ref: change shapefile to a single file

ReproNim · Jun 29, 2020 · b505eb2 · b505eb2
1 parent 3f52cb9
commit b505eb2
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Showing 11 changed files with 274 additions and 506 deletions.
diff --git a/reproschema/__init__.py b/reproschema/__init__.py
@@ -14,7 +14,7 @@
 def get_logger(name=None):
     """Return a logger to use
     """
-    return logging.getLogger("pydra_ml" + (".%s" % name if name else ""))
+    return logging.getLogger("reproschema" + (".%s" % name if name else ""))
 
 
 def set_logger_level(lgr, level):
@@ -34,7 +34,7 @@ def set_logger_level(lgr, level):
 
 lgr = get_logger()
 # Basic settings for output, for now just basic
-set_logger_level(lgr, os.environ.get("PYDRAML_LOG_LEVEL", logging.INFO))
+set_logger_level(lgr, os.environ.get("REPROSCHEMA_LOG_LEVEL", logging.INFO))
 FORMAT = "%(asctime)-15s [%(levelname)8s] %(message)s"
 logging.basicConfig(format=FORMAT)
 

diff --git a/reproschema/cli.py b/reproschema/cli.py
@@ -39,14 +39,14 @@ def main(log_level):
 
 
 @main.command()
-@click.option("--shapedir", default=None, type=click.Path(exists=True, dir_okay=True))
+@click.option("--shapefile", default=None, type=click.Path(exists=True, dir_okay=False))
 @click.argument("path", nargs=1, type=str)
-def validate(shapedir, path):
+def validate(shapefile, path):
     if not (path.startswith("http") or os.path.exists(path)):
         raise ValueError(f"{path} must be a URL or an existing file or directory")
     from .validate import validate
 
-    validate(shapedir, path)
+    validate(shapefile, path)
 
 
 @main.command()

diff --git a/reproschema/jsonldutils.py b/reproschema/jsonldutils.py
@@ -33,27 +33,6 @@ def load_file(path_or_url, started=False, http_kwargs={}):
     return data
 
 
-def file2shape(filename, shape_dir, started, http_kwargs={}):
-    data = load_file(filename, started, http_kwargs)
-    no_type = True
-    shape_file_path = []
-    for val in data:
-        if "@type" not in val:
-            continue
-        for schema_type in val["@type"]:
-            for key in ["Protocol", "Activity", "Field", "ResponseOption"]:
-                if schema_type.endswith(f"/{key}"):
-                    shape_file_path.append(os.path.join(shape_dir, f"{key}Shape.ttl"))
-                    no_type = False
-    if no_type:
-        raise ValueError(f"{filename} missing @type")
-    if len(shape_file_path) > 1:
-        raise ValueError(
-            f"Multiple reproschema types in {filename}. Not " f"supported yet"
-        )
-    return data, shape_file_path.pop()
-
-
 def validate_data(data, shape_file_path):
     """Validate an expanded jsonld document against a shape.
 

diff --git a/reproschema/tests/reproschema-shacl.ttl b/reproschema/tests/reproschema-shacl.ttl
@@ -0,0 +1,248 @@
+@prefix nidm: <http://purl.org/nidash/nidm#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix reproschema: <http://schema.repronim.org/> .
+@prefix schema: <http://schema.org/> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+
+reproschema:Activity a nidm:Assessment,
+        rdfs:Class,
+        prov:Entity,
+        prov:Plan ;
+    rdfs:label "Activity" ;
+    rdfs:comment "An assessment in a protocol." ;
+    rdfs:subClassOf schema:CreativeWork .
+
+reproschema:AdditionalProperty a rdfs:Class ;
+    rdfs:label "Additional properties" ;
+    rdfs:comment "An object to describe the various properties added to assessments and fields." .
+
+reproschema:AllowExport a rdfs:Class ;
+    rdfs:label "Allow export" ;
+    rdfs:comment "Indicates (by boolean) if data can be exported or not." .
+
+reproschema:AutoAdvance a rdfs:Class ;
+    rdfs:label "Auto advance" ;
+    rdfs:comment "Indicates (by boolean) if assessments in a protocol can auto advance or not." .
+
+reproschema:Choice a rdfs:Class ;
+    rdfs:label "Response choice" ;
+    rdfs:comment "An array to list the available options in responseOptions of the Field item." .
+
+reproschema:DisableBack a rdfs:Class ;
+    rdfs:label "Disable redo" ;
+    rdfs:comment "Indicates (by boolean) if we can go back to a completed assessment in a protocol." .
+
+reproschema:DontKnow a rdfs:Class ;
+    rdfs:label "Do not know" ;
+    rdfs:comment "An element to describe the choice when response is not known." .
+
+reproschema:Field a nidm:DataElement,
+        rdfs:Class,
+        prov:Entity ;
+    rdfs:label "Field" ;
+    rdfs:comment "An item in an assessment." ;
+    rdfs:subClassOf schema:CreativeWork .
+
+reproschema:Protocol a rdfs:Class,
+        prov:Entity,
+        prov:Plan ;
+    rdfs:label "Protocol" ;
+    rdfs:comment "A representation of a study which comprises one or more assessments." ;
+    rdfs:subClassOf schema:CreativeWork .
+
+reproschema:ResponseOption a rdfs:Class ;
+    rdfs:label "Response option" ;
+    rdfs:comment "An element (object or by URL)to describe the properties of response of the Field item." .
+
+reproschema:Scoring a rdfs:Class ;
+    rdfs:label "Scoring logic" ;
+    rdfs:comment "An object indicating score in an activity or protocol and the score Field item " .
+
+reproschema:Skipped a rdfs:Class ;
+    rdfs:label "Skipped" ;
+    rdfs:comment "An element to describe the choice when the item is skipped." .
+
+reproschema:TimedOut a rdfs:Class ;
+    rdfs:label "Response timed out" ;
+    rdfs:comment "A boolean element to describe if the response did not occur within the prescribed time." .
+
+schema:about schema:domainIncludes reproschema:Activity,
+        reproschema:Field,
+        reproschema:Protocol .
+
+schema:associatedMedia schema:domainIncludes reproschema:Field .
+
+schema:citation schema:domainIncludes reproschema:Activity .
+
+schema:description schema:domainIncludes reproschema:Activity,
+        reproschema:Field,
+        reproschema:Protocol .
+
+schema:image schema:domainIncludes reproschema:Choice .
+
+schema:isPartOf schema:domainIncludes reproschema:Field ;
+    schema:rangeIncludes reproschema:Activity .
+
+schema:maxValue schema:domainIncludes reproschema:ResponseOption .
+
+schema:minValue schema:domainIncludes reproschema:ResponseOption .
+
+schema:name schema:domainIncludes reproschema:Choice .
+
+schema:question schema:domainIncludes reproschema:Field .
+
+schema:readonlyValue schema:domainIncludes reproschema:Field .
+
+schema:schemaVersion schema:domainIncludes reproschema:Activity,
+        reproschema:Field,
+        reproschema:Protocol .
+
+schema:unitCode schema:domainIncludes reproschema:ResponseOption .
+
+schema:value schema:domainIncludes reproschema:Choice ;
+    schema:rangeIncludes reproschema:DontKnow,
+        reproschema:Skipped .
+
+schema:valueRequired schema:domainIncludes reproschema:AdditionalProperty .
+
+schema:version schema:domainIncludes reproschema:Activity,
+        reproschema:Field,
+        reproschema:Protocol .
+
+reproschema:addProperties a rdf:Property ;
+    rdfs:label "addProperties" ;
+    schema:domainIncludes reproschema:Activity,
+        reproschema:Protocol ;
+    schema:rangeIncludes reproschema:AdditionalProperty ;
+    rdfs:comment "An array of objects to describe the various properties added to assessments and fields." .
+
+reproschema:allow a rdf:Property ;
+    rdfs:label "allow" ;
+    schema:domainIncludes reproschema:Protocol ;
+    schema:rangeIncludes schema:Thing ;
+    rdfs:comment "An array of items indicating properties allowed on an activity or protocol " .
+
+reproschema:choices a rdf:Property ;
+    rdfs:label "choices" ;
+    schema:domainIncludes reproschema:ResponseOption ;
+    schema:rangeIncludes schema:URL,
+        reproschema:Choice ;
+    schema:sameAs schema:itemListElement ;
+    rdfs:comment "An array to list the available options in responseOptions of the Field item." .
+
+reproschema:datumType a rdf:Property ;
+    rdfs:label "datumType" ;
+    schema:domainIncludes reproschema:ResponseOption ;
+    schema:rangeIncludes schema:Text,
+        schema:URL ;
+    rdfs:comment "Indicates what type of datum the response is (e.g. range,count,scalar etc.) for the Field item." .
+
+reproschema:inputType a rdf:Property ;
+    rdfs:label "inputType" ;
+    schema:domainIncludes reproschema:Field ;
+    schema:rangeIncludes schema:Text ;
+    rdfs:comment "An element to describe the input type of a Field item." .
+
+reproschema:isAbout a rdf:Property ;
+    rdfs:label "isAbout" ;
+    schema:domainIncludes reproschema:AdditionalProperty ;
+    schema:rangeIncludes reproschema:Activity,
+        reproschema:Field ;
+    rdfs:comment "An element to define (by URL) the corresponding nodes." .
+
+reproschema:isVis a rdf:Property ;
+    rdfs:label "visibility" ;
+    schema:domainIncludes reproschema:AdditionalProperty ;
+    schema:rangeIncludes schema:Boolean,
+        schema:Text ;
+    rdfs:comment "An element to describe (by boolean or conditional statement) visibility conditions of items in an assessment." .
+
+reproschema:jsExpression a rdf:Property ;
+    rdfs:label "JavaScript Expression" ;
+    schema:domainIncludes reproschema:Scoring ;
+    schema:rangeIncludes schema:Boolean,
+        schema:Text ;
+    rdfs:comment "A JavaScript expression to compute a score from other variables." .
+
+reproschema:landingPage a rdf:Property ;
+    rdfs:label "Landing page content" ;
+    schema:domainIncludes reproschema:Protocol ;
+    schema:rangeIncludes schema:Text,
+        schema:URL ;
+    rdfs:comment "An element (by URL) to point to the protocol readme or landing page." .
+
+reproschema:multipleChoice a rdf:Property ;
+    rdfs:label "Multiple choice response expectation" ;
+    schema:domainIncludes reproschema:ResponseOption ;
+    schema:rangeIncludes schema:Boolean ;
+    rdfs:comment "Indicates (by bool) if response for the Field item has one or more answer." .
+
+reproschema:order a rdf:Property ;
+    rdfs:label "Order" ;
+    schema:domainIncludes reproschema:Activity,
+        reproschema:Protocol ;
+    schema:rangeIncludes schema:URL,
+        reproschema:Activity,
+        reproschema:Field ;
+    rdfs:comment "An ordered list to describe the order in which the items of an assessment or protocol appear in the user interface." .
+
+reproschema:preamble a rdf:Property ;
+    rdfs:label "Preamble" ;
+    schema:domainIncludes reproschema:Activity,
+        reproschema:Field ;
+    schema:rangeIncludes schema:Text,
+        rdf:langString ;
+    rdfs:comment "The preamble for an assessment" .
+
+reproschema:responseOptions a rdf:Property ;
+    rdfs:label "Response options" ;
+    schema:domainIncludes reproschema:Field ;
+    schema:rangeIncludes schema:URL,
+        reproschema:ResponseOption ;
+    rdfs:comment "An element (object or by URL)to describe the properties of response of the Field item." .
+
+reproschema:scoringLogic a rdf:Property ;
+    rdfs:label "Scoring logic objects" ;
+    schema:domainIncludes reproschema:Activity,
+        reproschema:Protocol ;
+    schema:rangeIncludes reproschema:Scoring ;
+    rdfs:comment "An array of objects indicating score in an activity or protocol and maps it to the score Field item " .
+
+reproschema:shuffle a rdf:Property ;
+    rdfs:label "Shuffle" ;
+    schema:domainIncludes reproschema:Activity,
+        reproschema:Protocol ;
+    schema:rangeIncludes schema:boolean ;
+    rdfs:comment "An element (bool) to determine if the list of items is shuffled or in order." .
+
+reproschema:statusOptions a rdf:Property ;
+    rdfs:label "Status options" ;
+    schema:rangeIncludes schema:Text ;
+    rdfs:comment "Provides information on whether or not a field item wants to be accompanied by the additional status option(s) defined in “statusOptions”" .
+
+reproschema:valueType a rdf:Property ;
+    rdfs:label "The type of the response" ;
+    schema:domainIncludes reproschema:ResponseOption ;
+    schema:rangeIncludes schema:Text,
+        rdf:langString ;
+    rdfs:comment "The type of the response of an item. For example, string, integer, etc." .
+
+reproschema:variableName a rdf:Property ;
+    rdfs:label "variableName" ;
+    schema:domainIncludes reproschema:AdditionalProperty,
+        reproschema:Scoring ;
+    schema:rangeIncludes schema:Text ;
+    rdfs:comment "The name used to represent an item." .
+
+skos:prefLabel a rdf:Property ;
+    rdfs:label "prefLabel" ;
+    schema:domainIncludes reproschema:Activity,
+        reproschema:AdditionalProperty,
+        reproschema:Field,
+        reproschema:Protocol ;
+    schema:rangeIncludes schema:Text ;
+    rdfs:comment "Indicates the label of an Activity or Field to be used as display name.",
+        "Indicates the label of the Field.",
+        "The preferred name of the assessment." .
diff --git a/reproschema/tests/test_validate.py b/reproschema/tests/test_validate.py
@@ -5,15 +5,15 @@
 
 def test_validate():
     os.chdir(os.path.dirname(__file__))
-    assert validate_dir("data", os.path.abspath("validation"))
+    assert validate_dir("data", os.path.abspath("reproschema-shacl.ttl"))
 
 
 def test_type_error():
     os.chdir(os.path.dirname(__file__))
     with pytest.raises(ValueError):
-        validate_dir("contexts", os.path.abspath("validation"))
+        validate_dir("contexts", os.path.abspath("reproschema-shacl.ttl"))
 
 
 def test_url():
     url = "https://raw.githubusercontent.com/ReproNim/reproschema-py/master/reproschema/tests/data/activities/activity1.jsonld"
-    assert validate(os.path.abspath("validation"), url)
+    assert validate(os.path.abspath("reproschema-shacl.ttl"), url)