Pull in refs fix from integration into rel/1.0.X

usnistgov · Jan 21, 2021 · c8e49dc · c8e49dc
2 parents 38066dc + fd13007
commit c8e49dc
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Showing 23 changed files with 732 additions and 508 deletions.
diff --git a/docker/jqfromsrc/Dockerfile b/docker/jqfromsrc/Dockerfile
@@ -7,7 +7,7 @@ RUN apt-get update && \
 WORKDIR /root
 RUN git clone http://github.com/stedolan/jq.git jq-dev && \
     cd jq-dev && \
-    git checkout 6306ac89667cf35f47ddc40aa0630546c57e387f && \
+    git checkout 80052e5275ae8c45b20411eecdd49c945a64a412 && \
     git submodule update --init && \
     autoreconf -fi && \
     ./configure --with-oniguruma=builtin && \

diff --git a/jq/pod2nerdm.jq b/jq/pod2nerdm.jq
@@ -21,19 +21,23 @@ include "urldecode";
 
 # the base NERDm JSON schema namespace
 #
-def nerdm_schema:  "https://data.nist.gov/od/dm/nerdm-schema/v0.3#";
+def nerdm_schema:  "https://data.nist.gov/od/dm/nerdm-schema/v0.4#";
 
-# the base NERDm JSON schema namespace
+# the NERDm pub schema extension namespace
+#
+def nerdm_pub_schema:  "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#";
+
+# the NERDm bib schema extension namespace
 #
-def nerdm_pub_schema:  "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#";
+def nerdm_bib_schema:  "https://data.nist.gov/od/dm/nerdm-schema/bib/v0.4#";
 
 # the NERDm context location
 #
 def nerdm_context: "https://data.nist.gov/od/dm/nerdm-pub-context.jsonld";
 
 # where the Datacite Document Reference types are defined
 #
-def dciteRefType: nerdm_schema + "/definitions/DCiteReference";
+def dciteRefType: nerdm_bib_schema + "/definitions/DCiteReference";
 
 # the resource identifier provided on the command line
 #
@@ -174,7 +178,7 @@ def ansc_coll_paths:
 def cvtref:  {
     "@type": ["deo:BibliographicReference"],
     "@id": ("#ref:" + (. | urlpath | sub("^/"; ""))),
-    "refType": "IsReferencedBy",
+    "refType": "IsSupplementTo",
     "location": .,
     "_extensionSchemas": [ dciteRefType ]
 };
@@ -230,7 +234,7 @@ def dist2download:
     .["filepath"] = ( .downloadURL | filepath ) |
     .["@type"] = [ "nrdp:DataFile", "nrdp:DownloadableFile", "dcat:Distribution" ] |
     .["@id"] = (. | componentID("cmps/")) |
-    .["_extensionSchemas"] = [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/DataFile" ] |
+    .["_extensionSchemas"] = [ nerdm_pub_schema + "/definitions/DataFile" ] |
     if .format then .format = { description: .format } else . end
 ;
 
@@ -244,7 +248,7 @@ def dist2checksum:
     .["filepath"] = ( .downloadURL | filepath ) |
     .["@type"] = [ "nrdp:ChecksumFile", "nrdp:DownloadableFile", "dcat:Distribution" ] |
     .["@id"] = (. | componentID("cmps/")) |
-    .["_extensionSchemas"] = [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/ChecksumFile" ] |
+    .["_extensionSchemas"] = [ nerdm_pub_schema + "/definitions/ChecksumFile" ] |
     .["mediaType"] = "text/plain" |
     .["algorithm"] = { "@type": "Thing", tag: (.filepath|extension) } |
     if .description then . else .["description"] = "SHA-256 checksum value for "+(.filepath|basename|remove_extension) end | 
@@ -284,7 +288,7 @@ def dist2inaccess:
 def dist2accesspage:
     .["@type"] = [ "nrdp:AccessPage", "dcat:Distribution" ] |
     .["@id"] = (. | componentID("#")) |
-    .["_extensionSchemas"] = [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/AccessPage" ] |
+    .["_extensionSchemas"] = [ nerdm_pub_schema + "/definitions/AccessPage" ] |
     if .format then .format = { description: .format } else . end
 ;
 

diff --git a/jq/tests/test_pod2nerdm.jqt b/jq/tests/test_pod2nerdm.jqt
@@ -10,14 +10,14 @@
 #
 include "pod2nerdm"; nerdm_schema
 null
-"https://data.nist.gov/od/dm/nerdm-schema/v0.3#"
+"https://data.nist.gov/od/dm/nerdm-schema/v0.4#"
 
 #--------------
 # testing nerdm_schema()
 #
 include "pod2nerdm"; nerdm_pub_schema
 null
-"https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#"
+"https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#"
 
 #--------------
 # testing nerdm_context()
@@ -31,7 +31,7 @@ null
 #
 include "pod2nerdm"; dciteRefType
 null
-"https://data.nist.gov/od/dm/nerdm-schema/v0.3#/definitions/DCiteReference"
+"https://data.nist.gov/od/dm/nerdm-schema/bib/v0.4#/definitions/DCiteReference"
 
 #--------------
 # testing resid()
@@ -91,7 +91,7 @@ include "pod2nerdm"; pdrLandingPageURL
 #
 include "pod2nerdm"; map(cvtref)
 [ "http://goob.net/doc1.txt", "https://goob.gov/doc2.txt" ]
-[{ "@type": ["deo:BibliographicReference"],"@id":"#ref:doc1.txt", "refType": "IsReferencedBy", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/v0.3#/definitions/DCiteReference" ], "location": "http://goob.net/doc1.txt"}, { "@type": ["deo:BibliographicReference"],"@id":"#ref:doc2.txt", "refType": "IsReferencedBy", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/v0.3#/definitions/DCiteReference" ], "location": "https://goob.gov/doc2.txt"}]
+[{ "@type": ["deo:BibliographicReference"],"@id":"#ref:doc1.txt", "refType": "IsSupplementTo", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/bib/v0.4#/definitions/DCiteReference" ], "location": "http://goob.net/doc1.txt"}, { "@type": ["deo:BibliographicReference"],"@id":"#ref:doc2.txt", "refType": "IsSupplementTo", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/bib/v0.4#/definitions/DCiteReference" ], "location": "https://goob.gov/doc2.txt"}]
 
 #---------------
 # testing filepath()
@@ -220,14 +220,14 @@ include "pod2nerdm"; map(componentID("#"))
 #
 include "pod2nerdm"; dist2download
 {"describedBy": "http://data.nist.gov/srd/srd_data/srd13_janaf-data-defs.json", "downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json", "mediaType": "application/json","title": "Titanium Boride" }
-{"describedBy": "http://data.nist.gov/srd/srd_data/srd13_janaf-data-defs.json", "downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json","mediaType": "application/json", "title": "Titanium Boride", "filepath":"srd13_B-101.json", "@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/srd13_B-101.json","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/DataFile"]}
+{"describedBy": "http://data.nist.gov/srd/srd_data/srd13_janaf-data-defs.json", "downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json","mediaType": "application/json", "title": "Titanium Boride", "filepath":"srd13_B-101.json", "@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/srd13_B-101.json","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/DataFile"]}
 
 #--------------
 # testing dist2checksum()
 #
 include "pod2nerdm"; dist2checksum
 {"downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json.sha256", "title": "Checksum for srd13_B-101.json" }
-{"downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json.sha256","mediaType": "text/plain", "description": "SHA-256 checksum value for srd13_B-101.json", "title": "Checksum for srd13_B-101.json", "filepath":"srd13_B-101.json.sha256", "algorithm": {"@type": "Thing","tag": "sha256"},"@type": ["nrdp:ChecksumFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/srd13_B-101.json.sha256","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/ChecksumFile"]}
+{"downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json.sha256","mediaType": "text/plain", "description": "SHA-256 checksum value for srd13_B-101.json", "title": "Checksum for srd13_B-101.json", "filepath":"srd13_B-101.json.sha256", "algorithm": {"@type": "Thing","tag": "sha256"},"@type": ["nrdp:ChecksumFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/srd13_B-101.json.sha256","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/ChecksumFile"]}
 
 #--------------
 # testing dist2hidden()
@@ -248,7 +248,7 @@ include "pod2nerdm"; dist2inaccess
 #
 include "pod2nerdm"; dist2accesspage
 {"accessURL": "https://doi.org/10.18434/T42C7D","title": "A Library to Enable the Modeling of Optical Imaging of Finite Multi-Line Arrays"}
-{"accessURL": "https://doi.org/10.18434/T42C7D","title": "A Library to Enable the Modeling of Optical Imaging of Finite Multi-Line Arrays","@type": [ "nrdp:AccessPage", "dcat:Distribution" ],"@id":"#10.18434/T42C7D","_extensionSchemas":["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/AccessPage"]}
+{"accessURL": "https://doi.org/10.18434/T42C7D","title": "A Library to Enable the Modeling of Optical Imaging of Finite Multi-Line Arrays","@type": [ "nrdp:AccessPage", "dcat:Distribution" ],"@id":"#10.18434/T42C7D","_extensionSchemas":["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/AccessPage"]}
 
 #--------------
 # testing dist2comp()
@@ -267,7 +267,7 @@ include "pod2nerdm"; dist2comp
 #
 include "pod2nerdm"; dist2comp
 {"describedBy": "http://data.nist.gov/srd/srd_data/srd13_janaf-data-defs.json", "downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json", "mediaType": "application/json","title": "Titanium Boride" }
-{"describedBy": "http://data.nist.gov/srd/srd_data/srd13_janaf-data-defs.json", "downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json","mediaType": "application/json", "title": "Titanium Boride", "filepath":"srd13_B-101.json", "@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/srd13_B-101.json","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/DataFile"]}
+{"describedBy": "http://data.nist.gov/srd/srd_data/srd13_janaf-data-defs.json", "downloadURL": "http://data.nist.gov/srd/srd_data/srd13_B-101.json","mediaType": "application/json", "title": "Titanium Boride", "filepath":"srd13_B-101.json", "@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/srd13_B-101.json","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/DataFile"]}
 
 #--------------
 # testing dist2comp()
@@ -277,7 +277,7 @@ include "pod2nerdm"; dist2comp
 #
 include "pod2nerdm"; dist2comp
 {"accessURL": "http://www.nsrl.nist.gov/Downloads.htm","conformsTo": "http://www.nsrl.nist.gov/Documents/Data-Formats-of-the-NSRL-Reference-Data-Set-16.pdf","downloadURL": "http://www.nsrl.nist.gov/RDS/rds_2.50/RDS_250.iso","format": "ISO 9660 disk image","mediaType": "application/zip" }
-{"accessURL": "http://www.nsrl.nist.gov/Downloads.htm","conformsTo": "http://www.nsrl.nist.gov/Documents/Data-Formats-of-the-NSRL-Reference-Data-Set-16.pdf","downloadURL": "http://www.nsrl.nist.gov/RDS/rds_2.50/RDS_250.iso","format": { "description": "ISO 9660 disk image"},"mediaType": "application/zip", "filepath":"RDS_250.iso", "@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/RDS_250.iso","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/DataFile"] }
+{"accessURL": "http://www.nsrl.nist.gov/Downloads.htm","conformsTo": "http://www.nsrl.nist.gov/Documents/Data-Formats-of-the-NSRL-Reference-Data-Set-16.pdf","downloadURL": "http://www.nsrl.nist.gov/RDS/rds_2.50/RDS_250.iso","format": { "description": "ISO 9660 disk image"},"mediaType": "application/zip", "filepath":"RDS_250.iso", "@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"],"@id":"cmps/RDS_250.iso","_extensionSchemas": ["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/DataFile"] }
 
 #--------------
 # testing dist2comp()
@@ -287,7 +287,7 @@ include "pod2nerdm"; dist2comp
 #
 include "pod2nerdm"; dist2comp
 {"accessURL": "http://webbook.nist.gov/chemistry/","description": "Landing page for the NIST Chemistry WebBook.","mediaType": "text/html"}
-{ "accessURL": "http://webbook.nist.gov/chemistry/","description": "Landing page for the NIST Chemistry WebBook.","mediaType": "text/html","@type": ["nrdp:AccessPage","dcat:Distribution"],"@id":"#chemistry/","_extensionSchemas":["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/AccessPage"]}
+{ "accessURL": "http://webbook.nist.gov/chemistry/","description": "Landing page for the NIST Chemistry WebBook.","mediaType": "text/html","@type": ["nrdp:AccessPage","dcat:Distribution"],"@id":"#chemistry/","_extensionSchemas":["https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/AccessPage"]}
 
 # testing dist2comp()
 #
@@ -389,13 +389,13 @@ include "pod2nerdm"; select_comp_type("nrdp:Subcollection"; "foo/bar")
 #
 include "pod2nerdm"; create_subcoll_for
 "a/b/foo"
-{"@id": "cmps/a/b/foo", "@type": ["nrdp:Subcollection"], "filepath": "a/b/foo", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/Subcollection" ]}
+{"@id": "cmps/a/b/foo", "@type": ["nrdp:Subcollection"], "filepath": "a/b/foo", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/Subcollection" ]}
 
 # testing insert_subcoll_comps
 #
 include "pod2nerdm"; insert_subcoll_comps
 [{ "title": "Titanium Boride", "filepath": "foo/srd13_B-101.json","@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"]},{ "title": "foo", "filepath": "foo", "@type": [ "nrdp:Subcollection"]},{"title": "Titanium Boride","filepath": "foo/bar/srd13_B-101.json","@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"]},{ "title": "foo bar goo", "filepath": "foo/bar/goo", "@type": ["nrdp:Subcollection"]}]
-[{"@id": "cmps/foo/bar", "@type": ["nrdp:Subcollection"], "filepath": "foo/bar", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/Subcollection" ]},{ "title": "Titanium Boride", "filepath": "foo/srd13_B-101.json","@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"]},{ "title": "foo", "filepath": "foo", "@type": [ "nrdp:Subcollection"]},{"title": "Titanium Boride","filepath": "foo/bar/srd13_B-101.json","@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"]},{ "title": "foo bar goo", "filepath": "foo/bar/goo", "@type": ["nrdp:Subcollection"]}]
+[{"@id": "cmps/foo/bar", "@type": ["nrdp:Subcollection"], "filepath": "foo/bar", "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/Subcollection" ]},{ "title": "Titanium Boride", "filepath": "foo/srd13_B-101.json","@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"]},{ "title": "foo", "filepath": "foo", "@type": [ "nrdp:Subcollection"]},{"title": "Titanium Boride","filepath": "foo/bar/srd13_B-101.json","@type": ["nrdp:DataFile","nrdp:DownloadableFile","dcat:Distribution"]},{ "title": "foo bar goo", "filepath": "foo/bar/goo", "@type": ["nrdp:Subcollection"]}]
 
 
 

diff --git a/jq/tests/test_podds2resource.py b/jq/tests/test_podds2resource.py
@@ -3,8 +3,9 @@
 import os, unittest, json, subprocess as subproc, types, pdb
 import ejsonschema as ejs
 
-nerdm = "https://data.nist.gov/od/dm/nerdm-schema/v0.3#"
-nerdmpub = "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#"
+nerdm = "https://data.nist.gov/od/dm/nerdm-schema/v0.4#"
+nerdmpub = "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#"
+nerdmbib = "https://data.nist.gov/od/dm/nerdm-schema/bib/v0.4#"
 datadir = os.path.join(os.path.dirname(__file__), "data")
 janaffile = os.path.join(datadir, "janaf_pod.json")
 corrfile =  os.path.join(datadir, "CORR-DATA.json")
@@ -29,7 +30,7 @@ def test_context(self):
 
     def test_schema(self):
         self.assertEquals(self.out['_schema'],
-                          "https://data.nist.gov/od/dm/nerdm-schema/v0.3#")
+                          "https://data.nist.gov/od/dm/nerdm-schema/v0.4#")
     def test_extsch(self):
 
         exts = self.out['_extensionSchemas']
@@ -101,13 +102,13 @@ def test_references(self):
         self.assertIsInstance(refs[0]['@type'], list)
         self.assertIsInstance(refs[0]['@type'][0], types.StringTypes)
         self.assertEquals(refs[0]['@type'], ["deo:BibliographicReference"])
-        self.assertEquals(refs[0]['refType'], "IsReferencedBy")
+        self.assertEquals(refs[0]['refType'], "IsSupplementTo")
         self.assertEquals(refs[0]['location'],
                           "http://www.nist.gov/data/PDFfiles/jpcrdS1V14.pdf")
 
         exts = refs[0]['_extensionSchemas']
         self.assertEquals(len(exts), 1)
-        self.assertIn(nerdm+"/definitions/DCiteReference", exts)
+        self.assertIn(nerdmbib+"/definitions/DCiteReference", exts)
 
     def test_hierarchy(self):
         self.assertIn("dataHierarchy", self.out,
@@ -142,7 +143,7 @@ def test_context(self):
 
     def test_schema(self):
         self.assertEquals(self.out['_schema'],
-                          "https://data.nist.gov/od/dm/nerdm-schema/v0.3#")
+                          "https://data.nist.gov/od/dm/nerdm-schema/v0.4#")
     def test_extsch(self):
 
         exts = self.out['_extensionSchemas']

diff --git a/model/examples/hitsc.json b/model/examples/hitsc.json
@@ -1,7 +1,7 @@
 {
     "@context": "https://data.nist.gov/od/dm/nerdm-pub-context.jsonld",
-    "_schema": "https://data.nist.gov/od/dm/nerdm-schema/v0.3#",
-    "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.3#/definitions/DataPublication" ],
+    "_schema": "https://data.nist.gov/od/dm/nerdm-schema/v0.4#",
+    "_extensionSchemas": [ "https://data.nist.gov/od/dm/nerdm-schema/pub/v0.4#/definitions/DataPublication" ],
 
     "@type": [ "nrdp:Database", "nrdp:SRD", "nrdp:PublishedDataResource" ],
     "@id": "ark:/88434/sdp0fjspek353",
@@ -48,12 +48,12 @@
     ],
     "references": [
         {
-            "@type": "deo:BibliographicReference",
+            "@type": [ "npg:Article", "schema:Article" ],
             "refType": "IsDocumentedBy",
             "label": "User Manual",
             "location": "https://srdata.nist.gov/CeramicDataPortal/Manual/HtsHelper",
             "_extensionSchemas": [
-                "https://data.nist.gov/od/dm/nerdm-schema/v0.3#/definitions/DCiteReference"
+                "https://data.nist.gov/od/dm/nerdm-schema/bib/v0.4#/definitions/DCiteReference"
             ]
         }
     ],