ZFMK/1650/733377/90217 gets redirected to https://id.zfmk.de/collection_ZFMK/rdf/xml/CollectionSpecimen/1650/733377/90217/?shorturl=1 and
2. by analysing the RDF via Apache Jena’s rdfparse it reveals that it describes something other: https://id.zfmk.de/collection_ZFMK/1650, but unrelated to the ID
3. http://id.zfmk.de/collection_ZFMK/1650/733377/90217 itself has no related description (rdf:Description) and “hangs somewhat in the air”
4. checking the website states a stable URL https://id.zfmk.de/collection_ZFMK/page/CollectionSpecimen/1650 but this very URL does not return any RDF

--Andreas Plank (talk) 12:29, 20 February 2020 (CET)

purl.org/nhmuio (NHMUO)

( Pending) The requested RDF does not describe the requested CETAF-ID http://purl.org/nhmuio/id/41d9cbb4-4590-4265-8079-ca44d46d27c3 itself, the ID “hangs somewhat in the air” (from a descriptive point of view):

1. http://purl.org/nhmuio/id/41d9cbb4-4590-4265-8079-ca44d46d27c3 gets redirected to https://data.gbif.no/resolver/O:L:14 and
2. by analysing the RDF via Apache Jena’s rdfparse it reveals that it describes something other: http://purl.org/gbifnorway/id/O:L:14, but unrelated to the ID
3. http://purl.org/nhmuio/id/41d9cbb4-4590-4265-8079-ca44d46d27c3 itself has no related description (rdf:Description) and “hangs somewhat in the air”

--Andreas Plank (talk) 13:30, 20 February 2020 (CET)

No RDF but HTML

col.smns-bw.org (SMNS)

( Pending) Requested RDF is instead an HTML fragment but RDF.--Andreas Plank (talk) 14:38, 18 February 2020 (CET)

For instance under Linux:

wget --header='Accept: application/rdf+xml'  --content-on-error --output-document="col.smns-bw.org⁄object⁄S10000227722006.rdf" "http://col.smns-bw.org/object/S10000227722006"
file col.smns-bw.org⁄object⁄S10000227722006.rdf
# col.smns-bw.org⁄object⁄S10000227722006.rdf: HTML document, ISO-8859 text, with very long lines, with CRLF line terminators

specimens.kew.org (RBGK)

( Pending) Requested RDF is instead HTML but RDF --Andreas Plank (talk) 14:32, 18 February 2020 (CET)

For instance under Linux:

wget --header='Accept: application/rdf+xml'  --content-on-error --output-document="specimens.kew.org⁄herbarium⁄K001116483.rdf" "http://specimens.kew.org/herbarium/K001116483"
file specimens.kew.org⁄herbarium⁄K001116483.rdf 
# specimens.kew.org⁄herbarium⁄K001116483.rdf: HTML document, ASCII text, with very long lines, with CRLF, LF line terminators

Fixed Issues

herbarium.bgbm.org (BGBM)

( Done) In some RDF files are invalid URI entries i.e. there is a tab/space character in the URI in owl:sameAs and this would break the whole import of data. The error log of triple store loader (tdbloader2) shows something like:

Bad URI: < http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/a86596ea-6f4d-4b97-bf6f-8d492c0fc8b2> Code: 0/ILLEGAL_CHARACTER in SCHEME: The character violates the grammar rules for URIs/IRIs. ERROR Bad character in IRI (space): <[space]...>

… see for instance in line 63:

62 <rdf:Description rdf:about="http://www.wikidata.org/entity/Q6382619">
63                     <owl:sameAs rdf:resource="	http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/a86596ea-6f4d-4b97-bf6f-8d492c0fc8b2" />
64                 <owl:sameAs rdf:resource="http://viaf.org/viaf/233473288" />
65           </rdf:Description>

The following objects were detected:

• http://herbarium.bgbm.org/data/rdf/B100000580 --Andreas Plank (talk) 16:21, 30 January 2020 (CET)  Done --Andreas Plank (talk) 11:45, 3 February 2020 (CET)
• http://herbarium.bgbm.org/data/rdf/B100000503 --Andreas Plank (talk) 16:21, 30 January 2020 (CET)  Done --Andreas Plank (talk) 11:45, 3 February 2020 (CET)
• http://herbarium.bgbm.org/data/rdf/B100000627 --Andreas Plank (talk) 16:21, 30 January 2020 (CET)  Done --Andreas Plank (talk) 11:45, 3 February 2020 (CET)