Add a gold standard example using data from chemotion repository

examples/PASTA/README_template.md

@@ -1,4 +1,9 @@
 ## PASTA ELN
 Its home is at: https://github.com/PASTA-ELN
 
+This folder contains two files:
+- PASTA.eln an export of the standard example of an installation with samples, measurements, devices, ...
+- A gold‑standard sibling triplet consists of an ELN file, a JSON‑LD file, and a Turtle file. The example shows
+  that the ELN file fully supersedes the JSON‑LD/Turtle files in terms of content. [more](goldStandard.md)
+
 

examples/PASTA/goldStandard.md

@@ -0,0 +1,61 @@
+# Gold‑standard example
+
+This gold‑standard sibling triplet consists of an ELN
+file, a JSON‑LD file, and a Turtle file. The example was created from the data
+for CRR‑25894 on chemotion‑repository.org. The triplet shows that FULL semantic information can be included into the ELN file.
+
+- **The JSON‑LD and Turtle files are equivalent:** the Turtle file was generated
+  from the JSON‑LD representation using rdflib.
+- **All data contained in the JSON‑LD/Turtle files are also present in the ELN file:** minor format conversions are summarized below.
+- **Binary and raw data contained in the ELN file are NOT included in the JSON‑LD or Turtle files.**
+
+**Therefore, the ELN file fully supersedes the JSON‑LD/Turtle files in terms of content** as also evident from the size although the json-ld file is packed less  dense.
+
+## Format conversion: JSON‑LD → ELN file
+
+1.  Create an empty folder and add the data files to it.
+2.  Ensure that every node has an `@id`. If a node lacks an identifier, create
+    one using the pattern `@type_@name`.
+3.  Flatten hierarchical dictionaries into a list of nodes, using `@id` values
+    to represent links.
+4.  Add the manifest nodes and include them in the node list.
+5.  Remove duplicate nodes.
+6.  Adjust dataset `@id` values to reflect the file locations of the
+    corresponding data sets:
+  - Add an additional file node to the node list for each data file. Each file
+    node must include `@id`, `@type`, `@name`, and `sha256`.
+  - Use the instrument information from `dataset-description.txt` as
+    supplemental metadata for the dataset.
+  - Link the additional data files via `hasPart` both in the dataset node and in
+    the root `./` node.
+7.  Restructure the root node:
+  - Set `@id` to `./` and `@type` to `Dataset`.
+  - Add all datasets and files under the root node using `hasPart`.
+8.  Rename protected keys:
+  - `author` → `authors`
+  - `keywords` → `keywordLists`
+  - Remove the protected `about` key if it only links back to the root node.
+  - rename @type: 'Study' -> 'CreativeWork'
+  - rename @type: 'QuantitativeValue' -> 'PropertyValue'
+  - for @type: Person, create name using givenName and familyName
+  - `affiliation` -> `worksFor`
+  - for @type: PropertyValue: add propertyID
+
+## Original data
+
+Source: CRR‑25894 from [chemotion‑repository.net](https://www.chemotion-repository.net/home/publications/collections/4916).
+
+The JSON‑LD files were downloaded manually and merged by copying the Analysis
+branches into the main Reaction tree to produce a single master JSON‑LD file.
+The files used include:
+
+- `JSON-LD_Reaction_7354-20251031....json`
+- `JSON-LD_Analysis_674242-20251031....json`
+- `JSON-LD_Analysis_674244-20251031....json`
+- `JSON-LD_Analysis_674246-20251031....json`
+- `JSON-LD_Analysis_674248-20251031....json`
+
+The master JSON‑LD file was converted to a Turtle file. A heuristic
+verification schema (`goldStandardShapes.ttl`) was created, and all files were
+validated against it.
+

examples/PASTA/goldStandardShapes.ttl

@@ -0,0 +1,232 @@
+@prefix dcterms: <http://purl.org/dc/terms/> .
+@prefix ex: <http://example.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<http://schema.org/ChemicalSubstanceShape> a sh:NodeShape ;
+    sh:property ex:alternateNamePropShape,
+        ex:descriptionPropShape,
+        ex:hasBioChemEntityPartPropShape,
+        ex:identifierPropShape,
+        ex:imagePropShape,
+        ex:namePropShape,
+        ex:subjectOfPropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/ChemicalSubstance> .
+
+<http://schema.org/CreativeWorkShape> a sh:NodeShape ;
+    sh:property ex:authorPropShape,
+        ex:namePropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/CreativeWork> .
+
+<http://schema.org/DataCatalogShape> a sh:NodeShape ;
+    sh:property ex:contributorPropShape,
+        ex:descriptionPropShape,
+        ex:isAccessibleForFreePropShape,
+        ex:keywordsPropShape,
+        ex:licensePropShape,
+        ex:namePropShape,
+        ex:providerPropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/DataCatalog> .
+
+<http://schema.org/DatasetShape> a sh:NodeShape ;
+    sh:property ex:authorPropShape,
+        ex:conformsToPropShape,
+        ex:creatorPropShape,
+        ex:descriptionPropShape,
+        ex:identifierPropShape,
+        ex:includedInDataCatalogPropShape,
+        ex:isPartOfPropShape,
+        ex:licensePropShape,
+        ex:measurementTechniquePropShape,
+        ex:namePropShape,
+        ex:publisherPropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/Dataset> .
+
+<http://schema.org/DefinedTermSetShape> a sh:NodeShape ;
+    sh:property ex:namePropShape ;
+    sh:targetClass <http://schema.org/DefinedTermSet> .
+
+<http://schema.org/DefinedTermShape> a sh:NodeShape ;
+    sh:property ex:alternateNamePropShape,
+        ex:inDefinedTermSetPropShape,
+        ex:namePropShape,
+        ex:termCodePropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/DefinedTerm> .
+
+<http://schema.org/MolecularEntityShape> a sh:NodeShape ;
+    sh:property ex:conformsToPropShape,
+        ex:inChIKeyPropShape,
+        ex:inChIPropShape,
+        ex:iupacNamePropShape,
+        ex:molecularFormulaPropShape,
+        ex:molecularWeightPropShape,
+        ex:namePropShape,
+        ex:smilesPropShape ;
+    sh:targetClass <http://schema.org/MolecularEntity> .
+
+<http://schema.org/OrganizationShape> a sh:NodeShape ;
+    sh:property ex:logoPropShape,
+        ex:namePropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/Organization> .
+
+<http://schema.org/PersonShape> a sh:NodeShape ;
+    sh:property ex:affiliationPropShape,
+        ex:familyNamePropShape,
+        ex:givenNamePropShape,
+        ex:identifierPropShape,
+        ex:namePropShape ;
+    sh:targetClass <http://schema.org/Person> .
+
+<http://schema.org/QuantitativeValueShape> a sh:NodeShape ;
+    sh:property ex:unitCodePropShape,
+        ex:valuePropShape ;
+    sh:targetClass <http://schema.org/QuantitativeValue> .
+
+<http://schema.org/StudyShape> a sh:NodeShape ;
+    sh:property ex:aboutPropShape,
+        ex:additionalTypePropShape,
+        ex:authorPropShape,
+        ex:citationPropShape,
+        ex:conformsToPropShape,
+        ex:contributorPropShape,
+        ex:creatorPropShape,
+        ex:dateCreatedPropShape,
+        ex:datePublishedPropShape,
+        ex:descriptionPropShape,
+        ex:identifierPropShape,
+        ex:keywordsPropShape,
+        ex:licensePropShape,
+        ex:namePropShape,
+        ex:providerPropShape,
+        ex:publisherPropShape,
+        ex:subjectOfPropShape,
+        ex:urlPropShape ;
+    sh:targetClass <http://schema.org/Study> .
+
+ex:aboutPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/about> .
+
+ex:additionalTypePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/additionalType> .
+
+ex:affiliationPropShape sh:nodeKind sh:BlankNode ;
+    sh:path <http://schema.org/affiliation> .
+
+ex:citationPropShape sh:nodeKind sh:BlankNode ;
+    sh:path <http://schema.org/citation> .
+
+ex:dateCreatedPropShape sh:datatype <http://schema.org/Date> ;
+    sh:path <http://schema.org/dateCreated> .
+
+ex:datePublishedPropShape sh:datatype <http://schema.org/Date> ;
+    sh:path <http://schema.org/datePublished> .
+
+ex:familyNamePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/familyName> .
+
+ex:givenNamePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/givenName> .
+
+ex:hasBioChemEntityPartPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/hasBioChemEntityPart> .
+
+ex:imagePropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/image> .
+
+ex:inChIKeyPropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/inChIKey> .
+
+ex:inChIPropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/inChI> .
+
+ex:inDefinedTermSetPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/inDefinedTermSet> .
+
+ex:includedInDataCatalogPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/includedInDataCatalog> .
+
+ex:isAccessibleForFreePropShape sh:datatype xsd:boolean ;
+    sh:path <http://schema.org/isAccessibleForFree> .
+
+ex:isPartOfPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/isPartOf> .
+
+ex:iupacNamePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/iupacName> .
+
+ex:logoPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/logo> .
+
+ex:measurementTechniquePropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/measurementTechnique> .
+
+ex:molecularFormulaPropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/molecularFormula> .
+
+ex:molecularWeightPropShape sh:nodeKind sh:BlankNode ;
+    sh:path <http://schema.org/molecularWeight> .
+
+ex:smilesPropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/smiles> .
+
+ex:termCodePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/termCode> .
+
+ex:unitCodePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/unitCode> .
+
+ex:valuePropShape sh:datatype xsd:double ;
+    sh:path <http://schema.org/value> .
+
+ex:alternateNamePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/alternateName> .
+
+ex:contributorPropShape sh:nodeKind sh:BlankNodeOrIRI ;
+    sh:path <http://schema.org/contributor> .
+
+ex:creatorPropShape sh:nodeKind sh:BlankNode ;
+    sh:path <http://schema.org/creator> .
+
+ex:keywordsPropShape
+    sh:or ( [ sh:datatype xsd:string ]
+            [ sh:nodeKind sh:IRI ] ) ;
+    sh:path <http://schema.org/keywords> .
+
+ex:providerPropShape sh:nodeKind sh:BlankNode ;
+    sh:path <http://schema.org/provider> .
+
+ex:publisherPropShape sh:nodeKind sh:BlankNode ;
+    sh:path <http://schema.org/publisher> .
+
+ex:subjectOfPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/subjectOf> .
+
+ex:authorPropShape
+    sh:or ( [ sh:datatype xsd:string ]
+            [ sh:nodeKind sh:BlankNodeOrIRI ; sh:class <http://schema.org/Person> ] ) ;
+    sh:path <http://schema.org/author> .
+
+ex:conformsToPropShape sh:nodeKind sh:IRI ;
+    sh:path dcterms:conformsTo .
+
+ex:licensePropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/license> .
+
+ex:descriptionPropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/description> .
+
+ex:identifierPropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/identifier> .
+
+ex:urlPropShape sh:nodeKind sh:IRI ;
+    sh:path <http://schema.org/url> .
+
+ex:namePropShape sh:datatype xsd:string ;
+    sh:path <http://schema.org/name> .
+

tests/checks.py

@@ -165,7 +165,7 @@ def checkSchema(fileName):
         metadataJsonFile = [i for i in elnFile.namelist() if i.endswith(METADATA_FILE)][0]
         metadataContent = json.loads(elnFile.read(metadataJsonFile))
         for error in sorted(validator.iter_errors(metadataContent), key=str):
-            log += f'- {error.message}'
+            log += f'- {error.message}\n'
             success = False
     return success, log