Use jsonpath to collect values when downloading a file

kgforge/core/archetypes/read_only_store.py

@@ -26,7 +26,7 @@
 )
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder
-from kgforge.core.reshaping import collect_values
+from kgforge.core.reshaping import collect_values, collect_values_jp
 from kgforge.core.wrappings import Filter
 from kgforge.core.wrappings.dict import DictWrapper
 
@@ -107,9 +107,13 @@ def download(
         # path: DirPath.
         urls = []
         store_metadata = []
+        constraint_dict = None
+        if content_type:
+            constraint_dict = {'encodingFormat': content_type}
         to_download = [data] if isinstance(data, Resource) else data
         for d in to_download:
-            collected_values = collect_values(d, follow, DownloadingError)
+            # collected_values = collect_values(d, follow, DownloadingError)
+            collected_values = collect_values_jp(d, follow, DownloadingError, constraint_dict)
             urls.extend(collected_values)
             store_metadata.extend(
                 [d._store_metadata for _ in range(len(collected_values))]

kgforge/core/reshaping.py

@@ -12,7 +12,8 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 
-from typing import Dict, Iterator, List, Union, Type
+from typing import Dict, Iterator, List, Union, Type, Optional
+import jsonpath_ng as jp
 
 from kgforge.core.resource import Resource
 from kgforge.core.commons.attributes import repr_class
@@ -106,3 +107,28 @@ def _collect(things: List) -> Iterator[str]:
         raise exception(
             f"An error occur when collecting values for path to follow '{follow}': {str(e)}"
         ) from e
+
+
+def collect_values_jp(data: Resource, follow: str,
+                      exception: Type[Exception] = Exception,
+                      constraint_dict: Optional[Dict] = None) -> List[str]:
+    try:
+        properties = follow.split('.')
+        pattern = f"$." + "[*].".join(properties)
+        jp_query = jp.parse(pattern)
+        data = as_json(data, False, False, None, None, None)
+        results = jp_query.find(data)
+        if len(results) == 0:
+            raise exception(f"Path not found")
+        if constraint_dict:
+            if len(constraint_dict) != 1:
+                raise NotImplementedError("Only one constraint can be impossed at the moment")
+            [(k, v)] = list(constraint_dict.items())
+            return [result.value for result in results if result.context.value[k] == v]
+        else:
+            return [result.value for result in results]
+
+    except Exception as e:
+        raise exception(
+            f"An error occur when collecting values for path to follow '{follow}': {str(e)}"
+        ) from e

kgforge/specializations/stores/bluebrain_nexus.py

@@ -601,8 +601,6 @@ def _download_one(
         params_download = copy.deepcopy(self.service.params.get("download", {}))
         headers = (
             self.service.headers_download
-            if not content_type
-            else update_dict(self.service.headers_download, {"Accept": content_type})
         )
 
         response = requests.get(

setup.py

@@ -51,7 +51,8 @@
         "owlrl>=5.2.3",
         "elasticsearch_dsl==7.4.0",
         "requests==2.32.0",
-        "typing-extensions"
+        "typing-extensions",
+        "jsonpath-ng"
     ],
     extras_require={
         "dev": [

tests/core/test_reshaping.py

@@ -16,7 +16,7 @@
 import pytest
 from kgforge.core.resource import Resource
 from kgforge.core.forge import KnowledgeGraphForge
-from kgforge.core.reshaping import collect_values, Reshaper
+from kgforge.core.reshaping import collect_values, collect_values_jp, Reshaper
 
 
 def test_collect_values():
@@ -43,6 +43,32 @@ def test_collect_values():
         collect_values(None, "hasPart.url",ValueError)
 
 
+def test_collect_values_jasonpath():
+    simple = Resource(type="Experiment", url="file.gz")
+    r = collect_values_jp(simple, "url")
+    assert simple.url in r, "url should be in the list"
+    deep = Resource(type="Experiment", level1=Resource(level2=Resource(url="file.gz")))
+    r = collect_values_jp(deep, "level1.level2.url")
+    assert deep.level1.level2.url in r, "url should be in the list"
+    files = [Resource(type="Experiment", url=f"file{i}") for i in range(3)]
+    files.append(Resource(type="Experiment", contentUrl=f"file3"))
+    data_set = Resource(type="Dataset", hasPart=files)
+    r = collect_values_jp(data_set, "hasPart.contentUrl")
+    assert ["file3"] == r, "one element should be in the list"
+    r = collect_values_jp(data_set, "hasPart.url")
+    assert ["file0", "file1", "file2"] == r, "three elements should be in the list"
+    files = [Resource(type="Experiment", url=f"file{i}", encodingFormat=f"application/{ext}") for i, ext in enumerate(['csv', 'swc'])] 
+    data_set = Resource(type="Dataset", hasPart=files)
+    r = collect_values_jp(data_set, "hasPart.url", constraint_dict={'encodingFormat': 'application/swc'})
+    assert ["file1"] == r, "only the file with encodingFormat `application/swc` must be returned"
+    with pytest.raises(Exception):
+        collect_values_jp(data_set, "hasPart.url", constraint_dict={'encodingFormat': 'application/swc', 'contentUrl': 'something'})
+    with pytest.raises(Exception):
+        collect_values_jp(data_set, "fake.path")
+    with pytest.raises(ValueError):
+        collect_values_jp(None, "hasPart.url", ValueError)
+
+
 def test_reshape(config):
     forge = KnowledgeGraphForge(config)
     reshaper = Reshaper(versioned_id_template="{x.id}?_version={x._store_metadata.version}")