Merge pull request #61 from oeg-upm/dev

Solving some issues and geomappings support

src/yatter/constants.py

@@ -211,7 +211,8 @@
     'csv': 'CSV',
     'json': 'JSONPath',
     'xpath': 'XPath',
-    'jsonpath': 'JSONPath'
+    'jsonpath': 'JSONPath',
+    "shp": "SHP"
 }
 
 YARRRML_DATABASES_DRIVER = {

src/yatter/mapping.py

@@ -1,4 +1,5 @@
 from .import *
+prefixes = {}
 
 
 def add_mapping(mapping, mappings, it):
@@ -11,6 +12,7 @@ def add_mapping(mapping, mappings, it):
 
 
 def add_prefix(data):
+    global prefixes
     template = []
     common_prefixes = []
     if YARRRML_PREFIXES in data:
@@ -121,5 +123,5 @@ def get_non_asserted_mappings(yarrrml_data, mapping_format):
 def merge_mapping_section_by_key(key,yarrrml_list):
     output = {key:{}}
     for yarrrml_mapping in yarrrml_list:
-        output[key] =  output[key] | yarrrml_mapping
+        output[key] = output[key] | yarrrml_mapping
     return output

src/yatter/predicateobject.py

@@ -4,9 +4,9 @@
 from .source import get_initial_sources, add_source, add_table
 from .subject import add_subject
 from .termmap import generate_rml_termmap, check_type
+from .mapping import prefixes
 from ruamel.yaml import YAML
 
-
 def get_object_access(predicate_object_map):
     if YARRRML_OBJECT in predicate_object_map:
         object_access = YARRRML_OBJECT
@@ -143,7 +143,7 @@ def add_predicate_object(data, mapping, predicate_object, mapping_format=RML_URI
     for pm in predicate_list:
         pm_value = pm
         execution = False
-        if YARRRML_VALUE in pm:
+        if YARRRML_VALUE in pm and type(pm) is dict:
             pm_value = pm[YARRRML_VALUE]
         elif YARRRML_FUNCTION in pm:
             pm_value = pm[YARRRML_FUNCTION]
@@ -165,8 +165,13 @@ def add_predicate_object(data, mapping, predicate_object, mapping_format=RML_URI
                 template += generate_rml_termmap(STAR_OBJECT, R2RML_OBJECT_CLASS,
                                                  object_value, "\t\t\t", mapping_format)
             else:
-                template += generate_rml_termmap(R2RML_OBJECT, R2RML_OBJECT_CLASS,
+                object_map = generate_rml_termmap(R2RML_OBJECT, R2RML_OBJECT_CLASS,
                                              object_value, "\t\t\t", mapping_format)
+
+                if object_value not in prefixes and ":" not in object_value and R2RML_CONSTANT in object_map:
+                    object_map = object_map.replace(object_value, f"\"{object_value}\"")
+
+                template += object_map
             if len(om) == 2:
                 types = check_type(om[1])
                 if types != "error":
@@ -201,7 +206,7 @@ def add_predicate_object(data, mapping, predicate_object, mapping_format=RML_URI
             else:
                template += ref_mapping(data, mapping, om, YARRRML_QUOTED, STAR_QUOTED, mapping_format)
         else:
-            if YARRRML_VALUE in om:
+            if YARRRML_VALUE in om and type(om) is dict:
                 object_value = om.get(YARRRML_VALUE)
             else:
                 object_value = om
@@ -311,7 +316,9 @@ def add_inverse_pom(mapping_id, rdf_mapping, classes, prefixes):
     yarrrml_poms = []
     yaml = YAML()
     for c in classes:
-        yarrrml_poms.append(['rdf:type', c.toPython()])
+        yarrrml_pom = yaml.seq(['rdf:type', c.toPython()])
+        yarrrml_pom.fa.set_flow_style()
+        yarrrml_poms.append(yarrrml_pom)
 
     query = f'SELECT ?predicate ?predicateValue ?object ?objectValue ?termtype ?datatype ?datatypeMapValue ' \
             f'?language ?languageMapValue ?parentTriplesMap ?child ?parent ?graphValue' \

src/yatter/source.py

@@ -1,3 +1,4 @@
+import os
 import re
 import rdflib
 from .constants import *
@@ -85,7 +86,7 @@ def add_source_simplified(mapping, source):
     source_rdf = ""
     file_path = re.sub("~.*", "", source[0])
     reference_formulation = source[0].split('~')[1]
-    source_extension = file_path.split('.')[1]
+    source_extension = os.path.splitext(file_path)[1].replace(".","")
     ref_formulation_rml = YARRRML_REFERENCE_FORMULATIONS[reference_formulation]
 
     if switch_in_reference_formulation(reference_formulation) != source_extension:
@@ -170,9 +171,7 @@ def database_source(mapping, source, db_identifier):
 
 def switch_in_reference_formulation(value):
     value = value.lower()
-    if value == "csv":
-        switcher = value
-    elif "json" in value:
+    if "json" in value:
         if "path" in value:
             switcher = "json"
         else:
@@ -182,6 +181,8 @@ def switch_in_reference_formulation(value):
             switcher = "xml"
         else:
             switcher = "xpath"
+    else:
+        switcher = value
     return switcher
 
 

src/yatter/subject.py

@@ -40,7 +40,7 @@ def add_subject(data, mapping, mapping_format):
             subject_termmap = generate_rml_termmap(STAR_SUBJECT, R2RML_SUBJECT_CLASS, individual_subject, "\t\t")
         else:
             subject_value = individual_subject
-            if YARRRML_VALUE in individual_subject:
+            if YARRRML_VALUE in individual_subject and type(individual_subject) is dict:
                 subject_value = individual_subject.get(YARRRML_VALUE)
             elif YARRRML_FUNCTION in individual_subject:
                 subject_value = individual_subject.get(YARRRML_FUNCTION)

src/yatter/termmap.py

@@ -23,7 +23,7 @@ def generate_rml_termmap(rml_property, rml_class, text, identation, mapping_form
     term_map = get_termmap_type(text, mapping_format)
     if term_map == R2RML_TEMPLATE:
         text = generate_rml_template(text)
-        text = text.replace('"',r'\"')
+        text = text.replace('"', r'\"')
     elif term_map == RML_REFERENCE or term_map == R2RML_COLUMN:
         text = text.replace("$(", "").replace(")", "")
         text = text.replace('"', r'\"')