add basic support for tool resource metadata schemas

hsmodels/schemas/__init__.py

@@ -31,13 +31,14 @@
     TimeSeriesMetadataInRDF,
     CSVFileMetadataInRDF,
 )
-from hsmodels.schemas.rdf.resource import CollectionMetadataInRDF, ResourceMap, ResourceMetadataInRDF
-from hsmodels.schemas.resource import CollectionMetadata, ResourceMetadata
+from hsmodels.schemas.rdf.resource import CollectionMetadataInRDF, ResourceMap, ResourceMetadataInRDF, WebAppMetadataInRDF
+from hsmodels.schemas.resource import CollectionMetadata, ResourceMetadata, WebAppMetadata
 
 rdf_schemas = {
     ORE.ResourceMap: ResourceMap,
     HSTERMS.CompositeResource: ResourceMetadataInRDF,
     HSTERMS.CollectionResource: CollectionMetadataInRDF,
+    HSTERMS.ToolResource: WebAppMetadataInRDF,
     HSTERMS.GeographicRasterAggregation: GeographicRasterMetadataInRDF,
     HSTERMS.GeographicFeatureAggregation: GeographicFeatureMetadataInRDF,
     HSTERMS.MultidimensionalAggregation: MultidimensionalMetadataInRDF,
@@ -53,6 +54,7 @@
 user_schemas = {
     ResourceMetadataInRDF: ResourceMetadata,
     CollectionMetadataInRDF: CollectionMetadata,
+    WebAppMetadataInRDF: WebAppMetadata,
     GeographicRasterMetadataInRDF: GeographicRasterMetadata,
     GeographicFeatureMetadataInRDF: GeographicFeatureMetadata,
     MultidimensionalMetadataInRDF: MultidimensionalMetadata,

hsmodels/schemas/fields.py

@@ -22,7 +22,6 @@ class Relation(BaseMetadata):
 
     type: RelationType = Field(title="Relation type", description="The type of relationship with the related resource")
     value: str = Field(
-        max_length=500,
         title="Value",
         description="String expressing the Full text citation, URL link for, or description of the related resource",
     )
@@ -38,7 +37,7 @@ class CellInformation(BaseMetadata):
     model_config = ConfigDict(title='Raster Cell Metadata')
 
     # TODO: Is there such a thing as "name" for CellInformation?
-    name: str = Field(default=None, max_length=500, title="Name", description="Name of the cell information",)
+    name: str = Field(default=None, title="Name", description="Name of the cell information",)
     rows: int = Field(default=None, title="Rows",
                       description="The integer number of rows in the raster dataset",)
     columns: int = Field(
@@ -72,6 +71,7 @@ class Rights(BaseMetadata):
     url: AnyUrl = Field(
         title="URL",
         description="An object containing the URL pointing to a description of the license or rights statement",
+        default=None
     )
 
     @classmethod
@@ -205,7 +205,7 @@ class Contributor(BaseMetadata):
         title="Organization",
         description="A string containing the name of the organization with which the contributor is affiliated",
     )
-    email: Optional[EmailStr] = Field(
+    email: Optional[str] = Field(
         default=None, title="Email", description="A string containing an email address for the contributor"
     )
     homepage: Optional[HttpUrl] = Field(
@@ -274,7 +274,7 @@ class BandInformation(BaseMetadata):
 
     model_config = ConfigDict(title='Raster Band Metadata')
 
-    name: str = Field(max_length=500, title="Name", description="A string containing the name of the raster band",
+    name: str = Field(title="Name", description="A string containing the name of the raster band",
                       )
     variable_name: Optional[str] = Field(
         default=None,
@@ -689,26 +689,26 @@ class BoxCoverage(base_models.BaseCoverage):
         description="A string containing a name for the place associated with the geographic coverage",
     )
     northlimit: float = Field(
-        gt=-90,
-        lt=90,
+        gte=-90,
+        lt3=90,
         title="North limit",
         description="A floating point value containing the constant coordinate for the northernmost face or edge of the bounding box",
     )
     eastlimit: float = Field(
-        gt=-180,
-        lt=180,
+        gte=-180,
+        lte=180,
         title="East limit",
         description="A floating point value containing the constant coordinate for the easternmost face or edge of the bounding box",
     )
     southlimit: float = Field(
-        gt=-90,
-        lt=90,
+        gte=-90,
+        lte=90,
         title="South limit",
         description="A floating point value containing the constant coordinate for the southernmost face or edge of the bounding box",
     )
     westlimit: float = Field(
-        gt=-180,
-        lt=180,
+        gte=-180,
+        lte=180,
         title="West limit",
         description="A floating point value containing the constant coordinate for the westernmost face or edge of the bounding box",
     )
@@ -725,6 +725,9 @@ class BoxCoverage(base_models.BaseCoverage):
     @model_validator(mode='after')
     def compare_north_south(self):
         if self.northlimit < self.southlimit:
+            if self.southlimit == 90 and self.northlimit == -90:
+                # special case for global coverage
+                return self
             raise ValueError(f"North latitude [{self.northlimit}] must be greater than or equal to South latitude [{self.southlimit}]")
         return self
 
@@ -824,10 +827,10 @@ class PointCoverage(base_models.BaseCoverage):
         description="A string containing a name for the place associated with the geographic coverage",
     )
     east: float = Field(
-        gt=-180, lt=180, title="East", description="The coordinate of the point location measured in the east direction"
+        gte=-180, lte=180, title="East", description="The coordinate of the point location measured in the east direction"
     )
     north: float = Field(
-        gt=-90, lt=90, title="North", description="The coordinate of the point location measured in the north direction"
+        gte=-90, lte=90, title="North", description="The coordinate of the point location measured in the north direction"
     )
     units: str = Field(
         title="Units", description="The units applying to the unlabelled numeric values of north and east"

hsmodels/schemas/rdf/fields.py

@@ -127,7 +127,7 @@ class DateInRDF(RDFBaseModel):
 
 class RightsInRDF(RDFBaseModel):
     statement: str = Field(json_schema_extra={"rdf_predicate": HSTERMS.rightsStatement})
-    url: AnyUrl = Field(json_schema_extra={"rdf_predicate": HSTERMS.URL})
+    url: AnyUrl = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.URL})
 
 
 class CreatorInRDF(RDFBaseModel):
@@ -153,7 +153,7 @@ class ContributorInRDF(RDFBaseModel):
     phone: str = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.phone})
     address: str = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.address})
     organization: str = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.organization})
-    email: EmailStr = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.email})
+    email: str = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.email})
     homepage: HttpUrl = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.homepage})
     hydroshare_user_id: int = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.hydroshare_user_id})
     ORCID: AnyUrl = Field(default=None, json_schema_extra={"rdf_predicate": HSTERMS.ORCID})

hsmodels/schemas/rdf/resource.py

@@ -85,7 +85,7 @@ class BaseResource(BaseModel):
     awards: List[AwardInfoInRDF] = Field(json_schema_extra={"rdf_predicate": HSTERMS.awardInfo}, default=[])
     coverages: List[CoverageInRDF] = Field(json_schema_extra={"rdf_predicate": DC.coverage}, default=[])
     publisher: PublisherInRDF = Field(json_schema_extra={"rdf_predicate": DC.publisher}, default=None)
-    citation: str = Field(json_schema_extra={"rdf_predicate": DCTERMS.bibliographicCitation})
+    citation: str = Field(default= None, json_schema_extra={"rdf_predicate": DCTERMS.bibliographicCitation})
 
     _parse_rdf_subject = model_validator(mode='before')(rdf_parse_rdf_subject)
     _parse_coverages = model_validator(mode='before')(parse_coverages)
@@ -130,3 +130,18 @@ class CollectionMetadataInRDF(BaseResource):
     @field_serializer('dc_type', 'rdf_type')
     def serialize_url(self, _type: URIRef, _info):
         return AnyUrl(_type)
+
+
+class WebAppMetadataInRDF(BaseResource):
+    dc_type: AnyUrl = Field(
+        json_schema_extra={"rdf_predicate": DC.type}, default=HSTERMS.ToolResource, frozen=True
+    )
+    rdf_type: AnyUrl = Field(
+        json_schema_extra={"rdf_predicate": RDF.type}, frozen=True, default=HSTERMS.ToolResource
+    )
+    _label_literal = Literal["Web App Resource"]
+    label: _label_literal = Field(default="Web App Resource", frozen=True, alias='label')
+
+    @field_serializer('dc_type', 'rdf_type')
+    def serialize_url(self, _type: URIRef, _info):
+        return AnyUrl(_type)

hsmodels/schemas/rdf/validators.py

@@ -79,8 +79,8 @@ def sort_creators(cls, creators):
         # assign creator_order to creators that don't have it
         creator_order_numbers = [c.creator_order for c in creators if c.creator_order is not None]
         if creator_order_numbers:
-            if len(creator_order_numbers) != len(set(creator_order_numbers)):
-                raise ValueError("creator_order values must be unique")
+            #if len(creator_order_numbers) != len(set(creator_order_numbers)):
+            #    raise ValueError("creator_order values must be unique")
             max_order_number = max(creator_order_numbers)
         else:
             max_order_number = 0

hsmodels/schemas/resource.py

@@ -196,3 +196,13 @@ class CollectionMetadata(BaseResourceMetadata):
         description="An object containing a URL that points to the HydroShare resource type selected from the hsterms namespace",
         json_schema_extra={"readOnly": True},
     )
+
+
+class WebAppMetadata(BaseResourceMetadata):
+    type: Literal['ToolResource'] = Field(
+        frozen=True,
+        default="ToolResource",
+        title="Resource Type",
+        description="An object containing a URL that points to the HydroShare resource type selected from the hsterms namespace",
+        json_schema_extra={"readOnly": True},
+    )

hsmodels/utils.py

@@ -3,9 +3,10 @@
 
 def to_coverage_dict(value):
     value_dict = {}
-    for key_value in value.split("; "):
-        k, v = key_value.split("=")
-        value_dict[k] = v
+    for key_value in value.split(";"):
+        if "=" in key_value:
+            k, v = key_value.split("=")
+            value_dict[k.strip()] = v.strip()
     return value_dict
 
 

setup.py

@@ -4,12 +4,12 @@
 
 setup(
     name='hsmodels',
-    version='1.0.4',
+    version='1.1.1',
     packages=find_packages(include=['hsmodels', 'hsmodels.*', 'hsmodels.schemas.*', 'hsmodels.schemas.rdf.*'],
                            exclude=("tests",)),
     install_requires=[
         'rdflib<6.0.0',
-        'pydantic==2.7.*',
+        'pydantic==2.8.*',
         'email-validator'
     ],
     url='https://github.com/hydroshare/hsmodels',

tests/data/json/webapp.json

@@ -0,0 +1,33 @@
+{
+  "title": "GeoTrust",
+  "abstract": "This app is used to execute the scuint package for the MODFLOW-NWT model. During testing of the work, this app is linked to a deployed EC2 machine on AWS. Full instruction is provided at https://github.com/uva-hydroinformatics/Sciunit_HydroShare_Implementation for how a user could deploy this on AWS to reproduce this work.",
+  "language": "eng",
+  "subjects": [
+    "MODFLOW-NWT-scuint"
+  ],
+  "creators": [
+    {
+      "name": "Bakinam Essawy",
+      "phone": "8034634471",
+      "organization": "University of Virginia",
+      "email": "btaessawy@gmail.com",
+      "creator_order": 1,
+      "hydroshare_user_id": 878,
+      "identifiers": {}
+    }
+  ],
+  "contributors": [],
+  "relations": [
+    {
+      "type": "The content of this resource is part of",
+      "value": "Essawy, B. (2018). ModflowNwtCollection, HydroShare, http://www.hydroshare.org/resource/bf598099ed384540aaa9284b7343a717"
+    }
+  ],
+  "additional_metadata": {},
+  "rights": {
+    "statement": "This resource is shared under the Creative Commons Attribution CC BY.",
+    "url": "http://creativecommons.org/licenses/by/4.0/"
+  },
+  "awards": [],
+  "citation": "Essawy, B. (2018). GeoTrust, HydroShare, http://www.hydroshare.org/resource/126701df868e4da9872d9b533db34ae6"
+}

tests/data/metadata/webapp_meta.xml

@@ -0,0 +1,62 @@
+<?xml version="1.0" encoding="utf-8"?>
+<rdf:RDF
+  xmlns:hsterms="https://www.hydroshare.org/terms/"
+  xmlns:dcterms="http://purl.org/dc/terms/"
+  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+  xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
+>
+  <hsterms:ToolResource rdf:about="http://www.hydroshare.org/resource/126701df868e4da9872d9b533db34ae6">
+    <dc:date>
+      <dcterms:modified>
+        <rdf:value>2018-06-12T17:35:56.675086+00:00</rdf:value>
+      </dcterms:modified>
+    </dc:date>
+    <dc:identifier>
+      <rdf:Description>
+        <hsterms:hydroShareIdentifier rdf:resource="http://www.hydroshare.org/resource/126701df868e4da9872d9b533db34ae6"/>
+      </rdf:Description>
+    </dc:identifier>
+    <dc:type>
+      <rdf:Description rdf:about="https://www.hydroshare.org/terms/ToolResource">
+        <rdfs:isDefinedBy rdf:resource="https://www.hydroshare.org/terms/"/>
+        <rdfs:label>Web App Resource</rdfs:label>
+      </rdf:Description>
+    </dc:type>
+    <dc:subject>MODFLOW-NWT-scuint</dc:subject>
+    <dc:language>eng</dc:language>
+    <dc:date>
+      <dcterms:created>
+        <rdf:value>2017-06-12T13:58:14.473992+00:00</rdf:value>
+      </dcterms:created>
+    </dc:date>
+    <dc:title>GeoTrust</dc:title>
+    <dc:description>
+      <rdf:Description>
+        <dcterms:abstract>This app is used to execute the scuint package for the MODFLOW-NWT model. During testing of the work, this app is linked to a deployed EC2 machine on AWS. Full instruction is provided at https://github.com/uva-hydroinformatics/Sciunit_HydroShare_Implementation for how a user could deploy this on AWS to reproduce this work.</dcterms:abstract>
+      </rdf:Description>
+    </dc:description>
+    <dc:rights>
+      <rdf:Description>
+        <hsterms:URL rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
+        <hsterms:rightsStatement>This resource is shared under the Creative Commons Attribution CC BY.</hsterms:rightsStatement>
+      </rdf:Description>
+    </dc:rights>
+    <dc:creator>
+      <rdf:Description>
+        <hsterms:email>btaessawy@gmail.com</hsterms:email>
+        <hsterms:name>Bakinam Essawy</hsterms:name>
+        <hsterms:creatorOrder rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</hsterms:creatorOrder>
+        <hsterms:hydroshare_user_id rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">878</hsterms:hydroshare_user_id>
+        <hsterms:phone>8034634471</hsterms:phone>
+        <hsterms:organization>University of Virginia</hsterms:organization>
+      </rdf:Description>
+    </dc:creator>
+    <dc:relation>
+      <rdf:Description>
+        <dcterms:isPartOf>Essawy, B. (2018). ModflowNwtCollection, HydroShare, http://www.hydroshare.org/resource/bf598099ed384540aaa9284b7343a717</dcterms:isPartOf>
+      </rdf:Description>
+    </dc:relation>
+    <dcterms:bibliographicCitation>Essawy, B. (2018). GeoTrust, HydroShare, http://www.hydroshare.org/resource/126701df868e4da9872d9b533db34ae6</dcterms:bibliographicCitation>
+  </hsterms:ToolResource>
+</rdf:RDF>

tests/test_defaults.py

@@ -24,12 +24,13 @@
     SingleFileMetadataInRDF,
     TimeSeriesMetadataInRDF,
 )
-from hsmodels.schemas.rdf.resource import CollectionMetadataInRDF, ResourceMetadataInRDF
-from hsmodels.schemas.resource import CollectionMetadata, ResourceMetadata
+from hsmodels.schemas.rdf.resource import CollectionMetadataInRDF, ResourceMetadataInRDF, WebAppMetadataInRDF
+from hsmodels.schemas.resource import CollectionMetadata, ResourceMetadata, WebAppMetadata
 
 schema_list_count = [
     (ResourceMetadata, 5),
     (CollectionMetadata, 5),
+    (WebAppMetadata, 5),
     (GeographicRasterMetadata, 1),
     (GeographicFeatureMetadata, 2),
     (MultidimensionalMetadata, 2),
@@ -41,6 +42,7 @@
     (ModelInstanceMetadata, 1),
     (ResourceMetadataInRDF, 8),
     (CollectionMetadataInRDF, 8),
+    (WebAppMetadataInRDF, 8),
     (GeographicRasterMetadataInRDF, 3),
     (GeographicFeatureMetadataInRDF, 4),
     (MultidimensionalMetadataInRDF, 4),

tests/test_metadata.py

@@ -55,6 +55,7 @@ def compare_metadatas(new_graph, original_metadata_file):
     'modelprogram_meta.xml',
     'modelinstance_meta.xml',
     'collection_meta.xml',
+    'webapp_meta.xml',
     'csvfile_meta.xml',
 ]
 

tests/test_metadata_json.py

@@ -55,6 +55,7 @@ def test_resource_additional_metadata_dictionary(res_md):
     (ModelProgramMetadataIn, 'modelprogram.json'),
     (ModelInstanceMetadataIn, 'modelinstance.json'),
     (ResourceMetadataIn, 'collection.json'),
+    (ResourceMetadataIn, 'webapp.json'),
     (CSVFileMetadataIn, 'csvfile.json'),
 ]
 
@@ -69,6 +70,8 @@ def test_metadata_json_serialization(metadata_json_input):
     from_schema = sorting(json.loads(md.model_dump_json()))
     from_file = sorting(json.loads(json_file_str))
     for i in range(1, len(from_file)):
+        if i >= len(from_schema):
+            assert False, f"Missing field {from_file[i]} in from_schema"
         assert from_file[i] == from_schema[i]
 
 

tests/test_schemas.py

@@ -2,6 +2,7 @@
 
 from hsmodels.schemas import (
     CollectionMetadata,
+    WebAppMetadata,
     FileSetMetadata,
     GeographicFeatureMetadata,
     GeographicRasterMetadata,
@@ -26,6 +27,7 @@
 read_only_fields = [
     (ResourceMetadata, ['type', 'identifier', 'created', 'modified', 'review_started', 'published', 'url']),
     (CollectionMetadata, ['type', 'identifier', 'created', 'modified', 'review_started', 'published', 'url']),
+    (WebAppMetadata, ['type', 'identifier', 'created', 'modified', 'review_started', 'published', 'url']),
     (GeographicRasterMetadata, ['type', 'url']),
     (ModelProgramMetadata, ['type', 'url']),
     (ModelInstanceMetadata, ['type', 'url']),
@@ -59,6 +61,7 @@ def test_readonly(read_only_field):
 additional_metadata_fields = [
     (ResourceMetadata, ['additional_metadata']),
     (CollectionMetadata, ['additional_metadata']),
+    (WebAppMetadata, ['additional_metadata']),
     (GeographicRasterMetadata, ['additional_metadata']),
     (GeographicFeatureMetadata, ['additional_metadata']),
     (MultidimensionalMetadata, ['additional_metadata']),