diff options
| -rw-r--r-- | python/Makefile | 7 | ||||
| -rw-r--r-- | python/refcat/attic.py | 1184 | ||||
| -rw-r--r-- | python/refcat/base.py | 2 | ||||
| -rw-r--r-- | python/refcat/cli.py | 29 | ||||
| -rw-r--r-- | python/refcat/report.py (renamed from python/refcat/techreport.py) | 5 | ||||
| -rw-r--r-- | python/refcat/utils.py | 31 |
6 files changed, 36 insertions, 1222 deletions
diff --git a/python/Makefile b/python/Makefile index 6821aed..d686297 100644 --- a/python/Makefile +++ b/python/Makefile @@ -38,13 +38,14 @@ else rsync -avP $^ ${DEPLOY_TARGET} endif -.PHONY: test -test: - pytest -v tests +# .PHONY: test +# test: +# pytest -v tests .PHONY: fmt fmt: yapf -p -i -r $(PKGNAME) tests + isort $(PKGNAME) .PHONY: clean clean: diff --git a/python/refcat/attic.py b/python/refcat/attic.py deleted file mode 100644 index 7633bab..0000000 --- a/python/refcat/attic.py +++ /dev/null @@ -1,1184 +0,0 @@ -# -# dBBBBBb dBBBBBBP dBBBBBBP dBP dBBBP -# BB -# dBP BB dBP dBP dBP dBP -# dBP BB dBP dBP dBP dBP -# dBBBBBBB dBP dBP dBP dBBBBP - - -class URLList(Refcat): - """ - TSV URL extracted, 44368911. - """ - def requires(self): - return URLTabs() - - def run(self): - stats = collections.Counter() - with self.input().open("rb") as f: - with self.output().open("w") as output: - for i, line in enumerate(f, start=1): - parts = line.decode("utf-8").strip().split("\t") - if len(parts) != 3: - stats["no-url"] += 1 - continue - urls = extract_urls(parts[2]) - stats["found-{}".format(len(urls))] += 1 - for link in urls: - link = link + "\n" - output.write(link.encode("utf-8")) - self.logger.debug(json.dumps(dict(stats))) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsDOI(Refcat): - """ - TSV with (ident, doi, full doc). - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - """ - Note: we want the full JSON document, so we use jq tostring, which - escapes "too much", hence we need to clean up with sed, unfortunately. - """ - # XXX: skate-doi could be an awk function, too. - # XXX: jq tostring might escape too much - output = shellout(r""" - zstdcat -T0 {input} | - LC_ALL=C tr -d '\t' | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.biblio.doi != null) | [.release_ident, .biblio.doi, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C awk -F $'\t' -v OFS='\t' '$2=tolower($2)' | - skate-to-doi -B -S -f 2 | - LC_ALL=C sort -S 30% --parallel 6 -T {tmpdir} -k2,2 | - zstd -c -T0 > {output} - """, - tmpdir=self.tmpdir, - n=self.n, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsPMID(Refcat): - """ - List of PMID, 74M refs seem to have one. - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.biblio.pmid != null and .biblio.doi == null) | [.release_ident, .biblio.pmid, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C sort -S 30% -T {tmpdir} -k2,2 | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - n=self.n, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsPMCID(Refcat): - """ - List of PMCID. - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.biblio.pmcid != null and .biblio.doi == null) | [.release_ident, .biblio.pmcid, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C sed -e 's@PMC@@g' | - LC_ALL=C sort -S 30% -T {tmpdir} -k2,2 | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - n=self.n, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsArxiv(Refcat): - """ - List of arxiv ids from refs. - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.biblio.arxiv_id != null and .biblio.doi == null) | [.release_ident, .biblio.arxiv_id, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C sort -S 30% -k2,2 -T {tmpdir} | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - n=self.n, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsTitles(Refcat): - """ - Extract titles. - - Contains many artifacts, e.g.: ! Accurate! and! efficient! insertional! - RNA!editing!in!isolated!Physarum!mitochondria.!RNA* - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.biblio.title != null and .biblio.doi == null) | - [.release_ident, (.biblio.title | ltrimstr(\" \") | rtrimstr(\" \") | gsub(\"\\n\"; \" \"))] | @tsv'" | - zstd -c -T0 > {output} - """, - input=self.input().path, - n=self.n) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsTitlesLower(Refcat): - """ - Unique lowercase titles; 223m46.443s. - """ - def requires(self): - return RefsTitles() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - tr '[:upper:]' '[:lower:]' | - LC_ALL=C sort -k2 | - zstd -T0 -c > {output} - """, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatDOI(Refcat): - """ - List of DOIs, lowercase on the fly. - """ - def requires(self): - return ReleaseExportReduced() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.ext_ids.doi != null) | [.ident, .ext_ids.doi, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C awk -F $'\t' -v OFS='\t' '$2=tolower($2)' | - LC_ALL=C sort -S 25% --parallel 6 -k2,2 -T {tmpdir} | - zstd -c -T0 > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path, - n=self.n) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatPMID(Refcat): - """ - List of PMID. - """ - def requires(self): - return ReleaseExportReduced() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.ext_ids.pmid != null) | [.ident, .ext_ids.pmid, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C sort -S 30% -T {tmpdir} -k2,2 | - zstd -c -T0 > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path, - n=self.n) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatPMCID(Refcat): - """ - List of PMCID. - """ - def requires(self): - return ReleaseExportReduced() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.ext_ids.pmcid != null) | [.ident, .ext_ids.pmcid, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C sed -e 's@PMC@@g' | - LC_ALL=C sort -S 30% -T {tmpdir} -k2,2 | - zstd -c -T0 > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path, - n=self.n) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatArxiv(Refcat): - """ - List of arxiv ids. - """ - def requires(self): - return ReleaseExportReduced() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.extra.arxiv.base_id != null) | [.ident, .extra.arxiv.base_id, (.|tostring)] | @tsv'" | - LC_ALL=C sed 's/\\\\/\\/g' | - LC_ALL=C sort -S 30% -k2,2 -T {tmpdir} | - zstd -c -T0 > {output}""", - tmpdir=self.tmpdir, - input=self.input().path, - n=self.n) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatTitles(Refcat): - """ - Get a list of non-normalized, sorted titles; ~104min. - """ - def requires(self): - return ReleaseExportReduced() - - def run(self): - output = shellout(r""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.title != null and .biblio.doi == null) | - [.ident, (.title | ltrimstr(\" \") | rtrimstr(\" \") | gsub(\"\\n\"; \" \"))] | @tsv'" | - zstd -c -T0 > {output} - """, - input=self.input().path, - n=self.n) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatTitlesLower(Refcat): - """ - Lowercase titles. - """ - def requires(self): - return FatcatTitles() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - tr '[:upper:]' '[:lower:]' | - LC_ALL=C sort -k2 | - zstd -T0 -c > {output} - """, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class FatcatSortedKeys(Refcat): - """ - Derive key and sort; key derivation (150M docs) took 39min; total 61min. - """ - def requires(self): - return ReleaseExportReduced() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-derive-key -b 50000 -verbose -f tsand | - LC_ALL=C sort -k2,2 -S 35% --parallel 6 --compress-program pzstd -T {tmpdir} | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class CommonDOI(Refcat): - """ - DOI that appear in the catalog and in the refs. - """ - def requires(self): - return { - "fatcat": FatcatDOI(), - "refs": RefsDOI(), - } - - def run(self): - f1 = shellout("zstdcat -T0 {fatcat} | cut -f2 > {output}", fatcat=self.input().get("fatcat").path) - f2 = shellout("zstdcat -T0 {refs} | cut -f2 > {output}", refs=self.input().get("refs").path) - output = shellout(""" LC_ALL=C comm {f1} {f2} | zstd -c > {output}""", f1=f1, f2=f2) - luigi.LocalTarget(output).move(self.output().path) - os.remove(f1) - os.remove(f2) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class CommonTitles(Refcat): - def requires(self): - return { - "fatcat": FatcatTitles(), - "refs": RefsTitles(), - } - - def run(self): - f1 = shellout("zstdcat -T0 {fatcat} | cut -f2 > {output}", fatcat=self.input().get("fatcat")) - f2 = shellout("zstdcat -T0 {refs} | cut -f2 > {output}", refs=self.input().get("refs")) - output = shellout(""" LC_ALL=C comm -12 {f1} {f2} | zstd -c > {output}""", f1=f1, f2=f2) - luigi.LocalTarget(output).move(self.output().path) - os.remove(f1) - os.remove(f2) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class CommonTitlesLower(Refcat): - def requires(self): - return { - "fatcat": FatcatTitlesLower(), - "refs": RefsTitlesLower(), - } - - def run(self): - f1 = shellout("zstdcat -T0 {fatcat} | cut -f2 > {output}", fatcat=self.input().get("fatcat").path) - f2 = shellout("zstdcat -T0 {refs} | cut -f2 > {output}", refs=self.input().get("refs").path) - output = shellout(""" comm -12 {f1} {f2} | zstd -c > {output}""", f1=f1, f2=f2) - luigi.LocalTarget(output).move(self.output().path) - os.remove(f1) - os.remove(f2) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsFatcatDOIJoin(Refcat): - """ - Join fatcat and refs DOI lists. - - Output will be like: - - ---- DOI -------------- ------ Fatcat ----------- -------- Refs ------------- - - 10.1001/2012.jama.10158 m7eoa3hbivcq5kgzzlepbifbna paygwq34z5hsnm5ypnwp2kz6wq - 10.1001/2012.jama.10159 xsw5qtrv3jg7pjoj67e3kijtwq 4ug6jvnedbau3nnkhuqegepw2q - 10.1001/2012.jama.10161 7m7yv5xkkjakxh3wuncqoctphe yllvkrxtgnhnfcyxwbj3swhegu - 10.1001/2012.jama.10368 dw2djv2qdzecncwmh4o7esg4ie ghgshdzpbranbcwsr4xsh3yfhy - - To count the number of citations per DOI, count occurences on the second - column. - - """ - def requires(self): - return { - "fatcat": FatcatDOI(), - "refs": RefsDOI(), - } - - def run(self): - output = shellout(""" - LC_ALL=C join -1 2 -2 2 <(zstdcat -T0 {fatcat}) <(zstdcat -T0 {refs}) | - zstd -T0 -c > {output} - """, - fatcat=self.input().get("fatcat").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst")) - - -class RefsFatcatPMIDJoin(Refcat): - """ - Join fatcat and refs PMID lists. - """ - def requires(self): - return { - "fatcat": FatcatPMID(), - "refs": RefsPMID(), - } - - def run(self): - output = shellout(""" - LC_ALL=C join -1 2 -2 2 <(zstdcat -T0 {fatcat}) <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - fatcat=self.input().get("fatcat").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst")) - - -class RefsFatcatPMCIDJoin(Refcat): - """ - Join fatcat and refs PMCID lists. - """ - def requires(self): - return { - "fatcat": FatcatPMCID(), - "refs": RefsPMCID(), - } - - def run(self): - output = shellout(""" - LC_ALL=C join -1 2 -2 2 <(zstdcat -T0 {fatcat}) <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - fatcat=self.input().get("fatcat").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst")) - - -class RefsFatcatArxivJoin(Refcat): - """ - Join fatcat, refs on arxiv (base) id. - """ - def requires(self): - return { - "fatcat": FatcatArxiv(), - "refs": RefsArxiv(), - } - - def run(self): - # TODO: We want a zippy join here (e.g. to generate biblioref docs). - output = shellout(""" - LC_ALL=C join -1 2 -2 2 <(zstdcat -T0 {fatcat}) <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - fatcat=self.input().get("fatcat").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst")) - - -class RefsFatcatTitleLowerJoin(Refcat): - """ - Join fatcat and refs titles. - - Output will be textfile (title, fatcat ident, refs ident). XXX: need to - filter out too common titles first. - """ - def requires(self): - return { - "fatcat": FatcatTitlesLower(), - "refs": RefsTitlesLower(), - } - - def run(self): - output = shellout(""" - LC_ALL=C join -1 2 -2 2 {fatcat} {refs} > {output} - """, - fatcat=self.input().get("fatcat").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv")) - - -class RefsFatcatGroupJoin(Refcat): - """ - Concat joins. - - 10.1001/2012.jama.11274 of7donzkmrbiddbyrr4guqbzum nncja4imynb4rajadrlbnoklxy - 10.1001/2012.jama.11274 of7donzkmrbiddbyrr4guqbzum noimcv5xdzd6hfqu2mebcrzr34 - 10.1001/2012.jama.11274 of7donzkmrbiddbyrr4guqbzum nqzg5lgdxvbhniy2hajlqd3aqi - ... - """ - def requires(self): - return [RefsFatcatDOIJoin(), RefsFatcatPMIDJoin(), RefsFatcatArxivJoin(), RefsFatcatPMCIDJoin()] - - def run(self): - _, tmpf = tempfile.mkstemp(prefix="refcat-") - for target in self.input(): - shellout("""cat {file} >> {output}""", file=target.path, output=tmpf) - luigi.LocalTarget(tmpf).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst")) - - -class RefsFatcatRanked(Refcat): - """ - Inbound count, ident; 32m34.142s. - - 15175 ui64apmob5gnrfwe7pwgk7egju - 15167 cejzj3ddszcdrmij7np36am5fa - 15165 2b2ok43pirduva7ai3745k5xa4 - 15158 cn4c33ctb5g5fax3touxjdmfle - 15155 rrlbmbro4rhwri3zawz3uhp5va - 15138 o62kjogy4zdyrlvy7cu7rlcs3m - """ - def requires(self): - return RefsFatcatGroupJoin() - - def run(self): - output = shellout(""" - zstdcat -T0 {file} | - LC_ALL=C sort -k2,3 -u | - LC_ALL=C cut -d ' ' -f 2 | - LC_ALL=C uniq -c | - LC_ALL=C sort -nr > {output} - """, - file=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv")) - - -# -# -# # TODO: merge refs docs and release docs, maybe add an source label, then -# # cluster; run verify and report on the number of similar records; generate a list of common titles -# # -# # TODO: find non-matched items and check for any pattern -# -# -class RefsCounter(Refcat): - """ - Key counts, see: ref_counter.py. - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - counts = collections.Counter() - with self.input().open("r") as f: - for i, line in enumerate(f): - obj = json.loads(line) - counts['total'] += 1 - for k in obj.keys(): - if k == 'biblio': - continue - elif k == 'ref_source': - counts["source_" + obj[k]] += 1 - elif obj.get(k): - counts["has_" + k] += 1 - biblio = obj.get('biblio') - if not biblio: - continue - for k in biblio.keys(): - if biblio.get(k): - counts["has_" + k] += 1 - if biblio.get('doi') or biblio.get('pmcid') or biblio.get('pmid') or biblio.get('arxiv_id'): - counts['has_any_extid'] += 1 - if biblio.get('container_name') and biblio.get('volume') and biblio.get('issue') and biblio.get( - 'pages'): - counts['has_container_volume_issue_pages'] += 1 - if biblio.get('title') and biblio.get('contrib_raw_names') and biblio.get('year'): - counts['has_title_contrib_year'] += 1 - if biblio.get('container_name') and biblio.get('contrib_raw_names') and biblio.get('year'): - counts['has_contrib_container_year'] += 1 - if biblio.get('title') and biblio.get('container_name') and biblio.get('year'): - counts['has_title_container_year'] += 1 - - if i % 1000000 == 0: - print(json.dumps(counts, indent=4, sort_keys=True), file=sys.stderr) - - with self.output().open("w") as output: - json.dump(counts, output) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json")) - - -class RefsKeyStats(Refcat): - """ - How many titles, DOI, etc. do we have in refs? - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - stats = { - "total": 0, - "no_biblio": 0, - "stats": collections.Counter(), - } - with self.input().open("r") as f: - for i, line in enumerate(f): - stats["total"] += 1 - doc = json.loads(line) - if "biblio" not in doc: - stats["no_biblio"] += 1 - continue - biblio = doc["biblio"] - key = "|".join(sorted(biblio.keys())) - stats["stats"][key] += 1 - if i % 1000000 == 0: - print(json.dumps(stats, indent=4, sort_keys=True), file=sys.stderr) - - with self.output().open("w") as output: - json.dumps(stats, output) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json")) - - -class RefsToRelease(Refcat): - """ - Convert a refs doc into a minimalistic release entity. Requires "skate" - tools - XXX: polish. - """ - def requires(self): - return RefsWithUnstructured() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-conv -f ref -w 24 -b 100000 | - zstd -T0 -c > {output} - """, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class RefsSortedKeys(Refcat): - """ - Derive key and sort; 1.8B json docs, took: 255min; 122k/s; key extration - almost 3h (might be faster with rust); 90G compressed. - - Keys based on title will have many empty keys; e.g. "2021-02-20", - 838,057,412 docs have no key. - """ - def requires(self): - return RefsToRelease() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-derive-key -skip-empty-keys -b 50000 -verbose -f tsand | - LC_ALL=C sort -k2,2 -S 35% --parallel 6 --compress-program pzstd -T {tmpdir} | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class RefsReleasesMerged(Refcat): - """ - Merge release and refs (in release form). - - wc: 1579687186 53137849922 913692185284 - """ - def requires(self): - return { - "release": ReleaseExportReduced(), - "refs": RefsToRelease(), - } - - def run(self): - _, f = tempfile.mkstemp(prefix="refcat-") - for k, v in self.input().items(): - shellout("cat {input} >> {output}", input=v.path, output=f) - luigi.LocalTarget(f).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class RefsTitleFrequency(Refcat): - """ - Dig into common titles. - """ - tmpdir = luigi.Parameter(default="/fast/tmp", description="set tempdir", significant=False) - - def requires(self): - return RefsTitlesLower() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - LC_ALL=C cut -f2 | - LC_ALL=C sort -T {tmpdir} -S20% --compress-program pzstd --parallel 6 | - LC_ALL=C uniq -c | - LC_ALL=C sort -nr | - zstd -c9 > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -# # XXX: After RefsReleasesMerged, we want to cluster. -# # python -m fuzzycat cluster -t tsandcrawler < data/re.json > cluster.json.zst -# # -# # Note: First run with no compression filled the disk, add zstd to fuzzycat. - - -class RefsFatcatSortedKeys(Refcat): - """ - Extract keys and sort. - """ - def requires(self): - return RefsReleasesMerged() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-derive-key -skip-empty-keys -b 50000 -verbose -f tsand | - LC_ALL=C sort -k2,2 -S 35% --parallel 6 --compress-program pzstd -T {tmpdir} | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class RefsFatcatClusters(Refcat): - """ - Group by clusters. Full set will be ~90GB compressed, about 40M clusters - (already filtered, so 2+ docs only, with at least on ref and one release, etc). - """ - def requires(self): - return RefsFatcatSortedKeys() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-cluster -both | - zstd -T0 -c9 > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -# ==== new style zippy biblioref generation - - -class BiblioRefFromFuzzyClusters(Refcat): - """ - Use "bref" mode to generate a biblioref document from verified clusters. - """ - def requires(self): - return RefsFatcatClusters() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-verify -m bref > {output} - """, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class BiblioRefZippyDOI(Refcat): - """ - Generate proposed biblioref docs from two sorted key files, sorted by DOI. - """ - def requires(self): - return { - "refs": RefsDOI(), - "releases": FatcatDOI(), - } - - def run(self): - output = shellout(r""" - skate-verify -m exact -r doi -R <(zstdcat -T0 {releases}) -F <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - releases=self.input().get("releases").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class BiblioRefZippyArxiv(Refcat): - """ - Generate proposed biblioref docs from two sorted key files, sorted by DOI. - """ - def requires(self): - return { - "refs": RefsArxiv(), - "releases": FatcatArxiv(), - } - - def run(self): - output = shellout(r""" - skate-verify -m exact -r arxiv -R <(zstdcat -T0 {releases}) -F <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - releases=self.input().get("releases").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class BiblioRefZippyPMID(Refcat): - """ - Generate proposed biblioref docs from two sorted key files, sorted by DOI. - """ - def requires(self): - return { - "refs": RefsPMID(), - "releases": FatcatPMID(), - } - - def run(self): - output = shellout(r""" - skate-verify -m exact -r pmid -R <(zstdcat -T0 {releases}) -F <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - releases=self.input().get("releases").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class BiblioRefZippyPMCID(Refcat): - """ - Generate proposed biblioref docs from two sorted key files, sorted by DOI. - """ - def requires(self): - return { - "refs": RefsPMCID(), - "releases": FatcatPMCID(), - } - - def run(self): - output = shellout(r""" - skate-verify -m exact -r pmcid -R <(zstdcat -T0 {releases}) -F <(zstdcat -T0 {refs}) | - zstd -c -T0 > {output} - """, - releases=self.input().get("releases").path, - refs=self.input().get("refs").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class BiblioRefV2(Refcat): - """ - A v1 set of biblioref schema docs. - """ - def requires(self): - return [ - BiblioRefZippyDOI(), - BiblioRefZippyArxiv(), - BiblioRefZippyPMID(), - BiblioRefZippyPMCID(), - BiblioRefFromFuzzyClusters() - ] - - def run(self): - _, tmpf = tempfile.mkstemp(prefix="refcat-") - for target in self.input(): - shellout(""" - zstdcat -T0 {input} | - skate-bref-id | - zstd -T0 >> {output} - """, - input=target.path, - output=tmpf) - luigi.LocalTarget(tmpf).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -# ==== V3 related - -# ==== RG title match example - - -class RGSitemapToRelease(Refcat): - """ - Turn sitemap data to skeleton release. - """ - def run(self): - link = "https://archive.org/download/rg_sitemap_2021_02_23/rg_sitemap_2021_02_23.ndj.zst" - output = shellout(""" - curl -sL {link} | - zstdcat -T0 | - parallel --block 10M -j 16 --pipe "jq -rc '{{\"title\": .title, \"extra\": {{\"rg\": {{\"sitemap\": true}}}}}}'" | - zstd -T0 -c > {output} - """, - link=link) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class RGSitemapFatcatMerged(Refcat): - """ - A minimal combined fatcat and RG dataset. - """ - def requires(self): - return [RGSitemapToRelease(), ReleaseExportTitleOnly()] - - def run(self): - _, tmpf = tempfile.mkstemp(prefix="refcat-") - for target in self.input(): - shellout("""cat {file} >> {output}""", file=target.path, output=tmpf) - luigi.LocalTarget(tmpf).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class RGSitemapFatcatSortedKeys(Refcat): - """ - Extract keys and sort. - """ - def requires(self): - return RGSitemapFatcatMerged() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-derive-key -b 50000 -verbose -f tsand | - LC_ALL=C sort -k2,2 -S 35% --parallel 6 --compress-program pzstd -T {tmpdir} | - zstd -T0 -c > {output}""", - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -# ==== MAG - - -class MAGDOI(Refcat): - """ - List of MAG DOI. - """ - def requires(self): - return MAGPapers() - - def run(self): - output = shellout(""" - unpigz -c {input} | - cut -f3 | - grep -v ^$ | - zstd -T0 -c > {output} - """, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -# ==== WikipediaCitations - - -class BiblioRefWikiDOISortedKeys(Refcat): - """ - Sorted DOI keys from wikipedia. - """ - def requires(self): - return WikipediaCitationsMinimalDataset() - - def run(self): - output = shellout(""" - cat {input} | - skate-wikipedia-doi | - LC_ALL=C sort -S 10% -k2,2 | - zstd -T0 -c > {output} - """, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd) - - -class BiblioRefWiki(Refcat): - def requires(self): - return { - "wiki": BiblioRefWikiDOISortedKeys(), - "releases": FatcatDOI(), - } - - def run(self): - output = shellout(r""" - skate-verify -m wiki -r doi -R <(zstdcat -T0 {releases}) -W <(zstdcat -T0 {wiki}) | - zstd -c -T0 > {output} - """, - releases=self.input().get("releases").path, - wiki=self.input().get("wiki").path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -# ==== Prepare unmatched - - -class BiblioRefSortedIdent(Refcat): - def requires(self): - return BiblioRefV2() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-derive-key -b 50000 -verbose -F source_release_ident | - LC_ALL=C sort -k2,2 -S 35% --parallel 6 --compress-program pzstd -T {tmpdir} | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class RefsSortedIdent(Refcat): - def requires(self): - return RefsWithUnstructured() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - skate-derive-key -b 50000 -verbose -F release_ident | - LC_ALL=C sort -k2,2 -S 35% --parallel 6 --compress-program pzstd -T {tmpdir} | - zstd -T0 -c > {output} - """, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -# OL - - -class WithISBN(Refcat): - """ - Keeps converted refs with isbn. - """ - def requires(self): - return RefsToRelease() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.ext_ids.isbn != null)'" | - zstd -T0 -c > {output} - """, - n=self.n, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) - - -class OpenLibraryWorks(Refcat): - """ - Extract just the works. - """ - def requires(self): - return OpenLibraryDump() - - def run(self): - output = shellout(""" - zstdcat -T0 {input} | - parallel -j {n} --block 10M --pipe "jq -rc 'select(.type == \\"work\\")'" | - zstd -T0 -c > {output} - """, - n=self.n, - tmpdir=self.tmpdir, - input=self.input().path) - luigi.LocalTarget(output).move(self.output().path) - - def output(self): - return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) diff --git a/python/refcat/base.py b/python/refcat/base.py index b36cae5..13e2324 100644 --- a/python/refcat/base.py +++ b/python/refcat/base.py @@ -4,13 +4,13 @@ Various utilities, copied from https://pypi.org/project/gluish/. import datetime import hashlib +import logging import os import random import re import string import subprocess import tempfile -import logging import luigi diff --git a/python/refcat/cli.py b/python/refcat/cli.py index a490553..6bb3073 100644 --- a/python/refcat/cli.py +++ b/python/refcat/cli.py @@ -18,6 +18,7 @@ To install completion run: $ source <(refcat.pyz completion) """ +import io import logging import os import subprocess @@ -32,9 +33,9 @@ from luigi.task_register import TaskClassNotFoundException from refcat import __version__ from refcat.deps import dump_deps, dump_deps_dot +from refcat.report import * from refcat.settings import LOGGING_CONF_FILE, settings from refcat.tasks import * -from refcat.techreport import * from refcat.utils import columnize # These are utility classes of luigi. @@ -58,6 +59,32 @@ suppress_task_names = [ ] +def columnize(lines, term_width=80, indent=0, pad=2): + n_lines = len(lines) + if n_lines == 0: + return + + col_width = max(len(line) for line in lines) + n_cols = int((term_width + pad - indent) / (col_width + pad)) + n_cols = min(n_lines, max(1, n_cols)) + + col_len = int(n_lines / n_cols) + (0 if n_lines % n_cols == 0 else 1) + if (n_cols - 1) * col_len >= n_lines: + n_cols -= 1 + + cols = [lines[i * col_len:i * col_len + col_len] for i in range(n_cols)] + + rows = list(zip(*cols)) + rows_missed = zip(*[col[len(rows):] for col in cols[:-1]]) + rows.extend(rows_missed) + + sio = io.StringIO() + for row in rows: + sio.write(" " * indent + (" " * pad).join(line.ljust(col_width) for line in row) + "\n") + + return sio.getvalue() + + def effective_task_names(): """ Runnable, relevant task names. diff --git a/python/refcat/techreport.py b/python/refcat/report.py index 4fe5771..8060aa3 100644 --- a/python/refcat/techreport.py +++ b/python/refcat/report.py @@ -2,8 +2,9 @@ Tasks for techreport. """ import luigi -from refcat.tasks import Refcat, OpenCitations, BrefWithDOI -from refcat.base import shellout, Zstd + +from refcat.base import Zstd, shellout +from refcat.tasks import BrefWithDOI, OpenCitations, Refcat class COCIDOIOnly(Refcat): diff --git a/python/refcat/utils.py b/python/refcat/utils.py deleted file mode 100644 index 30f3593..0000000 --- a/python/refcat/utils.py +++ /dev/null @@ -1,31 +0,0 @@ -""" -Assorted utilities. -""" - -import io - - -def columnize(lines, term_width=80, indent=0, pad=2): - n_lines = len(lines) - if n_lines == 0: - return - - col_width = max(len(line) for line in lines) - n_cols = int((term_width + pad - indent) / (col_width + pad)) - n_cols = min(n_lines, max(1, n_cols)) - - col_len = int(n_lines / n_cols) + (0 if n_lines % n_cols == 0 else 1) - if (n_cols - 1) * col_len >= n_lines: - n_cols -= 1 - - cols = [lines[i * col_len:i * col_len + col_len] for i in range(n_cols)] - - rows = list(zip(*cols)) - rows_missed = zip(*[col[len(rows):] for col in cols[:-1]]) - rows.extend(rows_missed) - - sio = io.StringIO() - for row in rows: - sio.write(" " * indent + (" " * pad).join(line.ljust(col_width) for line in row) + "\n") - - return sio.getvalue() |