diff options
| -rw-r--r-- | Pipfile | 2 | ||||
| -rw-r--r-- | Pipfile.lock | 501 | ||||
| -rw-r--r-- | fuzzycat/matching.py | 91 | ||||
| -rw-r--r-- | setup.py | 3 |
4 files changed, 376 insertions, 221 deletions
@@ -24,6 +24,8 @@ nltk = "*" regex = "*" pytest-cov = "*" glom = "*" +elasticsearch = "*" +elasticsearch-dsl = "*" [requires] python_version = "3.7" diff --git a/Pipfile.lock b/Pipfile.lock index 923ff3b..6f0fb6e 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "2302ed99d06867bc58dd112e5cc4cff090efda5f8be705ba1124c29771e31c82" + "sha256": "98b3f52b4b9617c7b902cf7288f34a4de6653446638e259de07cc0b639aa10b1" }, "pipfile-spec": 6, "requires": { @@ -26,22 +26,22 @@ }, "blis": { "hashes": [ - "sha256:19557b14763253ca3d4f6cfc9c9fe2eed3d65db14fa273ced8b0c17ce2bfda4a", - "sha256:221eef1b351063b0eb6682c7af2916884ce6c5015d95f6a28b7e45bea35e493c", - "sha256:3917491f366467a7339997dcfe501a282409cc50f461c6e1491d342a424442f1", - "sha256:55bacf2a1eb72ae728b665ac46433bcfee670de84f9bdf99987adf836fd92309", - "sha256:59cc549e904fd4169105f92d6fac94495eca228c357232f29444ae79981af974", - "sha256:6e65ef84205fadc1c41e59bd9d0d67fca8c41d463761b2dfe447003840172062", - "sha256:7f3e9564023e59a0abe9642a94408b3d2fe05ff205d800d512a67828b61819a8", - "sha256:9130e194f01124975a7bd76b8b65550f1f308610d596ec1992280b656e0c11be", - "sha256:ae53b880a1bca8115f1edccfa6e8800661c71347f9b75ed3f1af8549f080dd6b", - "sha256:b0fa63e4ca21a189698ca764367ae91ccba2274d885563c81205c1ac09f36fa6", - "sha256:c04165d196e16f652d21c2d1403a55fbae8721d74dbca1668fdfec6766687a12", - "sha256:ca0bccd31a216931ada487264ad07fa64a0b5a42b51c80cdebb1d3764b813d3b", - "sha256:e4e8b0dfd32e12f6d380b77a916ef15793756b856d8b00453a7d0ed4ba29f9ea" + "sha256:168fd7bd763ebe529aa25a066d3a6b89f4c3f492f6297f881df6942741b95787", + "sha256:4222bbc7b9c47bc3cf6f36f2241862c1512ca7ebac3828267a2e05ef6c47fc54", + "sha256:445e4838b809e99677f5c0982fb9af320f0d91328fb28c8097e5f1173c4df9d6", + "sha256:5b403deb2ad5515e1edb3c0867bccb5b974b461f24283d9219a3a761fd6dacc6", + "sha256:5c1a2023f7d8431daa8d87d32f539bb23e1a009500c37f9eba0ac7b3f20f73eb", + "sha256:5ecddc4c6daf80558154b091db0a9839bb15dbe65d2906a543a73b93fbce4f73", + "sha256:6814991b3e3193db4f9b2417174c6f24b9c0197409d864fa7628583bd2df1f0f", + "sha256:78a8e0ee72a42c3b2f5b9114500a781119995f76fa6c21d4b02c6fb9c21df2cc", + "sha256:7daa615a97d4f28db0f332b710bfe1900b15d0c25841c6d727965e4fd91e09cf", + "sha256:94890b2296f1449baa56aede46627ea7fc8de11c788f9c261ee38c2eb4a2cc7d", + "sha256:9f9b829480c12fc834549306821e5c51cb28b216ca5f88c5b2cfedbeb9daf67d", + "sha256:c2d8064217c326dd9a0dcbae294ffe8557263e2a00d76101ffa222b9c9d9c62d", + "sha256:d717b5dea407aac89a646908e7d9849105abab9c88a539c120518c200f899f4e" ], "markers": "python_version >= '3.6'", - "version": "==0.7.3" + "version": "==0.7.4" }, "boltons": { "hashes": [ @@ -60,10 +60,10 @@ }, "certifi": { "hashes": [ - "sha256:1f422849db327d534e3d0c5f02a263458c3955ec0aae4ff09b95f195c59f4edd", - "sha256:f05def092c44fbf25834a51509ef6e631dc19765ab8a57b4e7ab85531f0a9cf4" + "sha256:1a4995114262bffbc2413b159f2a1a480c969de6e6eb13ee966d470af86af59c", + "sha256:719a74fb9e33b9bd44cc7f3a8d94bc35e4049deebe19ba7d8e108280cfd59830" ], - "version": "==2020.11.8" + "version": "==2020.12.5" }, "chardet": { "hashes": [ @@ -122,21 +122,37 @@ }, "cymem": { "hashes": [ - "sha256:02c3994ee57003dd57d9a34417beb9597e51176e9378a757344347b72510ce8d", - "sha256:0f169ee07f30c2674ca811693cb13857e236dd7f92b4bc47b0f2bb201e27cc93", - "sha256:2baabeb408e4aaa0f51d7f6d8c53dd05f56decf34fb3f1f3180abe8755815890", - "sha256:2d40dfa4b4edf64541192966c67c2706e5058a9c6ce0bdc356e4d6ef1935c9ae", - "sha256:45b01ee36ce15aab6df041b4128de38016e3934274b934c44fec43de5100b64c", - "sha256:58f49a51bd8b76b260f38f8274ec2e4613c328423e0b543a503834de32dfa3c4", - "sha256:60b5d969f305a7598d86f34c93c37eb52b3388681e70b98081864f0f185da768", - "sha256:65e5759179b311b8350b82b29744324366e270f96095b16a8e249c73c3f9273f", - "sha256:7bb5791fde8dffa02005f158f5c98d64962adaf8501dac7a9b8156b8767c9a34", - "sha256:a61684d01a1413049e9874e073c9577d406d866eabe0d167c5ee15bbeae090a6", - "sha256:a61a4702dcc50ebd31fb86a90d1aba5526245af592d756c39c63d58d53360afc", - "sha256:ae283889f6f0036fb34d12358fe052d4ea9f5724f05177317f33f302f304b47c", - "sha256:f8f280f0aef46d32655b1b24ff049bea83b63365604b6c2decb112b44ed851fe" - ], - "version": "==2.0.4" + "sha256:01d3ea159f7a3f3192b1e800ed8207dac7586794d903a153198b9ea317f144bc", + "sha256:190e15d9cf2c3bde60ae37bddbae6568a36044dc4a326d84081a5fa08818eee0", + "sha256:1f0eb9b3d03623dcfc746cf8bff0663b0e347f4aea759965c8932087a0307ee9", + "sha256:3d48902d7441645835fefc7832df49feb5362c7300d182475b63a01d25ae44ef", + "sha256:4bd023c2477198b39b660c2a6b0242880649765ecee8461688a57fd4afd2bfc0", + "sha256:734d82d0d03c2ceb929bc1744c04dbe0a105e68a4947c8406056a36f86c41830", + "sha256:8ea57e6923f40eb51012352161bb5707c14a5a5ce901ff72021e59df06221655", + "sha256:9d72d69f7a62a280199c3aa7bc550685c47d6d0689b2d299e6492253b86d2437", + "sha256:a440d63577fcdc9c528c9cc026b7b4f8648193bac462bc0596c9eac10f9fba62", + "sha256:ce1e81c1d031f56b67bac2136e73b4512cbc794706cd570178972d54ba6115d8", + "sha256:d19f68b90411e02ab33b1654118337f96f41c13a3cd00c4f44f7abed2bc712e7", + "sha256:d307f7f6230d861a938837cae4b855226b6845a21c010242a15e9ce6853856cd", + "sha256:f2167c9959fcd639b95d51fa5efaa7c61eef8d686cb75a25412a914f428ce980" + ], + "version": "==2.0.5" + }, + "elasticsearch": { + "hashes": [ + "sha256:4ebd34fd223b31c99d9f3b6b6236d3ac18b3046191a37231e8235b06ae7db955", + "sha256:a725dd923d349ca0652cf95d6ce23d952e2153740cf4ab6daf4a2d804feeed48" + ], + "index": "pypi", + "version": "==7.10.1" + }, + "elasticsearch-dsl": { + "hashes": [ + "sha256:0ed75f6ff037e36b2397a8e92cae0ddde79b83adc70a154b8946064cb62f7301", + "sha256:9390d8e5cf82ebad3505e7f656e407259cf703f5a4035f211cef454127672572" + ], + "index": "pypi", + "version": "==7.3.0" }, "face": { "hashes": [ @@ -145,6 +161,14 @@ ], "version": "==20.1.1" }, + "fatcat-openapi-client": { + "hashes": [ + "sha256:2dfec611d1eb8396ba8812ea3c6dfdc250b098870aafcecf895ae31fa2a90c5f", + "sha256:fd7f3089d3cc223c1b560125b688e8ce0393ba76edfe87506464db7a1e38d0b1" + ], + "markers": "python_full_version >= '3.5.0'", + "version": "==0.3.2" + }, "ftfy": { "hashes": [ "sha256:51c7767f8c4b47d291fcef30b9625fb5341c06a31e6a3b627039c706c42f3720" @@ -196,33 +220,33 @@ }, "joblib": { "hashes": [ - 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"sha256:3d3f1470d26642e88bd3f73353cb6ff4c51ef7d5d7efef763238f4bc1f7e4e81", - "sha256:5ff3f5232b19fa4c5531641e480b7fad4598819f708a32eb815e6ea41c5fa313" + "sha256:38b658a3e4ecf9b4f6f8ff75ca16221ae3378b2e175d846b6b33ea3a20852cf5", + "sha256:d4f413aecb61c9779888c64ddf0c62910ad56dcbe857d8922bb505d4dbff0df1" ], "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", - "version": "==4.53.0" + "version": "==4.54.1" }, "traitlets": { "hashes": [ @@ -1104,6 +1162,7 @@ "sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c", "sha256:dafc7639cde7f1b6e1acc0f457842a83e722ccca8eef5270af2d74792619a89f" ], + "markers": "python_version < '3.8'", "version": "==3.7.4.3" }, "unidecode": { diff --git a/fuzzycat/matching.py b/fuzzycat/matching.py new file mode 100644 index 0000000..518198a --- /dev/null +++ b/fuzzycat/matching.py @@ -0,0 +1,91 @@ +import elasticsearch +from fatcat_openapi_client import ContainerEntity, ReleaseEntity + +def match_release_fuzzy(release: ReleaseEntity, size=5, es=None) -> List[ReleaseEntity]: + """ + Given a release entity, return a number similar release entities from + fatcat using Elasticsearch. + """ + assert isinstance(release, ReleaseEntity) + + if size is None or size == 0: + size = 10000 # or any large number + + if isinstance(es, str): + es = elasticsearch.Elasticsearch([es]) + if es is None: + es = elasticsearch.Elasticsearch() + + # Try to match by external identifier. + ext_ids = release.ext_ids + attrs = { + "doi": "doi", + "wikidata_qid": "wikidata_qid", + "isbn13": "isbn13", + "pmid": "pmid", + "pmcid": "pmcid", + "core": "code_id", + "arxiv": "arxiv_id", + "jstor": "jstor_id", + "ark": "ark_id", + "mag": "mag_id", + } + for attr, es_field in attrs.items(): + value = getattr(ext_ids, attr) + if not value: + continue + s = ( + elasticsearch_dsl.Search(using=es, index="fatcat_release") + .query("term", **{es_field: value}) + .extra(size=size) + ) + print(s) + resp = s.execute() + if len(resp) > 0: + return response_to_entity_list(resp, entity_type=ReleaseEntity) + + body = { + "query": {"match": {"title": {"query": release.title, "operator": "AND"}}}, + "size": size, + } + resp = es.search(body=body, index="fatcat_release") + if resp["hits"]["total"] > 0: + return response_to_entity_list(resp, entity_type=ReleaseEntity) + + # Get fuzzy. + # https://www.elastic.co/guide/en/elasticsearch/reference/current/common-options.html#fuzziness + body = { + "query": { + "match": { + "title": { + "query": release.title, + "operator": "AND", + "fuzziness": "AUTO", + } + } + }, + "size": size, + } + resp = es.search(body=body, index="fatcat_release") + if resp["hits"]["total"] > 0: + return response_to_entity_list(resp, entity_type=ReleaseEntity) + + # TODO: perform more queries on other fields. + return [] + + +def response_to_entity_list(response, size=5, entity_type=ReleaseEntity): + """ + Convert an elasticsearch result to a list of entities. Accepts both a + dictionary and an elasticsearch_dsl.response.Response. + + We take the ids from elasticsearch and retrieve entities via API. + """ + if isinstance(response, dict): + ids = [hit["_source"]["ident"] for hit in response["hits"]["hits"]][:size] + return retrieve_entity_list(ids, entity_type=entity_type) + elif isinstance(response, elasticsearch_dsl.response.Response): + ids = [hit.to_dict().get("ident") for hit in response] + return retrieve_entity_list(ids, entity_type=entity_type) + else: + raise ValueError("cannot convert {}".format(response)) @@ -31,6 +31,9 @@ with open("README.md", "r") as fh: "pydantic", "toml", "unidecode>=0.10", + "fatcat-openapi-client", # https://pypi.org/project/fatcat-openapi-client/ + "elasticsearch", + "elasticsearch-dsl", ], extras_require={"dev": [ "ipython", |