invenio-vocabularies 2.3.1__py2.py3-none-any.whl → 6.3.1__py2.py3-none-any.whl

invenio_vocabularies/contrib/names/config.py

@@ -28,12 +28,14 @@ class NamesSearchOptions(SearchOptions):
 
     suggest_parser_cls = SuggestQueryParser.factory(
         fields=[
-            "name^100",
-            "family_name^100",
             "given_name^100",
+            "name^70",
+            "family_name^50",
             "identifiers.identifier^20",
-            "affiliations.name^10",
+            "affiliations.name^20",
         ],
+        type="most_fields",  # https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-multi-match-query.html#multi-match-types
+        fuzziness="AUTO",
     )
 
     sort_default = "bestmatch"

invenio_vocabularies/contrib/names/datastreams.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2021-2022 CERN.
+# Copyright (C) 2021-2024 CERN.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -8,15 +8,123 @@
 
 """Names datastreams, transformers, writers and readers."""
 
+import csv
+import io
+import tarfile
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from datetime import timedelta
+
+import arrow
+import regex as re
+from flask import current_app
 from invenio_access.permissions import system_identity
 from invenio_records.dictutils import dict_lookup
 
+from invenio_vocabularies.contrib.names.s3client import S3OrcidClient
+
 from ...datastreams.errors import TransformerError
-from ...datastreams.readers import SimpleHTTPReader
+from ...datastreams.readers import BaseReader, SimpleHTTPReader
 from ...datastreams.transformers import BaseTransformer
 from ...datastreams.writers import ServiceWriter
 
 
+class OrcidDataSyncReader(BaseReader):
+    """ORCiD Data Sync Reader."""
+
+    def __init__(self, origin=None, mode="r", since=None, *args, **kwargs):
+        """Constructor.
+
+        :param origin: Data source (e.g. filepath).
+                       Can be none in case of piped readers.
+        """
+        super().__init__(origin=origin, mode=mode, *args, **kwargs)
+        self.s3_client = S3OrcidClient()
+        self.since = since
+
+    def _fetch_orcid_data(self, orcid_to_sync, bucket):
+        """Fetches a single ORCiD record from S3."""
+        # The ORCiD file key is located in a folder which name corresponds to the last three digits of the ORCiD
+        suffix = orcid_to_sync[-3:]
+        key = f"{suffix}/{orcid_to_sync}.xml"
+        try:
+            return self.s3_client.read_file(f"s3://{bucket}/{key}")
+        except Exception as e:
+            # TODO: log
+            return None
+
+    def _process_lambda_file(self, fileobj):
+        """Process the ORCiD lambda file and returns a list of ORCiDs to sync.
+
+        The decoded fileobj looks like the following:
+        orcid, path, date_created, last_modified
+        0000-0001-5109-3700, http://orcid.org/0000-0001-5109-3700, 2014-08-02 15:00:00.000,2021-08-02 15:00:00.000
+
+        Yield ORCiDs to sync until the last sync date is reached.
+        """
+        date_format = "YYYY-MM-DD HH:mm:ss.SSSSSS"
+        date_format_no_millis = "YYYY-MM-DD HH:mm:ss"
+        time_shift = current_app.config["VOCABULARIES_ORCID_SYNC_SINCE"]
+        if self.since:
+            time_shift = self.since
+        last_sync = arrow.now() - timedelta(**time_shift)
+
+        file_content = fileobj.read().decode("utf-8")
+
+        csv_reader = csv.DictReader(file_content.splitlines())
+
+        for row in csv_reader:  # Skip the header line
+            orcid = row["orcid"]
+
+            # Lambda file is ordered by last modified date
+            last_modified_str = row["last_modified"]
+            try:
+                last_modified_date = arrow.get(last_modified_str, date_format)
+            except arrow.parser.ParserError:
+                last_modified_date = arrow.get(last_modified_str, date_format_no_millis)
+
+            if last_modified_date < last_sync:
+                break
+            yield orcid
+
+    def _iter(self, orcids):
+        """Iterates over the ORCiD records yielding each one."""
+        with ThreadPoolExecutor(
+            max_workers=current_app.config["VOCABULARIES_ORCID_SYNC_MAX_WORKERS"]
+        ) as executor:
+            futures = [
+                executor.submit(
+                    self._fetch_orcid_data,
+                    orcid,
+                    current_app.config["VOCABULARIES_ORCID_SUMMARIES_BUCKET"],
+                )
+                for orcid in orcids
+            ]
+            for future in as_completed(futures):
+                result = future.result()
+                if result is not None:
+                    yield result
+
+    def read(self, item=None, *args, **kwargs):
+        """Streams the ORCiD lambda file, process it to get the ORCiDS to sync and yields it's data."""
+        # Read the file from S3
+        tar_content = self.s3_client.read_file(
+            "s3://orcid-lambda-file/last_modified.csv.tar"
+        )
+
+        orcids_to_sync = []
+        # Opens tar file and process it
+        with tarfile.open(fileobj=io.BytesIO(tar_content)) as tar:
+            # Iterate over each member (file or directory) in the tar file
+            for member in tar.getmembers():
+                # Extract the file
+                extracted_file = tar.extractfile(member)
+                if extracted_file:
+                    # Process the file and get the ORCiDs to sync
+                    orcids_to_sync.extend(self._process_lambda_file(extracted_file))
+
+        yield from self._iter(orcids_to_sync)
+
+
 class OrcidHTTPReader(SimpleHTTPReader):
     """ORCiD HTTP Reader."""
 
@@ -30,9 +138,26 @@ class OrcidHTTPReader(SimpleHTTPReader):
         super().__init__(origin, *args, **kwargs)
 
 
+DEFAULT_NAMES_EXCLUDE_REGEX = r"[\p{P}\p{S}\p{Nd}\p{No}\p{Emoji}--,.()\-']"
+"""Regex to filter out names with punctuations, symbols, decimal numbers and emojis."""
+
+
 class OrcidTransformer(BaseTransformer):
     """Transforms an ORCiD record into a names record."""
 
+    def __init__(
+        self, *args, names_exclude_regex=DEFAULT_NAMES_EXCLUDE_REGEX, **kwargs
+    ) -> None:
+        """Constructor."""
+        self._names_exclude_regex = names_exclude_regex
+        super().__init__()
+
+    def _is_valid_name(self, name):
+        """Check whether the name passes the regex."""
+        if not self._names_exclude_regex:
+            return True
+        return not bool(re.search(self._names_exclude_regex, name, re.UNICODE | re.V1))
+
     def apply(self, stream_entry, **kwargs):
         """Applies the transformation to the stream entry."""
         record = stream_entry.entry
@@ -42,6 +167,11 @@ class OrcidTransformer(BaseTransformer):
         name = person.get("name")
         if name is None:
             raise TransformerError(f"Name not found in ORCiD entry.")
+        if name.get("family-name") is None:
+            raise TransformerError(f"Family name not found in ORCiD entry.")
+
+        if not self._is_valid_name(name["given-names"] + name["family-name"]):
+            raise TransformerError(f"Invalid characters in name.")
 
         entry = {
             "id": orcid_id,
@@ -89,6 +219,7 @@ class NamesServiceWriter(ServiceWriter):
 
 VOCABULARIES_DATASTREAM_READERS = {
     "orcid-http": OrcidHTTPReader,
+    "orcid-data-sync": OrcidDataSyncReader,
 }
 
 
@@ -109,10 +240,15 @@ DATASTREAM_CONFIG = {
         {
             "type": "tar",
             "args": {
-                "regex": ".xml$",
+                "regex": "\\.xml$",
+            },
+        },
+        {
+            "type": "xml",
+            "args": {
+                "root_element": "record",
             },
         },
-        {"type": "xml"},
     ],
     "transformers": [{"type": "orcid"}],
     "writers": [
@@ -128,3 +264,35 @@ DATASTREAM_CONFIG = {
 
 An origin is required for the reader.
 """
+
+# TODO: Used on the jobs and should be set as a "PRESET" (naming to be defined)
+ORCID_PRESET_DATASTREAM_CONFIG = {
+    "readers": [
+        {
+            "type": "orcid-data-sync",
+        },
+        {
+            "type": "xml",
+            "args": {
+                "root_element": "record",
+            },
+        },
+    ],
+    "transformers": [{"type": "orcid"}],
+    "writers": [
+        {
+            "type": "async",
+            "args": {
+                "writer": {
+                    "type": "names-service",
+                }
+            },
+        }
+    ],
+    "batch_size": 1000,
+    "write_many": True,
+}
+"""ORCiD Data Stream configuration.
+
+An origin is required for the reader.
+"""

invenio_vocabularies/contrib/names/jsonschemas/names/name-v1.0.0.json

@@ -8,6 +8,9 @@
     "$schema": {
       "$ref": "local://definitions-v1.0.0.json#/$schema"
     },
+    "tags": {
+      "$ref": "local://vocabularies/definitions-v1.0.0.json#/tags"
+    },
     "scheme": {
       "description": "Identifier of the name scheme.",
       "$ref": "local://definitions-v1.0.0.json#/identifier"

invenio_vocabularies/contrib/names/mappings/os-v1/names/name-v1.0.0.json

@@ -24,6 +24,9 @@
       "id": {
         "type": "keyword"
       },
+      "tags": {
+        "type": "keyword"
+      },
       "name_sort": {
         "type": "keyword"
       },

invenio_vocabularies/contrib/names/mappings/os-v1/names/name-v2.0.0.json

@@ -0,0 +1,150 @@
+{
+  "settings": {
+    "analysis": {
+      "char_filter": {
+        "strip_special_chars": {
+          "type": "pattern_replace",
+          "pattern": "[\\p{Punct}\\p{S}]",
+          "replacement": ""
+        }
+      },
+      "analyzer": {
+        "accent_edge_analyzer": {
+          "tokenizer": "standard",
+          "type": "custom",
+          "char_filter": ["strip_special_chars"],
+          "filter": [
+            "lowercasepreserveoriginal",
+            "asciifoldingpreserveoriginal",
+            "edgegrams"
+          ]
+        },
+        "accent_analyzer": {
+          "tokenizer": "standard",
+          "type": "custom",
+          "char_filter": ["strip_special_chars"],
+          "filter": [
+            "lowercasepreserveoriginal",
+            "asciifoldingpreserveoriginal"
+          ]
+        }
+      },
+      "normalizer": {
+        "accent_normalizer": {
+          "type": "custom",
+          "char_filter": ["strip_special_chars"],
+          "filter": [
+            "lowercase",
+            "asciifolding"
+          ]
+        }
+      },
+      "filter": {
+        "lowercasepreserveoriginal": {
+          "type": "lowercase",
+          "preserve_original": true
+        },
+        "asciifoldingpreserveoriginal": {
+          "type": "asciifolding",
+          "preserve_original": true
+        },
+        "edgegrams": {
+          "type": "edge_ngram",
+          "min_gram": 2,
+          "max_gram": 20
+        }
+      }
+    }
+  },
+  "mappings": {
+    "dynamic": "strict",
+    "properties": {
+      "$schema": {
+        "type": "keyword",
+        "index": "false"
+      },
+      "created": {
+        "type": "date"
+      },
+      "updated": {
+        "type": "date"
+      },
+      "indexed_at": {
+        "type": "date"
+      },
+      "uuid": {
+        "type": "keyword"
+      },
+      "version_id": {
+        "type": "integer"
+      },
+      "id": {
+        "type": "keyword"
+      },
+      "tags": {
+        "type": "keyword"
+      },
+      "name_sort": {
+        "type": "keyword"
+      },
+      "name": {
+        "type": "text",
+        "analyzer": "accent_edge_analyzer",
+        "search_analyzer": "accent_analyzer",
+        "copy_to": "name_sort"
+      },
+      "given_name": {
+        "type": "text",
+        "analyzer": "accent_edge_analyzer",
+        "search_analyzer": "accent_analyzer"
+      },
+      "family_name": {
+        "type": "text"
+      },
+      "identifiers": {
+        "properties": {
+          "identifier": {
+            "type": "keyword",
+            "normalizer": "accent_normalizer"
+          },
+          "scheme": {
+            "type": "keyword"
+          }
+        }
+      },
+      "affiliations": {
+        "type": "object",
+        "properties": {
+          "@v": {
+            "type": "keyword"
+          },
+          "id": {
+            "type": "keyword"
+          },
+          "name": {
+            "type": "text",
+            "analyzer": "accent_edge_analyzer",
+            "search_analyzer": "accent_analyzer"
+          }
+        }
+      },
+      "pid": {
+        "type": "object",
+        "properties": {
+          "pk": {
+            "type": "integer"
+          },
+          "pid_type": {
+            "type": "keyword"
+          },
+          "obj_type": {
+            "type": "keyword"
+          },
+          "status": {
+            "type": "keyword"
+          }
+        }
+      }
+    }
+  }
+}

invenio_vocabularies/contrib/names/mappings/os-v2/names/name-v1.0.0.json

@@ -24,6 +24,9 @@
       "id": {
         "type": "keyword"
       },
+      "tags": {
+        "type": "keyword"
+      },
       "name_sort": {
         "type": "keyword"
       },

invenio_vocabularies/contrib/names/mappings/os-v2/names/name-v2.0.0.json

@@ -0,0 +1,150 @@
+{
+  "settings": {
+    "analysis": {
+      "char_filter": {
+        "strip_special_chars": {
+          "type": "pattern_replace",
+          "pattern": "[\\p{Punct}\\p{S}]",
+          "replacement": ""
+        }
+      },
+      "analyzer": {
+        "accent_edge_analyzer": {
+          "tokenizer": "standard",
+          "type": "custom",
+          "char_filter": ["strip_special_chars"],
+          "filter": [
+            "lowercasepreserveoriginal",
+            "asciifoldingpreserveoriginal",
+            "edgegrams"
+          ]
+        },
+        "accent_analyzer": {
+          "tokenizer": "standard",
+          "type": "custom",
+          "char_filter": ["strip_special_chars"],
+          "filter": [
+            "lowercasepreserveoriginal",
+            "asciifoldingpreserveoriginal"
+          ]
+        }
+      },
+      "normalizer": {
+        "accent_normalizer": {
+          "type": "custom",
+          "char_filter": ["strip_special_chars"],
+          "filter": [
+            "lowercase",
+            "asciifolding"
+          ]
+        }
+      },
+      "filter": {
+        "lowercasepreserveoriginal": {
+          "type": "lowercase",
+          "preserve_original": true
+        },
+        "asciifoldingpreserveoriginal": {
+          "type": "asciifolding",
+          "preserve_original": true
+        },
+        "edgegrams": {
+          "type": "edge_ngram",
+          "min_gram": 2,
+          "max_gram": 20
+        }
+      }
+    }
+  },
+  "mappings": {
+    "dynamic": "strict",
+    "properties": {
+      "$schema": {
+        "type": "keyword",
+        "index": "false"
+      },
+      "created": {
+        "type": "date"
+      },
+      "updated": {
+        "type": "date"
+      },
+      "indexed_at": {
+        "type": "date"
+      },
+      "uuid": {
+        "type": "keyword"
+      },
+      "version_id": {
+        "type": "integer"
+      },
+      "id": {
+        "type": "keyword"
+      },
+      "tags": {
+        "type": "keyword"
+      },
+      "name_sort": {
+        "type": "keyword"
+      },
+      "name": {
+        "type": "text",
+        "analyzer": "accent_edge_analyzer",
+        "search_analyzer": "accent_analyzer",
+        "copy_to": "name_sort"
+      },
+      "given_name": {
+        "type": "text",
+        "analyzer": "accent_edge_analyzer",
+        "search_analyzer": "accent_analyzer"
+      },
+      "family_name": {
+        "type": "text"
+      },
+      "identifiers": {
+        "properties": {
+          "identifier": {
+            "type": "keyword",
+            "normalizer": "accent_normalizer"
+          },
+          "scheme": {
+            "type": "keyword"
+          }
+        }
+      },
+      "affiliations": {
+        "type": "object",
+        "properties": {
+          "@v": {
+            "type": "keyword"
+          },
+          "id": {
+            "type": "keyword"
+          },
+          "name": {
+            "type": "text",
+            "analyzer": "accent_edge_analyzer",
+            "search_analyzer": "accent_analyzer"
+          }
+        }
+      },
+      "pid": {
+        "type": "object",
+        "properties": {
+          "pk": {
+            "type": "integer"
+          },
+          "pid_type": {
+            "type": "keyword"
+          },
+          "obj_type": {
+            "type": "keyword"
+          },
+          "status": {
+            "type": "keyword"
+          }
+        }
+      }
+    }
+  }
+}

invenio_vocabularies/contrib/names/mappings/v7/names/name-v1.0.0.json

@@ -24,6 +24,9 @@
       "id": {
         "type": "keyword"
       },
+      "tags": {
+        "type": "keyword"
+      },
       "name_sort": {
         "type": "keyword"
       },

invenio_vocabularies/contrib/names/names.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2021 CERN.
+# Copyright (C) 2021-2024 CERN.
 #
 # Invenio-Vocabularies is free software; you can redistribute it and/or
 # modify it under the terms of the MIT License; see LICENSE file for more
@@ -8,6 +8,7 @@
 
 """Vocabulary names."""
 
+from flask_resources import JSONSerializer, ResponseHandler
 from invenio_db import db
 from invenio_records.dumpers import SearchDumper
 from invenio_records.dumpers.indexedat import IndexedAtDumperExt
@@ -18,8 +19,10 @@ from invenio_records_resources.records.systemfields import (
     ModelPIDField,
     PIDListRelation,
 )
+from invenio_records_resources.resources.records.headers import etag_headers
+
+from invenio_vocabularies.contrib.names.permissions import NamesPermissionPolicy
 
-from ...services.permissions import PermissionPolicy
 from ..affiliations.api import Affiliation
 from .config import NamesSearchOptions, service_components
 from .schema import NameSchema
@@ -47,6 +50,7 @@ record_type = RecordTypeFactory(
     },
     schema_version="1.0.0",
     schema_path="local://names/name-v1.0.0.json",
+    index_name="names-name-v2.0.0",
     record_relations=name_relations,
     record_dumper=SearchDumper(
         model_fields={"pid": ("id", str)},
@@ -60,7 +64,15 @@ record_type = RecordTypeFactory(
     service_schema=NameSchema,
     search_options=NamesSearchOptions,
     service_components=service_components,
-    permission_policy_cls=PermissionPolicy,
+    permission_policy_cls=NamesPermissionPolicy,
     # Resource layer
     endpoint_route="/names",
+    resource_cls_attrs={
+        "response_handlers": {
+            "application/json": ResponseHandler(JSONSerializer(), headers=etag_headers),
+            "application/vnd.inveniordm.v1+json": ResponseHandler(
+                JSONSerializer(), headers=etag_headers
+            ),
+        }
+    },
 )

invenio_vocabularies/contrib/names/permissions.py

@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020-2024 CERN.
+#
+# Invenio-Vocabularies is free software; you can redistribute it and/or
+# modify it under the terms of the MIT License; see LICENSE file for more
+# details.
+
+"""Vocabulary permissions."""
+
+from invenio_records_permissions.generators import AuthenticatedUser, SystemProcess
+
+from ...services.permissions import PermissionPolicy
+
+
+class NamesPermissionPolicy(PermissionPolicy):
+    """Permission policy."""
+
+    can_search = [SystemProcess(), AuthenticatedUser()]
+    can_read = [SystemProcess(), AuthenticatedUser()]