diff options
| -rw-r--r-- | fuzzycat/config.py | 1 | ||||
| -rw-r--r-- | fuzzycat/matching.py | 77 | ||||
| -rw-r--r-- | fuzzycat/simple.py | 2 | ||||
| -rw-r--r-- | fuzzycat/utils.py | 2 | ||||
| -rw-r--r-- | fuzzycat/verify.py | 9 | ||||
| -rw-r--r-- | notes/2021_09_review.md | 129 | ||||
| -rw-r--r-- | notes/Makefile | 9 | ||||
| -rw-r--r-- | notes/known_issues.md | 17 | ||||
| -rw-r--r-- | notes/todo_manual_review.md (renamed from notes/todo.md) | 0 | ||||
| -rw-r--r-- | notes/workflow_schema.dot (renamed from notes/steps.dot) | 0 | ||||
| -rw-r--r-- | notes/workflow_schema.png (renamed from notes/steps.png) | bin | 29268 -> 29268 bytes | |||
| -rw-r--r-- | tests/test_matching.py | 45 | ||||
| -rw-r--r-- | tests/test_utils.py | 1 |
13 files changed, 272 insertions, 20 deletions
diff --git a/fuzzycat/config.py b/fuzzycat/config.py index 61050d1..d6989cf 100644 --- a/fuzzycat/config.py +++ b/fuzzycat/config.py @@ -1,4 +1,3 @@ - from dynaconf import Dynaconf settings = Dynaconf(envvar_prefix="FUZZYCAT") diff --git a/fuzzycat/matching.py b/fuzzycat/matching.py index c94a308..310dfc2 100644 --- a/fuzzycat/matching.py +++ b/fuzzycat/matching.py @@ -10,9 +10,9 @@ import requests from fatcat_openapi_client import ContainerEntity, DefaultApi, ReleaseEntity from fatcat_openapi_client.rest import ApiException +from fuzzycat.config import settings from fuzzycat.entities import entity_from_dict, entity_from_json from fuzzycat.utils import es_compat_hits_total -from fuzzycat.config import settings FATCAT_API_URL = settings.get("FATCAT_API_URL", "https://api.fatcat.wiki/v0") @@ -73,12 +73,83 @@ def match_release_fuzzy( if r: return [r] + + if release.title is not None and release.contribs is not None: + names = " ".join([c.raw_name for c in release.contribs]) + body = { + "track_total_hits": True, + "query": { + "bool": { + "must": [ + { + "match": { + "title": { + "query": release.title, + "operator": "AND", + "fuzziness": "AUTO", + }, + } + }, + { + "match": { + "contrib_names": { + "query": names, + "operator": "AND", + "fuzziness": "AUTO", + } + } + }, + ], + }, + }, + "size": size, + } + resp = es.search(body=body, index="fatcat_release") + if es_compat_hits_total(resp) > 0: + return response_to_entity_list(resp, entity_type=ReleaseEntity, size=size, api=api) + + body = { + "track_total_hits": True, + "query": { + "bool": { + "should": [ + { + "match": { + "title": { + "query": release.title, + "operator": "AND", + "fuzziness": "AUTO", + }, + } + }, + { + "match": { + "contrib_names": { + "query": names, + "operator": "AND", + "fuzziness": "AUTO", + } + } + }, + ], + }, + }, + "size": size, + } + resp = es.search(body=body, index="fatcat_release") + if es_compat_hits_total(resp) > 0: + return response_to_entity_list(resp, entity_type=ReleaseEntity, size=size, api=api) + + # Note: If the title is short, we will get lots of results here; do we need + # to check for title length or result set length length or result set + # length here? body = { + "track_total_hits": True, "query": { "match": { "title": { "query": release.title, - "operator": "AND" + "operator": "AND", } } }, @@ -91,6 +162,7 @@ def match_release_fuzzy( # Get fuzzy. # https://www.elastic.co/guide/en/elasticsearch/reference/current/common-options.html#fuzziness body = { + "track_total_hits": True, "query": { "match": { "title": { @@ -106,6 +178,7 @@ def match_release_fuzzy( if es_compat_hits_total(resp) > 0: return response_to_entity_list(resp, entity_type=ReleaseEntity, size=size, api=api) + # TODO: perform more queries on other fields. return [] diff --git a/fuzzycat/simple.py b/fuzzycat/simple.py index 8b206b1..ff59ba2 100644 --- a/fuzzycat/simple.py +++ b/fuzzycat/simple.py @@ -25,8 +25,8 @@ from fuzzycat.common import Reason, Status from fuzzycat.entities import entity_to_dict from fuzzycat.grobid_unstructured import grobid_parse_unstructured from fuzzycat.matching import match_release_fuzzy -from fuzzycat.verify import verify from fuzzycat.utils import clean_doi +from fuzzycat.verify import verify @dataclass diff --git a/fuzzycat/utils.py b/fuzzycat/utils.py index a1c5124..303daf6 100644 --- a/fuzzycat/utils.py +++ b/fuzzycat/utils.py @@ -81,6 +81,7 @@ def dict_key_exists(doc, path): else: return True + def clean_doi(raw: Optional[str]) -> Optional[str]: if not raw: return None @@ -95,6 +96,7 @@ def clean_doi(raw: Optional[str]) -> Optional[str]: raw = raw[:8] + raw[9:] return raw + def doi_prefix(v): """ Return the prefix of a DOI. diff --git a/fuzzycat/verify.py b/fuzzycat/verify.py index 1eeea40..5b90c47 100644 --- a/fuzzycat/verify.py +++ b/fuzzycat/verify.py @@ -90,9 +90,9 @@ from fuzzycat.common import Reason, Status from fuzzycat.data import (CONTAINER_NAME_BLACKLIST, PUBLISHER_BLACKLIST, TITLE_BLACKLIST, TITLE_FRAGMENT_BLACKLIST) from fuzzycat.entities import entity_to_dict -from fuzzycat.utils import (author_similarity_score, contains_chemical_formula, dict_key_exists, - doi_prefix, has_doi_prefix, jaccard, num_project, parse_page_string, - slugify_string, clean_doi) +from fuzzycat.utils import (author_similarity_score, clean_doi, contains_chemical_formula, + dict_key_exists, doi_prefix, has_doi_prefix, jaccard, num_project, + parse_page_string, slugify_string) Verify = collections.namedtuple("Verify", "status reason") @@ -597,8 +597,7 @@ def verify(a: Dict, b: Dict, min_title_length=5) -> Tuple[str, str]: try: a_parsed_pages = parse_page_string(glom(a, "pages")) b_parsed_pages = parse_page_string(glom(b, "pages")) - if (a_parsed_pages.count != None - and b_parsed_pages.count != None + if (a_parsed_pages.count != None and b_parsed_pages.count != None and abs(a_parsed_pages.count - b_parsed_pages.count) > 5): return Verify(Status.DIFFERENT, Reason.PAGE_COUNT) except (ValueError, PathAccessError): diff --git a/notes/2021_09_review.md b/notes/2021_09_review.md new file mode 100644 index 0000000..f15ed5b --- /dev/null +++ b/notes/2021_09_review.md @@ -0,0 +1,129 @@ +# Fuzzy matching review and retrospective + +> 2021-09-15 + +After [refcat](https://gitlab.com/internetarchive/refcat) has reached a +milestone, I'd like to review fuzzycat and fuzzy matching in general; this +should help pave the way to a slight redesign of the overall approach. + +## TL;DR + +* performance matters at scale and a faster language (e.g. Go) is essential +* for small scale, the api matters more than performance +* a lot of the code currently is base on specific schemas (e.g. release, a + specific elasticsearch mapping, etc), so not that much code is generic or + reusable - it also seems overkill to try to abstract the schema away + +## Ideas + +* [ ] use pydantic or dataclass to make schema more explicit +* [ ] extend type annotation coverage +* [ ] remove bulk stuff, remove clustering etc; improve the verification part +* [ ] use cases: work merging + +A few more things to revisit: + +* [ ] revisit journal matching; what is weak, strong? +* [ ] refactor: author list or string comparison +* [ ] go beyond title matching when querying elasticsearch +* [ ] better container name matching + +Take a look at: + +> https://github.com/djudd/human-name + +---- + +## Redesign ideas + +### Large scale processing + +JSON decoding and encoding does not seem to be the bottleneck, but working with +various, often optional fields gets expensive in Python (whereas in Go, we can +use a struct). + +The mapping stage in +[refcat/skate](https://gitlab.com/internetarchive/refcat/-/blob/3a79551dfe54ba668f7eee9de88625a0d33d9c7f/skate/map.go#L109-111) +is a simple operation (blob to fields), that can be implemented in isolation +and then [added to the command +line](https://gitlab.com/internetarchive/refcat/-/blob/3a79551dfe54ba668f7eee9de88625a0d33d9c7f/skate/cmd/skate-map/main.go#L67-87). +In skate, we already have over a dozen mappers working on various types. +There's even a bit of [map +middleware](https://gitlab.com/internetarchive/refcat/-/blob/3a79551dfe54ba668f7eee9de88625a0d33d9c7f/skate/map.go#L152-161). + +In fuzzycat, the +[Cluster](https://git.archive.org/webgroup/fuzzycat/-/blob/c587a084defe54103aa147b7ab91542a11a548b1/fuzzycat/cluster.py#L309-347) +class does mapping, via +[key](https://git.archive.org/webgroup/fuzzycat/-/blob/c587a084defe54103aa147b7ab91542a11a548b1/fuzzycat/cluster.py#L331), +[sorting](https://git.archive.org/webgroup/fuzzycat/-/blob/c587a084defe54103aa147b7ab91542a11a548b1/fuzzycat/cluster.py#L406-426), +and a specific +[grouping](https://git.archive.org/webgroup/fuzzycat/-/blob/c587a084defe54103aa147b7ab91542a11a548b1/fuzzycat/cluster.py#L428-454) +all in one go. + +For example, we did not use the single cluster document in refcat/skate anymore +(there, we keep two separate files and use an extra +[zipkey](https://gitlab.com/internetarchive/refcat/-/blob/3a79551dfe54ba668f7eee9de88625a0d33d9c7f/skate/zipkey/zipkey.go#L23-33) +type, which is a slightly generalized +[comm](https://en.wikipedia.org/wiki/Comm), e.g. it allows to run a function +over a cluster of documents (coming from currently two streams). + +A higher level command could encapsulate the whole pipeline, without needed an extra framework like luigi: + + inputs A B + | | + mapped M1 M2 + | | + sorted S1 S2 + \ / + \ / + reduced V + | + | + C + +> Not sure, if we need mappers at all, if we have them in refcat. + +An a command could look like this. + + $ fuzzycat pipeline -a A.json -b B.json --mapper-a "tn" --mapper-b "tn" --reduce "bref" + +Nice, if this would actually run fast. Could also be run programmatically: + + output = fuzzycat_pipeline(a="A.json", b="B.json", mapper_a="tn", mapper_b="tn", reduce="bref") + +Mappers should have a minimal scope; each mapper will have a format it can work +on. Reducers will have two inputs types specified. + +### Running continuously + +> With a couple of the inputs (metadata, extracted data, ...) getting updated +> all the time, it might for the moment be simpler to rerun the derivation in +> batch mode. + +A list of steps we would need to implement for continuous reference index updates: + +* a new metadata document arrives (e.g. via "changelog") +* if the metadata contains outbound references, nice; if not, we try to download the associated PDF, run grobid and get the references out that way + +At this point, we have the easier part - outbound references - covered. + +Where do the outbound references of all existing docs live? In the database +only, hence we cannot search for them currently. + +* [7ppmkfo5krb2zhefhwkwdp4mqe](https://search.fatcat.wiki/fatcat_release/_search?q=ident:7ppmkfo5krb2zhefhwkwdp4mqe) + says `ref_count` 12, but the list of refs we can only get via + [api](https://api.fatcat.wiki/v0/release/7ppmkfo5krb2zhefhwkwdp4mqe) + +We could add another elasticsearch index only for the raw refs. E.g. everytime +an item is updated, this index gets updated as well (taking refs from the API +and put them into ES). We can then query for any ID we find in the reference or +any string match, etc. Once we find e.g. ten documents, that have the document +in question in their reference list, we can update the reference index for each +of these documents. + +We could keep a (weekly) refs snapshot file around that would be used for +matching. The result would be the e.g. ten document, that refer to the document +in question. We can take their ids and update the document to establish the +link. The on-disk file (or files) should be all prepared, e.g. sorted by key, +so the lookup will be fast. + diff --git a/notes/Makefile b/notes/Makefile index 3a7dcaf..b4996f9 100644 --- a/notes/Makefile +++ b/notes/Makefile @@ -1,6 +1,11 @@ -steps.png: steps.dot +TARGETS = workflow_schema.png + +.PHONY: all +all: $(TARGETS) + +%.png: %.dot dot -Tpng $^ > $@ .PHONY: clean clean: - rm -rf steps.png + rm -rf $(TARGETS) diff --git a/notes/known_issues.md b/notes/known_issues.md index 32194fd..991de5c 100644 --- a/notes/known_issues.md +++ b/notes/known_issues.md @@ -102,3 +102,20 @@ $ python -m fuzzycat verify_single | jq . ] } ``` + +## "jaccard authors" can be too weak + +``` +$ python -m fuzzycat verify_single | jq . +{ + "extra": { + "q": "https://fatcat.wiki/release/search?q=canes" + }, + "a": "https://fatcat.wiki/release/ivhoiqvjt5cpxbdzzbuco7eciq", + "b": "https://fatcat.wiki/release/hprvn76ls5cbbkl2ypsyijojmu", + "r": [ + "strong", + "jaccard_authors" + ] +} +``` diff --git a/notes/todo.md b/notes/todo_manual_review.md index b3474f8..b3474f8 100644 --- a/notes/todo.md +++ b/notes/todo_manual_review.md diff --git a/notes/steps.dot b/notes/workflow_schema.dot index 365163f..365163f 100644 --- a/notes/steps.dot +++ b/notes/workflow_schema.dot diff --git a/notes/steps.png b/notes/workflow_schema.png Binary files differindex b321976..b321976 100644 --- a/notes/steps.png +++ b/notes/workflow_schema.png diff --git a/tests/test_matching.py b/tests/test_matching.py index 7ab7b11..90d1fee 100644 --- a/tests/test_matching.py +++ b/tests/test_matching.py @@ -9,7 +9,8 @@ from fatcat_openapi_client import ReleaseEntity from fuzzycat.entities import entity_from_dict from fuzzycat.matching import anything_to_entity, match_release_fuzzy -warnings.filterwarnings("ignore") # InsecureRequestWarning: Unverified HTTPS request is being made to host ... +warnings.filterwarnings( + "ignore") # InsecureRequestWarning: Unverified HTTPS request is being made to host ... from fuzzycat.matching import anything_to_entity, match_release_fuzzy from fuzzycat.config import settings @@ -28,6 +29,7 @@ FATCAT_SEARCH_URL = settings.get("FATCAT_SEARCH_URL", "https://search.fatcat.wik def is_not_reachable(url, timeout=3): return not is_reachable(url) + def is_reachable(url, timeout=3): """ Return true, if URL is reachable and returns HTTP 200. @@ -37,14 +39,21 @@ def is_reachable(url, timeout=3): except Exception: return False + @pytest.fixture def es_client(): return elasticsearch.Elasticsearch([FATCAT_SEARCH_URL]) -@pytest.mark.skipif(is_not_reachable(FATCAT_SEARCH_URL), - reason="{} not reachable, use e.g. FUZZYCAT_FATCAT_SEARCH_URL=localhost:9200 to override".format(FATCAT_SEARCH_URL)) +@pytest.mark.skipif( + is_not_reachable(FATCAT_SEARCH_URL), + reason="{} not reachable, use e.g. FUZZYCAT_FATCAT_SEARCH_URL=localhost:9200 to override". + format(FATCAT_SEARCH_URL)) def test_match_release_fuzzy(es_client, caplog): + """ + This test is tied to the current index contents, so if that changes, this + test may fail as well. + """ cases = ( ("wtv64ahbdzgwnan7rllwr3nurm", 1), ("eqcgtpav3na5jh56o5vjsvb4ei", 1), @@ -63,17 +72,35 @@ def test_match_release_fuzzy(es_client, caplog): "ext_ids": {} }, 5), ({ - "title": "The Future of Digital Scholarship", - "contribs": [{ - "raw_name": "Costantino Thanos" - }], + "title": "unlikelytitle", + "ext_ids": {} + }, 0), + ({ + "title": "Imminent dystopia", + "ext_ids": {} + }, 2), + ({ + "title": "", + "contribs": [{"raw_name": "Aristoteles"}], "ext_ids": {} }, 5), + # ({ + # "title": "Letter", + # "contribs": [{"raw_name": "Claudel"}], + # "ext_ids": {} + # }, 1), + # ({ + # "title": "The Future of Digital Scholarship", + # "contribs": [{ + # "raw_name": "Costantino Thanos" + # }], + # "ext_ids": {} + # }, 5), ) for i, (doc, count) in enumerate(cases): entity = entity_from_dict(doc, ReleaseEntity) result = match_release_fuzzy(entity, es=es_client) with caplog.at_level(logging.INFO): - logging.info("[{}] given {}, found {}, {}".format(i, entity.title, len(result), + logging.info("[{}] given title '{}', found {}, {}".format(i, entity.title, len(result), [v.title for v in result])) - assert len(result) == count + assert len(result) == count, doc diff --git a/tests/test_utils.py b/tests/test_utils.py index 21b85a4..957203f 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -124,6 +124,7 @@ def test_es_compat_hits_total(): for r, expected in cases: assert es_compat_hits_total(r) == expected + def test_clean_doi(): assert clean_doi(None) == None assert clean_doi("blah") == None |
