From 6a224c316869ba2651094ad47e1d92e102524f85 Mon Sep 17 00:00:00 2001 From: Martin Czygan Date: Tue, 21 Sep 2021 15:55:11 +0200 Subject: reorganize notes --- notes/2021_09_review.md | 129 ++++++++++++++++++++++++++++++++++++++++++++ notes/Makefile | 9 +++- notes/known_issues.md | 17 ++++++ notes/steps.dot | 16 ------ notes/steps.png | Bin 29268 -> 0 bytes notes/todo.md | 94 -------------------------------- notes/todo_manual_review.md | 94 ++++++++++++++++++++++++++++++++ notes/workflow_schema.dot | 16 ++++++ notes/workflow_schema.png | Bin 0 -> 29268 bytes 9 files changed, 263 insertions(+), 112 deletions(-) create mode 100644 notes/2021_09_review.md delete mode 100644 notes/steps.dot delete mode 100644 notes/steps.png delete mode 100644 notes/todo.md create mode 100644 notes/todo_manual_review.md create mode 100644 notes/workflow_schema.dot create mode 100644 notes/workflow_schema.png 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/steps.dot b/notes/steps.dot deleted file mode 100644 index 365163f..0000000 --- a/notes/steps.dot +++ /dev/null @@ -1,16 +0,0 @@ -digraph steps { - node [shape=plaintext, fontname="helvetica"]; - graph [fontname = "helvetica"]; - edge [fontname = "helvetica"]; - - "release_export_expanded.json" -> "clustered"; - "clustered" -> "verified"; - "verified" -> "manual review"; - "manual review" -> "discover pattern"; - "manual review" -> "fix codepath"; - "fix codepath" -> "add verification test case"; - "discover pattern" -> "add verification test case"; - "discover pattern" -> "fix codepath"; - "fix codepath" -> "discover pattern"; - "add verification test case" -> "clustered"; -} diff --git a/notes/steps.png b/notes/steps.png deleted file mode 100644 index b321976..0000000 Binary files a/notes/steps.png and /dev/null differ diff --git a/notes/todo.md b/notes/todo.md deleted file mode 100644 index b3474f8..0000000 --- a/notes/todo.md +++ /dev/null @@ -1,94 +0,0 @@ -# TODO - -## Case mining - -* 2805572 undecided items - -## Examples - -* [x] https://fatcat.wiki/release/73pcaauzwbalvi7aqhv6vopxl4 https://fatcat.wiki/release/xp3oxb7tqbgaxdzkzbchfkcjn4 - -> "reference-entry", "entry" - vs other type, e.g. article - -* [x] https://fatcat.wiki/release/63g4ukdxajcqhdytqla6du3t3u https://fatcat.wiki/release/rz72bzfevzeofdeb342c6z45qu - -This example comes from datacite, the original md: - -* [https://api.datacite.org/dois/10.14288/1.0151581](https://api.datacite.org/dois/10.14288/1.0151581) - -Metadata similarly off on: - -* [https://commons.datacite.org/doi.org/10.14288/1.0011045?query=%2210.14288%22](https://commons.datacite.org/doi.org/10.14288/1.0011045?query=%2210.14288%22) -* [https://api.datacite.org/application/vnd.datacite.datacite+json/10.14288/1.0011045](https://api.datacite.org/application/vnd.datacite.datacite+json/10.14288/1.0011045) - -Picture categorized as article. Added custom rule as workaround. - -* [ ] https://fatcat.wiki/release/fwghjz4q7bdulismftuvagmgfu https://fatcat.wiki/release/jwbn7qohu5ggtc5okm4m7s5vja - -This seems to be a rerun or repackage of a science article: - -* https://stke.sciencemag.org/content/2006/316/tw466 -* https://science.sciencemag.org/content/310/5756/1865.6/tab-pdf - -STKE "fulltext" link does not lead anywhere; discontinued. - -* [x] https://fatcat.wiki/release/hhyyhosajjflpkufecx26gncwe https://fatcat.wiki/release/yxqwe4ns5vbntjzcse5igkgxk4 - -> book vs article-journal - -* [x] https://fatcat.wiki/release/ij3yuoh6lrh3tkrv5o7gfk6yyi https://fatcat.wiki/release/tur236mqljdfdnlzbbnks2sily - -> preprint and IEEE published article - -* [x] https://fatcat.wiki/release/neznj5fb4nf3tdqnotnbe34b6e https://fatcat.wiki/release/gcqdvvjiq5bphl7lpc4invi4vy - -> a standard document; DOI and DOIu -- which means "undated" (as per URL) -- -> https://landingpage.bsigroup.com/LandingPage/Undated?UPI=000000000030281171 - -* [ ] https://fatcat.wiki/release/fmi7hmpb3beotnj5kfyjjkolcy https://fatcat.wiki/release/isihxweh6ffxxhhrw2fthqymfa - -> Interestingly, the same item, altough different doi and URL, but image ID seems to be the same. - -* [x] https://fatcat.wiki/release/he334wpbobegxhptpkvvrufioq https://fatcat.wiki/release/td3ouhgtzbbe7ctevfnldqkoba - -> datacite version - -* [ ] https://fatcat.wiki/release/5zybwzmlsjexri6c3ma6tczf7q https://fatcat.wiki/release/35gerfmlirelfh3af6qug2oz4q -* [x] https://fatcat.wiki/release/rnso2swxzvfonemgzrth3arumi https://fatcat.wiki/release/caxa7qbfqvg3bkgz4nwvapgnvi - -> too common title - -* [ ] https://fatcat.wiki/release/tfhflmc2gnfrncsv2pm2b4oraq https://fatcat.wiki/release/gp7cnryj5bczhao6oor5sbjaoe Status.AMBIGUOUS OK.DUMMY - -> Two items, datacite, but both version 1; one lead to an inaccessible item - -* [ ] https://fatcat.wiki/release/s4kjrs3g5ndlvixz2fgpydeuja https://fatcat.wiki/release/jn25jn44vzbc3nsubabl2wndsa Status.AMBIGUOUS OK.DUMMY -* [ ] https://fatcat.wiki/release/5xbugnniynea3k3pllzrb4lfeu https://fatcat.wiki/release/e52xw23ec5cxzi6mkyfyxifvhu Status.AMBIGUOUS OK.DUMMY - -* [ ] https://fatcat.wiki/release/6udxu4cnk5egrcxtfrrqt3jcli https://fatcat.wiki/release/ett4oyembjfahhe3iwoc44dnja Status.AMBIGUOUS OK.DUMMY - -> todo: distinguish by page - -* [ ] https://fatcat.wiki/release/ehu6pdvzvvcmdoyq4l2yf4vciu https://fatcat.wiki/release/2omou6ehgjccbe6yjvr4wgnsha Status.AMBIGUOUS OK.DUMMY - -Blacklist fragment. - -* [ ] https://fatcat.wiki/release/zkqujozrx5cnjitmglclt6heqq https://fatcat.wiki/release/urr2gs4dsbbwdl7asgyqnwwtxy Status.AMBIGUOUS OK.DUMMY - -Blacklist fragment. - -* [ ] https://fatcat.wiki/release/yy2wzuaxhba7jht72mcjhxuaju https://fatcat.wiki/release/5b3lb2ebmrdp5nzxvohefmadre Status.AMBIGUOUS OK.DUMMY - -> Meeting abstract (ma) versus document. - -* [ ] https://fatcat.wiki/release/iwtrxnov2repzlgoi2at2md6tm https://fatcat.wiki/release/s5hm65waingwjmgf3plu76hzu4 Status.AMBIGUOUS OK.DUMMY - -> 10.1126 issue with moved items? - -* [ ] https://fatcat.wiki/release/b6wfpvotwrecdbygyn27kmihne https://fatcat.wiki/release/3vflegbxtrg4fknx4zyq3rf4im Status.AMBIGUOUS OK.DUMMY - -> The same content, but hard to separate. - -* [ ] https://fatcat.wiki/release/zlywxoy7cfexvaatziqp4ip5m4 https://fatcat.wiki/release/phqelg6oc5hs5dehhgmodcnh5u Status.AMBIGUOUS OK.DUMMY - -> one item contains more md, but the physical entity seems to be the same; 0058904_001 vs 0058904 diff --git a/notes/todo_manual_review.md b/notes/todo_manual_review.md new file mode 100644 index 0000000..b3474f8 --- /dev/null +++ b/notes/todo_manual_review.md @@ -0,0 +1,94 @@ +# TODO + +## Case mining + +* 2805572 undecided items + +## Examples + +* [x] https://fatcat.wiki/release/73pcaauzwbalvi7aqhv6vopxl4 https://fatcat.wiki/release/xp3oxb7tqbgaxdzkzbchfkcjn4 + +> "reference-entry", "entry" - vs other type, e.g. article + +* [x] https://fatcat.wiki/release/63g4ukdxajcqhdytqla6du3t3u https://fatcat.wiki/release/rz72bzfevzeofdeb342c6z45qu + +This example comes from datacite, the original md: + +* [https://api.datacite.org/dois/10.14288/1.0151581](https://api.datacite.org/dois/10.14288/1.0151581) + +Metadata similarly off on: + +* [https://commons.datacite.org/doi.org/10.14288/1.0011045?query=%2210.14288%22](https://commons.datacite.org/doi.org/10.14288/1.0011045?query=%2210.14288%22) +* [https://api.datacite.org/application/vnd.datacite.datacite+json/10.14288/1.0011045](https://api.datacite.org/application/vnd.datacite.datacite+json/10.14288/1.0011045) + +Picture categorized as article. Added custom rule as workaround. + +* [ ] https://fatcat.wiki/release/fwghjz4q7bdulismftuvagmgfu https://fatcat.wiki/release/jwbn7qohu5ggtc5okm4m7s5vja + +This seems to be a rerun or repackage of a science article: + +* https://stke.sciencemag.org/content/2006/316/tw466 +* https://science.sciencemag.org/content/310/5756/1865.6/tab-pdf + +STKE "fulltext" link does not lead anywhere; discontinued. + +* [x] https://fatcat.wiki/release/hhyyhosajjflpkufecx26gncwe https://fatcat.wiki/release/yxqwe4ns5vbntjzcse5igkgxk4 + +> book vs article-journal + +* [x] https://fatcat.wiki/release/ij3yuoh6lrh3tkrv5o7gfk6yyi https://fatcat.wiki/release/tur236mqljdfdnlzbbnks2sily + +> preprint and IEEE published article + +* [x] https://fatcat.wiki/release/neznj5fb4nf3tdqnotnbe34b6e https://fatcat.wiki/release/gcqdvvjiq5bphl7lpc4invi4vy + +> a standard document; DOI and DOIu -- which means "undated" (as per URL) -- +> https://landingpage.bsigroup.com/LandingPage/Undated?UPI=000000000030281171 + +* [ ] https://fatcat.wiki/release/fmi7hmpb3beotnj5kfyjjkolcy https://fatcat.wiki/release/isihxweh6ffxxhhrw2fthqymfa + +> Interestingly, the same item, altough different doi and URL, but image ID seems to be the same. + +* [x] https://fatcat.wiki/release/he334wpbobegxhptpkvvrufioq https://fatcat.wiki/release/td3ouhgtzbbe7ctevfnldqkoba + +> datacite version + +* [ ] https://fatcat.wiki/release/5zybwzmlsjexri6c3ma6tczf7q https://fatcat.wiki/release/35gerfmlirelfh3af6qug2oz4q +* [x] https://fatcat.wiki/release/rnso2swxzvfonemgzrth3arumi https://fatcat.wiki/release/caxa7qbfqvg3bkgz4nwvapgnvi + +> too common title + +* [ ] https://fatcat.wiki/release/tfhflmc2gnfrncsv2pm2b4oraq https://fatcat.wiki/release/gp7cnryj5bczhao6oor5sbjaoe Status.AMBIGUOUS OK.DUMMY + +> Two items, datacite, but both version 1; one lead to an inaccessible item + +* [ ] https://fatcat.wiki/release/s4kjrs3g5ndlvixz2fgpydeuja https://fatcat.wiki/release/jn25jn44vzbc3nsubabl2wndsa Status.AMBIGUOUS OK.DUMMY +* [ ] https://fatcat.wiki/release/5xbugnniynea3k3pllzrb4lfeu https://fatcat.wiki/release/e52xw23ec5cxzi6mkyfyxifvhu Status.AMBIGUOUS OK.DUMMY + +* [ ] https://fatcat.wiki/release/6udxu4cnk5egrcxtfrrqt3jcli https://fatcat.wiki/release/ett4oyembjfahhe3iwoc44dnja Status.AMBIGUOUS OK.DUMMY + +> todo: distinguish by page + +* [ ] https://fatcat.wiki/release/ehu6pdvzvvcmdoyq4l2yf4vciu https://fatcat.wiki/release/2omou6ehgjccbe6yjvr4wgnsha Status.AMBIGUOUS OK.DUMMY + +Blacklist fragment. + +* [ ] https://fatcat.wiki/release/zkqujozrx5cnjitmglclt6heqq https://fatcat.wiki/release/urr2gs4dsbbwdl7asgyqnwwtxy Status.AMBIGUOUS OK.DUMMY + +Blacklist fragment. + +* [ ] https://fatcat.wiki/release/yy2wzuaxhba7jht72mcjhxuaju https://fatcat.wiki/release/5b3lb2ebmrdp5nzxvohefmadre Status.AMBIGUOUS OK.DUMMY + +> Meeting abstract (ma) versus document. + +* [ ] https://fatcat.wiki/release/iwtrxnov2repzlgoi2at2md6tm https://fatcat.wiki/release/s5hm65waingwjmgf3plu76hzu4 Status.AMBIGUOUS OK.DUMMY + +> 10.1126 issue with moved items? + +* [ ] https://fatcat.wiki/release/b6wfpvotwrecdbygyn27kmihne https://fatcat.wiki/release/3vflegbxtrg4fknx4zyq3rf4im Status.AMBIGUOUS OK.DUMMY + +> The same content, but hard to separate. + +* [ ] https://fatcat.wiki/release/zlywxoy7cfexvaatziqp4ip5m4 https://fatcat.wiki/release/phqelg6oc5hs5dehhgmodcnh5u Status.AMBIGUOUS OK.DUMMY + +> one item contains more md, but the physical entity seems to be the same; 0058904_001 vs 0058904 diff --git a/notes/workflow_schema.dot b/notes/workflow_schema.dot new file mode 100644 index 0000000..365163f --- /dev/null +++ b/notes/workflow_schema.dot @@ -0,0 +1,16 @@ +digraph steps { + node [shape=plaintext, fontname="helvetica"]; + graph [fontname = "helvetica"]; + edge [fontname = "helvetica"]; + + "release_export_expanded.json" -> "clustered"; + "clustered" -> "verified"; + "verified" -> "manual review"; + "manual review" -> "discover pattern"; + "manual review" -> "fix codepath"; + "fix codepath" -> "add verification test case"; + "discover pattern" -> "add verification test case"; + "discover pattern" -> "fix codepath"; + "fix codepath" -> "discover pattern"; + "add verification test case" -> "clustered"; +} diff --git a/notes/workflow_schema.png b/notes/workflow_schema.png new file mode 100644 index 0000000..b321976 Binary files /dev/null and b/notes/workflow_schema.png differ -- cgit v1.2.3