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authorMartin Czygan <martin.czygan@gmail.com>2021-03-21 00:36:54 +0100
committerMartin Czygan <martin.czygan@gmail.com>2021-03-21 00:36:54 +0100
commite00e979a8b144231ce16aafe6b8482e4104f5e37 (patch)
tree942af1fbb0eeb71625438a2aaa0b1d783b84db0e
parentc8d9268759f7da1e050658e135fac0c8f0b6fc53 (diff)
downloadrefcat-e00e979a8b144231ce16aafe6b8482e4104f5e37.tar.gz
refcat-e00e979a8b144231ce16aafe6b8482e4104f5e37.zip
initial import of python tasks
Diffstat
-rw-r--r--README.md2
-rw-r--r--python/.env.sample2
-rw-r--r--python/.gitignore135
-rw-r--r--python/.style.yapf5
-rw-r--r--python/Makefile50
-rw-r--r--python/README.md68
-rw-r--r--python/conf/logging.ini47
-rw-r--r--python/conf/settings.ini36
-rw-r--r--python/notes/data/oci_v1_10_1056_nejmoa1606220.json5825
-rw-r--r--python/notes/data/oci_v1_10_1056_nejmoa1606220_lookup.json647
-rw-r--r--python/notes/data_quality.md11
-rw-r--r--python/notes/version_0.md468
-rw-r--r--python/notes/version_1.md491
-rw-r--r--python/notes/version_1_fuzzy_stats.txt30
-rw-r--r--python/notes/version_2.md219
-rw-r--r--python/notes/version_3.md187
-rw-r--r--python/notes/wikipedia_citations_2020-07-14.md51
-rw-r--r--python/refcat/__init__.py1
-rw-r--r--python/refcat/cli.py251
-rw-r--r--python/refcat/deps.py29
-rw-r--r--python/refcat/settings.py16
-rw-r--r--python/refcat/tasks.py1366
-rw-r--r--python/refcat/utils.py268
-rw-r--r--python/setup.py42
-rw-r--r--python/tests/test_utils.py41
25 files changed, 10287 insertions, 1 deletions
diff --git a/README.md b/README.md
index f866297..680990a 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,3 @@
# cgraph
-Scholarly citation graph related code. \ No newline at end of file
+Scholarly citation graph related code.
diff --git a/python/.env.sample b/python/.env.sample
new file mode 100644
index 0000000..c2a7b7d
--- /dev/null
+++ b/python/.env.sample
@@ -0,0 +1,2 @@
+# Where the single executable is rsynced to (via Makefile).
+DEPLOY_TARGET=user@host:/path/to/bin
diff --git a/python/.gitignore b/python/.gitignore
new file mode 100644
index 0000000..e5a4723
--- /dev/null
+++ b/python/.gitignore
@@ -0,0 +1,135 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Text Editors
+*~
+*.swp
+
+settings.local.ini
+
+/tmp
+/refcat.pyz
diff --git a/python/.style.yapf b/python/.style.yapf
new file mode 100644
index 0000000..f518dee
--- /dev/null
+++ b/python/.style.yapf
@@ -0,0 +1,5 @@
+[style]
+
+based_on_style = pep8
+split_before_logical_operator = true
+column_limit = 160
diff --git a/python/Makefile b/python/Makefile
new file mode 100644
index 0000000..647a3c3
--- /dev/null
+++ b/python/Makefile
@@ -0,0 +1,50 @@
+# Makefile for refcat.
+
+# use .env if present, https://lithic.tech/blog/2020-05/makefile-dot-env
+ifneq (,$(wildcard ./.env))
+ include .env
+ export
+endif
+
+SHELL := /bin/bash
+PY_FILES := $(shell find . -name \*.py -print)
+PKGNAME := refcat
+
+# The "zipapp" we build, cf. PEP441, https://www.python.org/dev/peps/pep-0441/,
+# https://shiv.readthedocs.io/
+ZIPAPP := $(PKGNAME).pyz
+
+# IMPORTANT: Python version on dev and target must match (up to minor version)
+# e.g. for aitio, you might want to use:
+# make refcat.pyz PYTHON_INTERPRETER='"/usr/bin/env python3.7"'
+PYTHON_INTERPRETER := "/usr/bin/env python3.7"
+
+.PHONY: test
+test:
+ pytest -v tests
+
+$(ZIPAPP): $(PY_FILES)
+ # https://shiv.readthedocs.io/en/latest/cli-reference.html
+ # note: use SHIV_ROOT envvar to override expansion dir (e.g. if home is networked)
+ shiv --reproducible --compressed --entry-point refcat.cli:main --python $(PYTHON_INTERPRETER) --output-file $(ZIPAPP) .
+
+.PHONY: deploy
+deploy: $(ZIPAPP)
+ifndef DEPLOY_TARGET
+$(error DEPLOY_TARGET is not set)
+else
+ rsync -avP $^ ${DEPLOY_TARGET}
+endif
+
+.PHONY: fmt
+fmt:
+ yapf -p -i -r $(PKGNAME) tests
+
+.PHONY: clean
+clean:
+ rm -rf .pytest_cache/
+ rm -rf build/
+ rm -rf $(PKGNAME).egg-info/
+ rm -rf $(ZIPAPP)
+ find . -name "__pycache__" -exec rm -rf "{}" +
+
diff --git a/python/README.md b/python/README.md
new file mode 100644
index 0000000..81db0b0
--- /dev/null
+++ b/python/README.md
@@ -0,0 +1,68 @@
+# refcat (wip)
+
+Citation graph related tasks.
+
+* compagnon repository: [skate](https://github.com/miku/skate)
+
+Objective: Given data about
+[releases](https://guide.fatcat.wiki/entity_release.html) and references derive
+various artifacts, e.g.:
+
+* a citation graph; nodes are releases and an edge is a citation (currently, this graph has about 50M nodes and 870M edges)
+* a list of referenced entities, like ISSN (container), ISBN (book), URL (webpage), datasets (by URL, DOI, name, ...)
+
+## Ongoing Notes
+
+* [notes/version_0.md](version 0) (id only)
+* [notes/version_1.md](version 1) (id plus title)
+* [notes/version_2.md](version 2) (v1, full schema)
+
+## Deployment
+
+We are testing a zipapp based deployment (20s for packaging into a 10MB zip
+file, and copying to target).
+
+Caveat: The development machine needs the same python version (e.g. 3.7) as the
+target, e.g. for native dependencies. It is relatively easy to have multiple
+versions of Python available with [pyenv](https://github.com/pyenv/pyenv).
+
+```
+$ make refcat.pyz && rsync -avP refcat.pyz user@host:/usr/local/bin
+```
+
+On the target you can call (first run will be slower, e.g. 4s, subsequent runs
+at around 1s startup time).
+
+```
+$ refcat.pyz
+
+
+ ____ __
+ ________ / __/________ _/ /_
+ / ___/ _ \/ /_/ ___/ __ `/ __/
+ / / / __/ __/ /__/ /_/ / /_
+/_/ \___/_/ \___/\__,_/\__/
+
+Command line entry point for running various data tasks.
+
+General usage:
+
+ $ refcat TASK
+
+BASE: /bigger/.cache
+
+BiblioRef KeyDistribution RefsFatcatSortedKeys
+BiblioRefFromJoin RefCounter RefsFatcatTitleLowerJoin
+BiblioRefFuzzy Refcat RefsKeyStats
+CommonDOIs RefsArxiv RefsPMCID
+CommonTitles RefsDOIs RefsPMID
+CommonTitlesLower RefsDOIsLower RefsReleasesMerged
+FatcatArxiv RefsFatcatArxivJoin RefsTitleFrequency
+FatcatDOIs RefsFatcatClusterVerify RefsTitles
+FatcatDOIsLower RefsFatcatClusters RefsTitlesLower
+FatcatPMCID RefsFatcatDOIJoin RefsToRelease
+FatcatPMID RefsFatcatGroupJoin ReleaseExportExpanded
+FatcatTitles RefsFatcatPMCIDJoin URLList
+FatcatTitlesLower RefsFatcatPMIDJoin URLTabs
+Input RefsFatcatRanked
+```
diff --git a/python/conf/logging.ini b/python/conf/logging.ini
new file mode 100644
index 0000000..12d91f5
--- /dev/null
+++ b/python/conf/logging.ini
@@ -0,0 +1,47 @@
+# Logging config for luigi: https://luigi.readthedocs.io/en/stable/logging.html
+
+[loggers]
+keys=root,luigi_interface,gluish,urllib3
+
+[handlers]
+keys=consoleHandler
+
+[formatters]
+keys=simpleFormatter
+
+
+
+[logger_root]
+level = INFO
+handlers = consoleHandler
+propagate = 0
+
+[logger_luigi_interface]
+level = INFO
+handlers = consoleHandler
+qualname = luigi-interface
+propagate = 0
+
+[logger_gluish]
+level = DEBUG
+handlers = consoleHandler
+qualname = gluish
+propagate = 0
+
+[logger_urllib3]
+level = INFO
+handlers = consoleHandler
+qualname = urllib3
+propagate = 0
+
+[handler_consoleHandler]
+class = StreamHandler
+formatter = simpleFormatter
+args = (sys.stderr,)
+
+
+
+[formatter_simpleFormatter]
+format = [%(asctime)s][%(name)s][%(levelname)-8s] %(message)s
+datefmt = %Y-%m-%d %H:%M:%S
+
diff --git a/python/conf/settings.ini b/python/conf/settings.ini
new file mode 100644
index 0000000..4996374
--- /dev/null
+++ b/python/conf/settings.ini
@@ -0,0 +1,36 @@
+[default]
+
+# Where all task outputs go.
+BASE = "/bigger/.cache"
+TMPDIR = "/bigger/tmp"
+
+# The raw input containing a single reference per line and sha1 of compressed
+# file.
+#
+# {
+# "biblio": {
+# "container_name": "IEEE Trans. Pattern Anal. Mach. Intell",
+# "contrib_raw_names": [
+# "M Ben-Ezra",
+# "S K Nayar"
+# ],
+# "issue": "6",
+# "pages": "689-698",
+# "title": "Motion-based motion deblurring",
+# "unstructured": "M. Ben-Ezra and S. K. Nayar. Motion-based motion deblurring. IEEE Trans. Pattern Anal. Mach. Intell., 26(6):689-698, 2004. 2",
+# "volume": "26",
+# "year": 2004
+# },
+# "index": 0,
+# "key": "b0",
+# "ref_source": "grobid",
+# "release_ident": "26qgat7mzrerjacrlsz3gdmcgy",
+# "release_year": 2014,
+# "work_ident": "aaaoe2wcbvdjthnv36dlqgkray"
+# }
+#
+REFS_FILE = "/bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst"
+
+# Release docs from database export.
+RELEASE_EXPORT_EXPANDED_FILE = "/bigger/citations/release_export_expanded.json.zst"
+
diff --git a/python/notes/data/oci_v1_10_1056_nejmoa1606220.json b/python/notes/data/oci_v1_10_1056_nejmoa1606220.json
new file mode 100644
index 0000000..0549967
--- /dev/null
+++ b/python/notes/data/oci_v1_10_1056_nejmoa1606220.json
@@ -0,0 +1,5825 @@
+[
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010737010137000905-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-03",
+ "citing": "10.1016/j.juro.2017.11.095",
+ "journal_sc": "no",
+ "timespan": "P1Y5M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010737010137010106-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-05",
+ "citing": "10.1016/j.juro.2017.11.116",
+ "journal_sc": "no",
+ "timespan": "P1Y7M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010737010237000603-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-06",
+ "citing": "10.1016/j.juro.2017.12.063",
+ "journal_sc": "no",
+ "timespan": "P1Y8M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010837000137000002-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-04",
+ "citing": "10.1016/j.juro.2018.01.002",
+ "journal_sc": "no",
+ "timespan": "P1Y6M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020010001063619371930272437020001083700023703000804-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-09",
+ "citing": "10.1016/j.juro.2018.02.3084",
+ "journal_sc": "no",
+ "timespan": "P1Y11M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010837000437000700-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-11",
+ "citing": "10.1016/j.juro.2018.04.070",
+ "journal_sc": "no",
+ "timespan": "P2Y1M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010837000437000708-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-10",
+ "citing": "10.1016/j.juro.2018.04.078",
+ "journal_sc": "no",
+ "timespan": "P2Y0M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100010636193719302724370200010837000537010201-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-10",
+ "citing": "10.1016/j.juro.2018.05.121",
+ "journal_sc": "no",
+ "timespan": "P2Y0M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020010009033618111336183535010705-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-08-14",
+ "citing": "10.1093/ibd/izz175",
+ "journal_sc": "no",
+ "timespan": "P2Y10M1D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "0200100080036000206050607030637020001093701060502070703-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019",
+ "citing": "10.1080/02656736.2019.1652773",
+ "journal_sc": "no",
+ "timespan": "P3Y"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020010107073601050507090808030108070800080501-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-06-07",
+ "citing": "10.1177/1557988318780851",
+ "journal_sc": "no",
+ "timespan": "P1Y7M25D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362801020600096300010963000300066302-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-07-19",
+ "citing": "10.1007/s12609-019-0306-2",
+ "journal_sc": "no",
+ "timespan": "P2Y9M6D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010763000401026306-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2017-05-17",
+ "citing": "10.1007/s00120-017-0412-6",
+ "journal_sc": "no",
+ "timespan": "P0Y7M4D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010763000501016304-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2017-10-05",
+ "citing": "10.1007/s00120-017-0511-4",
+ "journal_sc": "no",
+ "timespan": "P0Y11M22D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010863000607056306-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-06-05",
+ "citing": "10.1007/s00120-018-0675-6",
+ "journal_sc": "no",
+ "timespan": "P1Y7M23D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010863000703056334-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-07-24",
+ "citing": "10.1007/s00120-018-0735-y",
+ "journal_sc": "no",
+ "timespan": "P1Y9M11D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010963000809046305-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-03",
+ "citing": "10.1007/s00120-019-0894-5",
+ "journal_sc": "no",
+ "timespan": "P2Y5M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010963000809096300-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-03-11",
+ "citing": "10.1007/s00120-019-0899-0",
+ "journal_sc": "no",
+ "timespan": "P2Y4M26D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010963000900036308-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-03-11",
+ "citing": "10.1007/s00120-019-0903-8",
+ "journal_sc": "no",
+ "timespan": "P2Y4M26D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007362800000102006300010963000902016306-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-04-23",
+ "citing": "10.1007/s00120-019-0921-6",
+ "journal_sc": "no",
+ "timespan": "P2Y6M10D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020020107043601050608000206060109060606010900010205010405080306-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-03-26",
+ "citing": "10.2174/1568026619666190125145836",
+ "journal_sc": "no",
+ "timespan": "P2Y5M13D"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020010009073622133700000000000000000000000102050004-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2018-10",
+ "citing": "10.1097/md.0000000000012504",
+ "journal_sc": "no",
+ "timespan": "P2Y0M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020010009073622133700000000000000000000000106010202-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-06",
+ "citing": "10.1097/md.0000000000016122",
+ "journal_sc": "no",
+ "timespan": "P2Y8M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "020010009073622133700000000000000000000000106010903-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019-07",
+ "citing": "10.1097/md.0000000000016193",
+ "journal_sc": "no",
+ "timespan": "P2Y9M"
+ },
+ {
+ "author_sc": "no",
+ "oci": "02001000007360907086303630301096307060405076303490103-020010005063623141922241001060006020200",
+ "cited": "10.1056/nejmoa1606220",
+ "creation": "2019",
+ "citing": "10.1007/978-3-319-76457-3_13",
+ "journal_sc": "no",
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+{"doi":"10.1371/journal.pone.0210194","status":200}
+{"doi":"10.1007/s11654-017-0004-3","status":200}
+{"doi":"10.1007/s11654-017-0002-5","status":200}
+{"doi":"10.1007/s11654-019-00179-2","status":200}
+{"doi":"10.1007/978-3-319-96809-4_8","status":200}
+{"doi":"10.1002/9781119129875.ch26","status":200}
+{"doi":"10.1007/s11255-017-1714-8","status":200}
+{"doi":"10.1002/9781118990957.ch13","status":200}
+{"doi":"10.1080/15384047.2017.1323600","status":200}
+{"doi":"10.1111/ecc.12699","status":200}
+{"doi":"10.1038/s41598-018-26682-0","status":200}
+{"doi":"10.2217/fon-2017-0074","status":200}
+{"doi":"10.2217/fon-2017-0337","status":200}
+{"doi":"10.1111/ecc.13076","status":200}
+{"doi":"10.2217/fon-2017-0531","status":200}
+{"doi":"10.1530/eje-18-0117","status":200}
+{"doi":"10.1530/erc-18-0058","status":200}
+{"doi":"10.1530/erc-17-0155","status":200}
+{"doi":"10.1007/s11469-019-00108-y","status":200}
+{"doi":"10.1038/s41571-018-0116-x","status":200}
+{"doi":"10.1038/s41576-018-0018-x","status":200}
+{"doi":"10.1038/s41585-018-0024-y","status":200}
+{"doi":"10.1038/s41585-018-0060-7","status":200}
+{"doi":"10.1038/s41585-018-0073-2","status":200}
+{"doi":"10.1093/jjco/hyaa027","status":200}
+{"doi":"10.1007/s00520-019-05268-0","status":200}
+{"doi":"10.1038/s41585-019-0167-5","status":200}
+{"doi":"10.1002/wnan.1607","status":200}
+{"doi":"10.1038/s41585-018-0140-8","status":200}
+{"doi":"10.3389/fendo.2018.00736","status":200}
+{"doi":"10.1038/s41585-019-0212-4","status":200}
+{"doi":"10.2214/ajr.19.21836","status":200}
+{"doi":"10.1007/978-3-662-55793-8_48-1","status":200}
+{"doi":"10.1007/978-3-030-21447-0_25","status":200}
+{"doi":"10.1002/jmri.27147","status":200}
+{"doi":"10.3390/nano8060360","status":200}
+{"doi":"10.1111/iju.14202","status":200}
+{"doi":"10.1038/s41598-020-57618-2","status":200}
+{"doi":"10.3390/ijms21030905","status":200}
+{"doi":"10.1007/s00345-019-03024-x","status":200}
+{"doi":"10.1007/s00345-019-03056-3","status":200}
+{"doi":"10.1007/s00345-020-03111-4","status":200}
+{"doi":"10.1177/2051415819889552","status":200}
+{"doi":"10.1007/s00345-020-03154-7","status":200}
+{"doi":"10.1371/journal.pone.0224151","status":200}
+{"doi":"10.1177/1457496919883962","status":200}
+{"doi":"10.1007/s00120-020-01123-x","status":200}
+{"doi":"10.1002/14651858.cd012816.pub2","status":200}
+{"doi":"10.1111/bju.14910","status":200}
+{"doi":"10.1111/bju.14918","status":200}
+{"doi":"10.1111/bju.14935","status":200}
+{"doi":"10.1111/bju.14951","status":200}
+{"doi":"10.1111/bju.14987","status":200}
+{"doi":"10.1111/bju.15003","status":200}
+{"doi":"10.1097/pas.0000000000001345","status":200}
+{"doi":"10.1111/bju.15037","status":200}
+{"doi":"10.1136/jim-2017-000627","status":200}
+{"doi":"10.1007/s00330-019-06505-0","status":200}
+{"doi":"10.1186/s13148-020-00836-2","status":200}
+{"doi":"10.1007/978-3-030-22254-3_16","status":200}
+{"doi":"10.1007/978-3-030-28599-9_35","status":200}
+{"doi":"10.1002/cam4.2920","status":200}
+{"doi":"10.1002/cam4.2685","status":200}
+{"doi":"10.1056/nejmoa1910038","status":200}
+{"doi":"10.2217/fon-2019-0635","status":200}
+{"doi":"10.18632/oncotarget.22981","status":200}
+{"doi":"10.18632/oncotarget.21519","status":200}
+{"doi":"10.1007/s00261-020-02547-x","status":200}
+{"doi":"10.1002/cncr.32821","status":200}
+{"doi":"10.1002/cam4.3073","status":200}
+{"doi":"10.1007/s11764-020-00888-6","status":200}
+{"doi":"10.1080/17434440.2020.1755258","status":200}
+{"doi":"10.1111/his.14064","status":200}
+{"doi":"10.1590/1678-4685-gmb-2018-0329","status":200}
+{"doi":"10.1002/mp.14169","status":200}
+{"doi":"10.1136/bmjopen-2018-026438","status":200}
+{"doi":"10.1590/s1677-5538.ibju.2020.04.03","status":200}
+{"doi":"10.1186/s13014-020-01527-1","status":200}
+{"doi":"10.1056/nejmms1914228","status":200}
+{"doi":"10.1111/bju.15021","status":200}
+{"doi":"10.1007/s12094-020-02355-1","status":200}
+{"doi":"10.18632/oncotarget.20078","status":200}
+{"doi":"10.1111/bju.15100","status":200}
+{"doi":"10.1111/bju.15153","status":200}
+{"doi":"10.1007/s00066-020-01657-1","status":200}
+{"doi":"10.1002/1878-0261.12712","status":200}
+{"doi":"10.1007/s00066-020-01661-5","status":200}
+{"doi":"10.1002/14651858.cd006590.pub3","status":200}
+{"doi":"10.1177/0300891620943953","status":200}
+{"doi":"10.1371/journal.pone.0235616","status":200}
+{"doi":"10.1089/end.2020.0042","status":200}
+{"doi":"10.1007/s00330-020-06997-1","status":200}
+{"doi":"10.1038/s41585-020-0356-2","status":200}
+{"doi":"10.1186/s13063-020-04425-9","status":200}
+{"doi":"10.1097/rli.0000000000000685","status":200}
+{"doi":"10.1007/s12032-020-01397-3","status":200}
+{"doi":"10.1002/pon.5375","status":200}
+{"doi":"10.1093/jjco/hyaa105","status":200}
+{"doi":"10.1002/pros.24040","status":200}
+{"doi":"10.1093/jjco/hyaa132","status":200}
+{"doi":"10.1186/s12916-020-01681-z","status":200}
+{"doi":"10.1002/cam4.3197","status":200}
+{"doi":"10.1007/s00261-020-02683-4","status":200}
+{"doi":"10.1007/s00345-020-03301-0","status":200}
+{"doi":"10.1007/s00345-020-03304-x","status":200}
+{"doi":"10.1177/0091217420938896","status":200}
+{"doi":"10.1007/s10865-020-00171-0","status":200}
+{"doi":"10.1007/s40487-020-00119-z","status":200}
+{"doi":"10.1038/s41416-020-0978-4","status":200}
+{"doi":"10.1056/nejmsb2000250","status":200}
+{"doi":"10.1200/go.20.00255","status":200}
+{"doi":"10.1200/jco.19.03114","status":200}
+{"doi":"10.1001/jamanetworkopen.2020.14674","status":200}
+{"doi":"10.1111/iju.14321","status":200}
+{"doi":"10.1111/iju.14358","status":200}
+{"doi":"10.1001/jamaoncol.2020.4922","status":200}
+{"doi":"10.1001/jamanetworkopen.2020.18318","status":200}
+{"doi":"10.1007/s00761-020-00811-9","status":200}
+{"doi":"10.1111/jgs.16794","status":200}
+{"doi":"10.1148/rycan.2020190078","status":200}
+{"doi":"10.1111/ajt.16318","status":200}
+{"doi":"10.1155/2020/5395312","status":200}
+{"doi":"10.3390/cancers12082208","status":200}
+{"doi":"10.1097/md.0000000000021642","status":200}
+{"doi":"10.1111/bju.15231","status":200}
+{"doi":"10.1038/s41585-020-0354-4","status":200}
+{"doi":"10.1590/s1677-5538.ibju.2020.s106","status":200}
+{"doi":"10.1007/s40487-020-00132-2","status":200}
+{"doi":"10.1038/s41391-020-00291-3","status":200}
+{"doi":"10.1007/978-3-030-54482-9_9","status":200}
+{"doi":"10.1038/s41598-020-72088-2","status":200}
+{"doi":"10.1002/cam4.3482","status":200}
+{"doi":"10.1002/cam4.3341","status":200}
+{"doi":"10.1007/s00345-020-03471-x","status":200}
+{"doi":"10.1007/s00345-020-03485-5","status":200}
+{"doi":"10.1007/s00345-020-03494-4","status":200}
+{"doi":"10.17816/uroved102133-142","status":200}
+{"doi":"10.1007/978-3-030-47963-3_27","status":200}
+{"doi":"10.5694/mja2.50794","status":200}
+{"doi":"10.3389/fonc.2020.01349","status":200}
+{"doi":"10.3389/fonc.2020.564068","status":200}
+{"doi":"10.3390/cells9112342","status":200}
+{"doi":"10.2147/rru.s243088","status":200}
+{"doi":"10.1097/coc.0000000000000721","status":200}
+{"doi":"10.1007/s11934-020-00987-y","status":200}
+{"doi":"10.1111/pin.13026","status":200}
+{"doi":"10.1186/s12885-020-07276-4","status":200}
+{"doi":"10.1186/s12885-020-07244-y","status":200}
+{"doi":"10.1186/s13073-020-00770-1","status":200}
+{"doi":"10.23736/s0393-2249.19.03637-3","status":200}
+{"doi":"10.32322/jhsm.758558","status":404}
+{"doi":"10.23736/s0393-2249.20.03780-7","status":200}
+{"doi":"10.3310/hta24370","status":200}
+{"doi":"10.1093/ndt/gfaa209","status":200}
+{"doi":"10.23736/s0393-2249.20.03782-0","status":200}
+{"doi":"10.1007/s41669-020-00226-7","status":200}
+{"doi":"10.1007/s11701-020-01144-w","status":200}
+{"doi":"10.1111/ctr.14080","status":200}
+{"doi":"10.1002/pon.5513","status":200}
+{"doi":"10.1259/bjr.20200571","status":200}
+{"doi":"10.1259/bjr.20200848","status":200}
+{"doi":"10.1002/pros.24075","status":200}
+{"doi":"10.1007/978-3-662-61494-5_11","status":200}
+{"doi":"10.1007/s00432-020-03327-2","status":200}
+{"doi":"10.1111/ecc.13301","status":200}
+{"doi":"10.1200/op.20.00508","status":200}
+{"doi":"10.1038/s41443-020-00364-w","status":200}
+{"doi":"10.1186/s12943-020-01264-9","status":200}
+{"doi":"10.4103/iju.iju_115_20","status":200}
+{"doi":"10.1007/978-3-319-57415-8_34","status":200}
+{"doi":"10.2147/cmar.s257441","status":200}
+{"doi":"10.1097/mou.0000000000000683","status":200}
+{"doi":"10.1634/theoncologist.2018-0679","status":200}
+{"doi":"10.1200/jco.19.01904","status":200}
+{"doi":"10.1200/jco.19.02768","status":200}
+{"doi":"10.1200/jco.19.02267","status":200}
diff --git a/python/notes/data_quality.md b/python/notes/data_quality.md
new file mode 100644
index 0000000..e386914
--- /dev/null
+++ b/python/notes/data_quality.md
@@ -0,0 +1,11 @@
+# Data quality issues
+
+## Mismatched PDFs
+
+* https://fatcat.wiki/release/iwvep44l5jdqlpwrzjmfdtxdrio
+
+Two SHA1, titles match roughly, but these are different docs:
+
+* [https://file.scirp.org/pdf/JSS_2017121115100474.pdf](https://file.scirp.org/pdf/JSS_2017121115100474.pdf)
+* [http://eprints.lincoln.ac.uk/id/eprint/38840/1/polcice%20journal.pdf](http://eprints.lincoln.ac.uk/id/eprint/38840/1/polcice%20journal.pdf)
+
diff --git a/python/notes/version_0.md b/python/notes/version_0.md
new file mode 100644
index 0000000..a6108be
--- /dev/null
+++ b/python/notes/version_0.md
@@ -0,0 +1,468 @@
+# Version Zero Graph
+
+* ~1.8B refs
+* ~250M w/ titles
+* ~40M URLs
+* ~25M titles exact match w/ fatcat
+
+```
+127589929 fatcat_lower.tsv
+251934865 refs_lower.tsv
+
+ 34931967 common_lower.tsv
+ 26840211 common.tsv
+```
+
+----
+
+# Input
+
+Heavy intermediate schema from
+[fatcat-scholar](https://git.archive.org/webgroup/fatcat-scholar/), raw names
+of journal titles, partial metadata.
+
+Example line:
+
+```json
+{
+ "biblio": {
+ "contrib_raw_names": [
+ "Maria Azevedo E Castro",
+ "Gabriela"
+ ],
+ "title": "Imaginação em Paul Ricoeur",
+ "unstructured": "AZEVEDO E CASTRO, Maria Gabriela. Imaginação em Paul Ricoeur."
+ },
+ "index": 0,
+ "key": "b0",
+ "ref_source": "grobid",
+ "release_ident": "ruhcoyvxxnbc5ljsgtwhnolx3i",
+ "release_year": 2018,
+ "work_ident": "aaaes3j4argnjbkzdvud5r4zdi"
+}
+```
+
+280M docs per file:
+
+```
+$ unpigz -c fatcat_scholar_work_fulltext.split_00.refs.json.gz | wc -l
+285004451
+```
+
+Around 1,733,267,886 total reference entries. Sample completeness (10M, 1M
+docs, ...):
+
+```
+{
+ "biblio": 10000000,
+ "biblio.arxiv_id": 23227,
+ "biblio.container_name": 5760760,
+ "biblio.contrib_raw_names": 7156385,
+ "biblio.doi": 3584451,
+ "biblio.issue": 763784,
+ "biblio.pages": 3331911,
+ "biblio.pmcid": 776,
+ "biblio.pmid": 471338,
+ "biblio.publisher": 398305,
+ "biblio.title": 5164864,
+ "biblio.unstructured": 6304402,
+ "biblio.url": 256771,
+ "biblio.volume": 5202508,
+ "biblio.year": 7055442,
+ "index": 10000000,
+ "key": 8986307,
+ "locator": 2390436,
+ "ref_source": 10000000,
+ "release_ident": 10000000,
+ "release_year": 9629380,
+ "target_release_id": 419033,
+ "work_ident": 10000000
+}
+```
+
+A smaller sample:
+
+```
+{
+ "biblio": 1000000,
+ "biblio.arxiv_id": 1804,
+ "biblio.container_name": 580018,
+ "biblio.contrib_raw_names": 722526,
+ "biblio.doi": 355664,
+ "biblio.issue": 79145,
+ "biblio.pages": 337716,
+ "biblio.pmcid": 241,
+ "biblio.pmid": 47500,
+ "biblio.publisher": 39840,
+ "biblio.title": 518449,
+ "biblio.unstructured": 643743,
+ "biblio.url": 27535,
+ "biblio.volume": 526148,
+ "biblio.year": 713331,
+ "index": 1000000,
+ "key": 904205,
+ "locator": 241850,
+ "ref_source": 1000000,
+ "release_ident": 1000000,
+ "release_year": 966723,
+ "target_release_id": 42333,
+ "work_ident": 1000000
+}
+```
+
+
+----
+
+## DOI graph (v2020-01-22)
+
+* 615514019 lines joined
+
+We have "inbound" links for 41950903 records.
+
+However, the top ranked docs seem invalid, datasets from a few prefixes, mostly
+from datacite.
+
+A few paper examples:
+
+* https://fatcat.wiki/release/6ykebula5vgtbinbqhftun7jcy
+
+> Effect of intensive blood-glucose control with metformin on complications in overweight patients with type 2 diabetes (UKPDS 34)
+
+* Google Scholar: [7981](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Effect+of+intensive+blood-glucose+control+with+metformin+on+complications+in+overweight+&btnG=)
+* CG: 2105
+
+----
+
+* https://fatcat.wiki/release/3katpfxlafezdb2rmgoesgbhkq
+
+> The pyramid of corporate social responsibility
+
+* GS: [12690](https://scholar.google.com/scholar?cluster=13669080523806449819&hl=en&as_sdt=0,5&sciodt=0,5)
+* CG: 2100
+
+----
+
+> Policy Paradigms, Social Learning, and the State
+
+* https://fatcat.wiki/release/m3kxbmcsxnfhzajp5zrdmvirlm
+* GS: [8675](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Policy+Paradigms%2C+Social+Learning%2C+and+the+State&btnG=)
+* CG: 2077
+* OCI: [2457](https://opencitations.net/index/coci/api/v1/citations/10.2307/422246)
+
+----
+
+> Efficacy and safety of sorafenib in patients in the Asia-Pacific
+
+* GS: [4780](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=%22Efficacy+and+safety+of+sorafenib+in+patients+in+the+Asia-Pacific%22&btnG=)
+* CG: 1829
+* OCI: [2326](https://opencitations.net/index/coci/api/v1/citations/10.1016/s1470-2045(08)70285-7)
+
+----
+
+* https://fatcat.wiki/release/qbdkrwg2dzbpfcdcsczy7ekjk4
+* GS: [4172](https://scholar.google.com/scholar?cluster=10863619180312621990&hl=en&as_sdt=0,5&sciodt=0,5)
+* CG: 1303
+* OCI: [1776](https://opencitations.net/index/coci/api/v1/citations/10.1038/18884), 48, https://opencitations.net/browser/br/107462
+
+----
+
+> Oxidative stress and some antioxidant systems in acid rain-treated bean plants
+
+* https://fatcat.wiki/release/qrsuwvixbvgvpn4qzlum7btysi
+* GS: [2613](https://scholar.google.com/scholar?cluster=13765746500938441584&hl=en&as_sdt=2005&sciodt=0,5)
+* CG: 940
+* OCI: [1042](https://opencitations.net/index/coci/api/v1/citations/10.1016/s0168-9452(99)00197-1)
+
+Not sure, what this interface does, but it says "20" (?):
+[https://opencitations.net/search?text=10.1016%2Fs0168-9452%2899%2900197-1&rule=doi](https://opencitations.net/search?text=10.1016%2Fs0168-9452%2899%2900197-1&rule=doi), https://opencitations.net/browser/br/808900
+
+----
+
+> Weak pairwise correlations imply strongly correlated network states in a neural population
+
+* https://fatcat.wiki/release/zga73tc25nabdpt42m5ehm2kmm
+* GS: [1597](https://scholar.google.com/scholar?cluster=3499093978246315979&hl=en&as_sdt=0,5&sciodt=0,5)
+* CG: 706
+* OCI: [794](https://opencitations.net/index/coci/api/v1/citations/10.1038/nature04701)
+
+----
+
+* https://fatcat.wiki/release/fm3ni5ppyzbknj2ke3rcn3qwva
+* GS: [3118](https://scholar.google.com/scholar?cluster=495710774871014506&hl=en&as_sdt=0,5&sciodt=0,5)
+* CG: 679
+* OCI: [1092](https://opencitations.net/index/coci/api/v1/citations/10.1056/nejm199505183322008)
+
+----
+
+* https://fatcat.wiki/release/5i5j4qejbjey5pt56n25qmxque
+* GS: [1043](https://scholar.google.de/scholar?cluster=2106266772718631212&hl=en&as_sdt=2005&sciodt=0,5)
+* CG: 421
+* OCI: [406](https://opencitations.net/index/coci/api/v1/citations/10.1029/2003wr002086)
+
+----
+
+* https://fatcat.wiki/release/agrh573u7nc4hd5pmyptoasvua
+* GS: [1391](https://scholar.google.de/scholar?cluster=17826621684475874878&hl=en&as_sdt=2005&sciodt=0,5)
+* CG: 388
+* OCI: [444](https://opencitations.net/index/coci/api/v1/citations/10.1136/bjsm.2006.033548)
+
+----
+
+* https://fatcat.wiki/release/ellwakbl7rdlvgqcu7d3ss7wwa
+* GS: [593](https://scholar.google.com/scholar?cluster=537065614856795966&hl=en&as_sdt=2005&sciodt=0,5)
+* CG: 315
+* OCI: [348](https://opencitations.net/index/coci/api/v1/citations/10.1038/nature05136)
+
+----
+
+* https://fatcat.wiki/release/dj6pufwjnnhfvpwj7tuyfl43mq
+* GS: [1948](https://scholar.google.com/scholar?q=A%20Simple%20Approximate%20Long-Memory%20Model%20of%20Realized%20Volatility)
+* CG: 275
+* OCI: [336](https://opencitations.net/index/coci/api/v1/citations/10.1093/jjfinec/nbp001)
+
+## Refs completeness
+
+Use `ref_counter.py` and `ref_key_counter.py` to assess completeness of refs.
+
+Example (1.8B):
+
+```json
+{
+ "has_any_extid": 700483339,
+ "has_arxiv_id": 4229730,
+ "has_container_name": 998375407,
+ "has_container_volume_issue_pages": 99419112,
+ "has_contrib_container_year": 951540575,
+ "has_contrib_raw_names": 1243059610,
+ "has_doi": 620638102,
+ "has_index": 1682302484,
+ "has_issue": 132575565,
+ "has_key": 1559104305,
+ "has_locator": 415631451,
+ "has_pages": 578644324,
+ "has_pmcid": 129593,
+ "has_pmid": 80598430,
+ "has_publisher": 68809489,
+ "has_release_ident": 1733948346,
+ "has_release_year": 1671156907,
+ "has_target_release_id": 71771437,
+ "has_title": 895913346,
+ "has_title_container_year": 608802846,
+ "has_title_contrib_year": 800324815,
+ "has_unstructured": 1095871772,
+ "has_url": 44860180,
+ "has_volume": 901926534,
+ "has_work_ident": 1733948346,
+ "has_year": 1224602612,
+ "source_crossref": 716691444,
+ "source_datacite": 97088644,
+ "source_fatcat": 31681853,
+ "source_grobid": 778474113,
+ "source_pubmed": 110012292,
+ "total": 1733948346
+}
+```
+
+Overview of field cooccurences (running):
+
+```shell
+$ zstdcat -T0 /bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst | pv -l | \
+ parallel -j 16 --pipe --roundrobin python extra/ref_key_counter.py > ref_key_counter.json
+$ python extra/ref_key_counter_merge.py < ref_key_counter.json
+```
+
+Top 3 key combinations:
+
+```
+$ jq -r '.c | to_entries[] | [.key, .value] | @tsv' ref_key_counter_merge.json | sort -nrk2,2 2> /dev/null | head -30 | column -t
+container_name|contrib_raw_names|pages|title|unstructured|volume|year 259790699
+doi 257006166
+container_name|contrib_raw_names|issue|pages|title|unstructured|volume|year 82516807
+container_name|contrib_raw_names|doi|unstructured|volume|year 76858089
+pmid|unstructured 74462682
+container_name|contrib_raw_names|doi|title|volume|year 70821103
+container_name|contrib_raw_names|year 64064559
+container_name|contrib_raw_names|doi|volume|year 62559951
+unstructured 61711602
+contrib_raw_names|pages|title|unstructured|volume|year 61557246
+container_name|contrib_raw_names|volume|year 49701699
+container_name|contrib_raw_names|unstructured|volume|year 36401044
+contrib_raw_names|title|unstructured|year 35976833
+container_name|contrib_raw_names|doi|pages|title|unstructured|volume|year 32506970
+contrib_raw_names|publisher|title|unstructured|year 29668363
+container_name|contrib_raw_names|title|volume|year 27447296
+container_name|contrib_raw_names|unstructured|year 26663422
+container_name|contrib_raw_names|pages|title|unstructured|year 18216147
+contrib_raw_names|unstructured 16731608
+container_name|contrib_raw_names|title|unstructured|year 15103791
+doi|unstructured 14464285
+container_name|contrib_raw_names|doi|unstructured|year 14207167
+contrib_raw_names|pages|title|unstructured|year 14198485
+container_name|contrib_raw_names|doi|year 13159340
+contrib_raw_names|title|year 12980769
+contrib_raw_names|title|unstructured 12595768
+title|unstructured 12391968
+contrib_raw_names|title|volume|year 10636816
+container_name|contrib_raw_names|doi|title|year 10438502
+container_name|contrib_raw_names|pages|publisher|title|unstructured|year 8343539
+```
+
+Loaded key sets and counts into sqlite3.
+
+```
+sqlite> select sum(count) from card;
+1733948346
+
+sqlite> select sum(count) from card where key like '%doi%' or key like '%pmid%' or key like '%pmcid%' or key like '%arxiv%';
+700483341
+
+sqlite> select sum(count) from card where key like '%title%';
+895913346
+
+sqlite> select sum(count) from card where key like '%doi%';
+620638104
+
+sqlite3> select sum(count) from card where key like '%doi%' and key like '%title%';
+166109956
+
+sqlite> select sum(count) from card where key like '%doi%' and key not like '%title%';
+454528148
+
+sqlite> select sum(count) from card where key like 'unstructured';
+61711602
+
+sqlite> select sum(count) from card where key not like '%pmid%' and key not like '%doi%' and key not like '%title%';
+309033306
+
+sqlite> select * from card order by count desc limit 20;
+container_name|contrib_raw_names|pages|title|unstructured|volume|year 259790699
+doi 257006166
+container_name|contrib_raw_names|issue|pages|title|unstructured|volum 82516807
+container_name|contrib_raw_names|doi|unstructured|volume|year 76858089
+pmid|unstructured 74462682
+container_name|contrib_raw_names|doi|title|volume|year 70821103
+container_name|contrib_raw_names|year 64064559
+container_name|contrib_raw_names|doi|volume|year 62559951
+unstructured 61711602
+contrib_raw_names|pages|title|unstructured|volume|year 61557246
+container_name|contrib_raw_names|volume|year 49701699
+container_name|contrib_raw_names|unstructured|volume|year 36401044
+contrib_raw_names|title|unstructured|year 35976833
+container_name|contrib_raw_names|doi|pages|title|unstructured|volume| 32506970
+contrib_raw_names|publisher|title|unstructured|year 29668363
+container_name|contrib_raw_names|title|volume|year 27447296
+container_name|contrib_raw_names|unstructured|year 26663422
+container_name|contrib_raw_names|pages|title|unstructured|year 18216147
+contrib_raw_names|unstructured 16731608
+container_name|contrib_raw_names|title|unstructured|year 15103791
+
+sqlite> select * from card where key not like '%pmid%' and key not like '%doi%' and key not like '%title%' order by count desc limit 30;
+container_name|contrib_raw_names|year|64064559
+unstructured|61711602
+container_name|contrib_raw_names|volume|year|49701699
+container_name|contrib_raw_names|unstructured|volume|year|36401044
+container_name|contrib_raw_names|unstructured|year|26663422
+contrib_raw_names|unstructured|16731608
+contrib_raw_names|unstructured|year|7668998
+container_name|year|4946373
+contrib_raw_names|pages|unstructured|4574398
+|3931030
+container_name|volume|year|3879804
+contrib_raw_names|year|3634698
+container_name|contrib_raw_names|2530058
+contrib_raw_names|pages|unstructured|volume|1963485
+container_name|contrib_raw_names|issue|unstructured|volume|year|1895141
+contrib_raw_names|pages|unstructured|volume|year|1825755
+contrib_raw_names|pages|unstructured|year|1759744
+contrib_raw_names|publisher|unstructured|year|1652931
+contrib_raw_names|1533772
+container_name|contrib_raw_names|volume|1183234
+year|1057837
+container_name|contrib_raw_names|issue|volume|year|857175
+contrib_raw_names|unstructured|volume|850630
+container_name|unstructured|year|842953
+contrib_raw_names|unstructured|url|year|764268
+contrib_raw_names|unstructured|url|644762
+contrib_raw_names|unstructured|volume|year|591568
+contrib_raw_names|publisher|unstructured|579832
+container_name|471755
+contrib_raw_names|pages|publisher|unstructured|year|402852
+```
+
+## Refs as releases
+
+We convert refs to release like docs in order to run clustering on it.
+
+About 530M refs have to title, yet they have some kind of identifier (e.g. doi,
+pmid, arxiv, ...).
+
+```
+$ zstdcat -T0 sha1-ef1756a5856085807742966f48d95b4cb00299a0.tsv.zst | LC_ALL=C grep -c -v -F "title"
+529498074
+```
+
+We have 895M refs with title.
+
+Rough metadata, extracted, partial or wrong, e.g "LANCET" as title.
+
+How many items have both title and `ext_ids` - via:
+
+```
+$ zstdcat -T0 with_title.json.zst | LC_ALL=C rg -c -F "ext_ids"
+```
+
+170985267 have both title and some identifier.
+
+Another performance data point: grepping through 300G on disk, uncompressed
+takes about twice the time to uncompress (zstd) a 60G file on the fly.
+
+Sampling with `awk` - `cat 1B.txt | awk 'NR % 1000000 == 0'`
+
+## Ref only DOIs
+
+There are 2649552 unique strings identified as DOI in refs, which do not match
+any DOI in fatcat (normalized to lowercase). However, a link check of a sample
+of 2K reveals that only 20% of those DOI actually resolve.
+
+There may be around 500K DOI in references that do not appear in fatcat.
+
+## Fuzzy matches
+
+* [x] convert refs docs into partial release entities
+* [x] concatenate with fatcat releases
+* [-] cluster; note: huge file, stopped
+
+Ran a sample on 11M (1.4G compressed) docs (10M refs, 1M fatcat), clustered in
+18min.
+
+Found 15214 clusters, but all with fatcat, not refs/fatcat. Need to extend the dataset size.
+
+Running sample with 110M docs (100M refs, 10M fatcat; 14G compressed; clustered
+96min); found 231998 clusters, but again none between the refs and fatcat
+groups.
+
+## Quality observations
+
+A case, where we seem to have GROBID output in the refs dataset, from a PDF, which does not fit the PDF linked:
+
+* https://fatcat.wiki/release/5al5q6ksx5dxhhtmt4cjajehge (should be an article, 157-187), but:
+* [https://smartech.gatech.edu/bitstream/handle/1853/26610/zhang_lei_200812_phd.pdf](https://smartech.gatech.edu/bitstream/handle/1853/26610/zhang_lei_200812_phd.pdf) is a thesis (150+ pages)
+
+## Approximate string match
+
+* in refs: "Turkish Cypriots fear implications of Cyprus EU presidency" - but
+ we have: https://fatcat.wiki/release/vp4h6jp65bfuro2wrkh3qg3ody, "Turkey's
+boycott of the Cyprus EU presidency" plus duplication. We would need an approx. string match, or substring match.
+
+
+# Lookup storage
+
+* Can we convert our JSON into parquet for faster queries? Should we index by
+ release? By title?
+
+# Funnel Setup
+
+* [ ] refs with a DOI (620,638,104); lookup the DOI; keep (refrid, rid)
+* [ ] refs with other extids; lookup id in extracted lists from fatcat
+* [ ] refs w/o extids, but with a title
+
diff --git a/python/notes/version_1.md b/python/notes/version_1.md
new file mode 100644
index 0000000..50a38cc
--- /dev/null
+++ b/python/notes/version_1.md
@@ -0,0 +1,491 @@
+# Version 1
+
+Includes:
+
+* doi, pmid, pmcid, arxiv
+* title-lower exact matches
+
+Title join yields 16B+ matches (16761492658), since we have many generic rows, e.g.
+"introduction". 180G compressed, about 53 min for a one pass.
+
+```
+$ LC_ALL=C time join -t ' ' -1 2 -2 2 <(zstdcat FatcatTitlesLower/sha1-ef1756a5856085807742966f48d95b4cb00299a0.tsv.zst) \
+ <(zstdcat RefsTitlesLower/sha1-ef1756a5856085807742966f48d95b4cb00299a0.tsv.zst) | zstd -c > title.tsv.zst
+```
+
+Filter and sample with `awk`, e.g. via:
+
+```
+$ zstdcat -T0 title.tsv.zst | LC_ALL=C grep -E '^[[:alnum:]]' | awk 'length($1) > 30' | awk 'NR%1000==0'
+```
+
+Need to pre-filter before join, to keep join smaller.
+
+Basic inspection of the "exact lower title" set.
+
+* 16B+ candidates
+* as the join keys are already sorted, we can run uniq
+
+```
+$ time zstdcat -T0 title.tsv.zst | LC_ALL=C cut -f 1 | LC_ALL=C pv -l | LC_ALL=C uniq -c | zstd -c > title_counts.tsv.zst
+
+real 92m28.442s
+user 142m49.627s
+sys 46m9.473s
+```
+
+Some manual sampling:
+
+Different release, but same references (585):
+
+* https://fatcat.wiki/release/zvd5r6grcvd6tnmeovijvx4soq/references
+* https://fatcat.wiki/release/4zutv5pmhjgs7nfvqy2zws6icm/references
+
+There are duplicates in the join, need to filter them out.
+
+```
+$ time zstdcat -T0 title.tsv.zst | LC_ALL=C uniq | LC_ALL=C pv -l | zstd -T0 -c > title_uniq.tsv.zst
+```
+
+Left with about 13B uniq.
+
+OCI, example:
+
+* https://opencitations.net/index/coci/api/v1/citations/10.1056/nejmoa1606220
+* OCI: 646 citations
+
+we have 356 via doi, pmid, about 112 via title, 468 total; which one do we miss?
+
+However, we do have all but one of the OCI DOIs in fatcat:
+
+```
+$ jq -r '.[].citing' oci_v1_10_1056_nejmoa1606220.json | tigris-doi > oci_v1_10_1056_nejmoa1606220_lookup.json
+```
+
+Example, DOI not in OCI:
+
+* https://opencitations.net/index/coci/api/v1/citations/10.14236/ewic/eva2014.30
+
+Possible mitigations:
+
+* ignore common titles
+* ignore numbers only
+
+Examples: `42` appeards 3816 times
+
+Harder cases:
+
+* "41st annual meeting" - too generic, and wrong
+
+
+Generic DOI lookup from OCI in fatcat:
+
+```
+$ curl -sL https://opencitations.net/index/coci/api/v1/citations/10.1016/j.cell.2010.03.012 | jq -rc '.[].citing' | tigris-doi -w 256 | jq -rc .
+{"doi":"10.1530/erc-16-0228","status":200}
+{"doi":"10.1371/journal.pone.0080023","status":200}
+{"doi":"10.1074/jbc.m114.566141","status":200}
+...
+```
+
+Overall:
+
+* 31344136 unique titles
+
+most common join title:
+
+* 11,939,631,644 introduction
+* also: "science", "preface", "book reviews", ..., "cell", ...
+
+Filtering:
+
+```
+$ zstdcat -T0 title_counts.tsv.zst | \
+ LC_ALL=C awk '($1 > 5000 && length($0) < 30) || ($1 > 15000 && length($0) < 40)'
+```
+
+About 7275 titles to filter out, e.g.
+
+```
+...
+ 475300 abstracts of papers
+ 20502 ac
+ 13892 aca
+ 7881 academic freedom
+...
+ 5047 community policing
+ 157176 community-acquired pneumonia
+ 68222 commutative algebra
+ 5512 comorbidity
+ 5516 compact stars
+ 8865 company
+...
+ 7353 facebook
+ 6461 facial pain
+ 8977 facilities
+ 5238 facing the future
+ 5064 fact
+ 11198 fact sheet
+...
+```
+
+Trying fuzzycat clustering, with 0.1.13, which allows to compress `-C`
+intermediate artifacts.
+
+```
+$ time zstdcat \
+ RefsReleasesMerged/sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | \
+ parallel -j 16 --block 10M --roundrobin --pipe 'TMPDIR=/bigger/tmp python -m \
+ fuzzycat cluster -t tsandcrawler -C' | pv -l | zstd -T0 -c > cluster.ndj.zst
+```
+
+Using fuzzycat 0.1.13 with compression; all fine until:
+
+```
+$ time zstdcat \
+ RefsReleasesMerged/sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | pv \
+ -l | parallel -j 16 --block 10M --roundrobin --pipe 'TMPDIR=/bigger/tmp python \
+ -m fuzzycat clust er -t tsandcrawler -C' | zstd -T0 -c > cluster.ndj.zst
+
+1.58G 6:35:39 [66.5k/s] [ <=> ]
+parallel: Error: Output is incomplete.
+parallel: Error: Cannot append to buffer file in /tmp.
+parallel: Error: Is the disk full?
+parallel: Error: Change $TMPDIR with --tmpdir or use --compress.
+
+real 1013m20.128s
+user 2696m14.290s
+sys 119m29.419s
+```
+
+A run with `--compress` and `--tmpdir` set on parallel worked:
+
+```
+$ time zstdcat
+ RefsReleasesMerged/sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst |
+ parallel --compress --tmpdir /fast/tmp -j 4 --block 10M --roundrobin --pipe
+ 'TMPDIR=/bigger/tmp python -m fuzzycat cluster -t tsandcrawler -C' |
+ zstd -T0 -c > cluster.ndj.zst
+
+real 1301m26.206s
+user 2778m20.635s
+sys 140m32.121s
+```
+
+* 21h, finds 5850385 clusters (seems too low)
+
+# Sample generation
+
+Created samples, filtered by years (1895, 1955, 1995, 2015) for refs and releases:
+
+* ~114M refs
+* ~7M releases
+
+Adjusted `tasks.py` to use a different sha1 and updated settings.ini with
+sample file locations.
+
+# First clustering
+
+Key extraction (KE), sorting and clustering took 14h, when the merged dataset
+is already there (it takes ~80min to convert refs to releases, plus a bit more
+to concatenate the files).
+
+```
+$ ./run.sh RefsFatcatClusters
+
+real 841m45.169s
+user 2872m35.481s
+sys 561m14.231s
+```
+
+Resulting file is 154G compressed.
+
+Cluster count and sizes:
+
+```
+$ zstdcat -T0 sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | \
+ LC_ALL=C pv -l | LC_ALL=C jq -rc '[(.v|length), .k] | @tsv' > sizes.tsv
+```
+
+Follow up tasks:
+
+* each cluster will have ref and non-ref items
+* we want at least one non-ref item
+
+```
+$ skate-cluster -both ...
+```
+
+Will keep only those clusters that contain at least one ref and one non-ref
+entry.
+
+Found 40257623 clusters, iteration over the 89GB compressed file takes 28min.
+
+Raw synopsis:
+
+```
+$ zstdcat sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | \
+ jq -c -C 'select(.v|length == 2) | [(.v[] | [.ext_ids.doi[0:2], .title[0:10], .ident, .extra.skate.status == "ref"])]' | less -r
+```
+
+Some numbers:
+
+* [ ] number of 2-clusters, where not both entries have a doi?
+
+Verification.
+
+* needed a different batch verifier, since we do not need pairwise comparisons;
+
+```
+$ cut -d ' ' -f 3-4 cluster_ref_verify.tsv | LC_ALL=C sort -S20% | uniq -c | sort -nr
+8390899 Status.DIFFERENT Reason.YEAR
+6191622 Status.EXACT Reason.DOI
+5468805 Status.STRONG Reason.JACCARD_AUTHORS
+3848964 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY
+3306728 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH
+1263329 Status.STRONG Reason.TOKENIZED_AUTHORS
+ 424441 Status.AMBIGUOUS Reason.UNKNOWN
+ 199157 Status.EXACT Reason.TITLE_AUTHOR_MATCH
+ 138144 Status.AMBIGUOUS Reason.SHORT_TITLE
+ 92054 Status.DIFFERENT Reason.PAGE_COUNT
+ 25122 Status.AMBIGUOUS Reason.BLACKLISTED
+ 22964 Status.EXACT Reason.WORK_ID
+ 17702 Status.STRONG Reason.VERSIONED_DOI
+ 16236 Status.DIFFERENT Reason.COMPONENT
+ 14462 Status.STRONG Reason.PREPRINT_PUBLISHED
+ 9632 Status.STRONG Reason.PMID_DOI_PAIR
+ 3429 Status.STRONG Reason.ARXIV_VERSION
+ 3288 Status.STRONG Reason.CUSTOM_IEEE_ARXIV
+ 729 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW
+ 195 Status.STRONG Reason.FIGSHARE_VERSION
+ 76 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN
+ 74 Status.DIFFERENT Reason.TITLE_FILENAME
+ 43 Status.DIFFERENT Reason.NUM_DIFF
+ 22 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916
+ 11 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT
+ 1 Status.STRONG Reason.CUSTOM_BSI_UNDATED
+```
+
+Guessing: Maybe 30% "strong", so maybe ~120M new edges?
+
+
+----
+
+# Manual sampling and issues
+
+```
+https://fatcat.wiki/release/tiqp3w67sjhzdorc6whizpnbyy https://fatcat.wiki/release/lbmqfamyoveldeyvv5xktq5ayi Status.DIFFERENT Reason.YEAR
+```
+
+Grobid output:
+
+```xml
+<biblStruct xml:id="b77">
+ <analytic>
+ <title level="a" type="main">The Social Construction of Planning Systems: A Strategic-Relational Institutionalist Approach</title>
+ <author>
+ <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">L</forename><surname>Servillo</surname></persName>
+ </author>
+ <author>
+ <persName xmlns="http://www.tei-c.org/ns/1.0"><surname>Van Den</surname></persName>
+ </author>
+ <author>
+ <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">P</forename><surname>Broeck</surname></persName>
+ </author>
+ <idno type="DOI">10.1080/02697459.2012.661179&gt;</idno>
+ <idno>En línea] 2012 [Fecha de consulta: 21 de agosto 2015</idno>
+ <ptr target="&lt;http://dx.doi.org/10.1080/02697459.2012.661179&gt;" />
+ </analytic>
+ <monogr>
+ <title level="j">En: Planning Practice and Research</title>
+ <imprint>
+ <biblScope unit="volume">27</biblScope>
+ <biblScope unit="issue">1</biblScope>
+ <biblScope unit="page" from="41" to="61" />
+ </imprint>
+ </monogr>
+</biblStruct>
+```
+
+There are dates, but not explicit clean 2012.
+
+Another issue:
+
+```
+https://fatcat.wiki/release/2n7pyugxenb73gope52bn6m2ru https://fatcat.wiki/release/p4bettvcszgn5d3zls5ogdjk4u Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH
+```
+
+Very similar titles:
+
+"... nephrotic syndrome in childhood" vs "... nephrotic syndrome in childred" ...
+
+* year do not match, but fuzzycat does not check from that (1995, vs 2004 in the refs)
+
+Intermediate match results:
+
+```
+141970958 Status.DIFFERENT Reason.YEAR
+106734288 Status.EXACT Reason.DOI
+ 91205561 Status.STRONG Reason.JACCARD_AUTHORS
+ 66894403 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY
+ 53693804 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH
+ 20889423 Status.STRONG Reason.TOKENIZED_AUTHORS
+ 7449880 Status.AMBIGUOUS Reason.UNKNOWN
+ 3507120 Status.EXACT Reason.TITLE_AUTHOR_MATCH
+ 1199761 Status.DIFFERENT Reason.PAGE_COUNT
+ 1121611 Status.AMBIGUOUS Reason.SHORT_TITLE
+ 395710 Status.EXACT Reason.WORK_ID
+ 362089 Status.DIFFERENT Reason.COMPONENT
+ 351654 Status.AMBIGUOUS Reason.BLACKLISTED
+ 326730 Status.STRONG Reason.VERSIONED_DOI
+ 239924 Status.STRONG Reason.PREPRINT_PUBLISHED
+ 171594 Status.STRONG Reason.PMID_DOI_PAIR
+ 54646 Status.STRONG Reason.ARXIV_VERSION
+ 49248 Status.STRONG Reason.CUSTOM_IEEE_ARXIV
+ 17135 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW
+ 5219 Status.DIFFERENT Reason.TITLE_FILENAME
+ 2451 Status.AMBIGUOUS Reason.APPENDIX
+ 1874 Status.STRONG Reason.FIGSHARE_VERSION
+ 1231 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN
+ 774 Status.DIFFERENT Reason.NUM_DIFF
+ 448 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916
+ 123 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT
+ 17 Status.STRONG Reason.CUSTOM_BSI_UNDATED
+ 17 Status.DIFFERENT Reason.CUSTOM_PREFIX_10_14288
+ 6 Status.STRONG Reason.CUSTOM_BSI_SUBDOC
+```
+
+Another false negative:
+
+* https://fatcat.wiki/release/sqrld55t4zdrhf23oq75azo67a
+* http://real.mtak.hu/78943/1/acs.jctc.8b00072.pdf, https://fatcat.wiki/release/gx7owpu4gbcglfwlyzdh5qlfji
+
+```
+https://fatcat.wiki/release/sqrld55t4zdrhf23oq75azo67a https://fatcat.wiki/release/gx7owpu4gbcglfwlyzdh5qlfji Status.DIFFERENT Reason.YEAR
+```
+
+Both docs contain 1972?
+
+```xml
+<biblStruct xml:id="b67">
+ <analytic>
+ <title level="a" type="main">Variational Wavefunctions for H2 +</title>
+ <author>
+ <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">F</forename><surname>Weinhold</surname></persName>
+ </author>
+ </analytic>
+ <monogr>
+ <title level="j">J. Chem. Phys</title>
+ <imprint>
+ <biblScope unit="volume">56</biblScope>
+ <biblScope unit="page" from="3798" to="3801" />
+ <date type="published" when="1972" />
+ </imprint>
+ </monogr>
+</biblStruct>
+```
+
+----
+
+Running:
+
+```
+$ time zstdcat -T0 sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | parallel --tmpdir /bigger/tmp --blocksize 4M --pipe -j 16 'python -m fuzzycat verify_ref' > clus
+ter_ref_verify.tsv
+```
+
+resulted in a 69GB tsv file and took 3056m5.322s (~50h), 512033197 comparisons.
+
+Stats:
+
+```
+$ TMPDIR=/bigger/tmp LC_ALL=C time zstdcat -T0
+ cluster_ref_verify_2021_02_16.tsv.zst | cut -d ' ' -f 3-4 | TMPDIR=/bigger/tmp
+ LC_ALL=C sort -S20% | uniq -c | sort -nr
+
+146095427 Status.DIFFERENT Reason.YEAR
+110052214 Status.EXACT Reason.DOI
+ 94300998 Status.STRONG Reason.JACCARD_AUTHORS
+ 68986574 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY
+ 55199653 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH
+ 21545821 Status.STRONG Reason.TOKENIZED_AUTHORS
+ 7746937 Status.AMBIGUOUS Reason.UNKNOWN
+ 3626713 Status.EXACT Reason.TITLE_AUTHOR_MATCH
+ 1265506 Status.DIFFERENT Reason.PAGE_COUNT
+ 1171178 Status.AMBIGUOUS Reason.SHORT_TITLE
+ 409043 Status.EXACT Reason.WORK_ID
+ 374051 Status.DIFFERENT Reason.COMPONENT
+ 356772 Status.AMBIGUOUS Reason.BLACKLISTED
+ 336588 Status.STRONG Reason.VERSIONED_DOI
+ 249723 Status.STRONG Reason.PREPRINT_PUBLISHED
+ 177547 Status.STRONG Reason.PMID_DOI_PAIR
+ 56445 Status.STRONG Reason.ARXIV_VERSION
+ 51776 Status.STRONG Reason.CUSTOM_IEEE_ARXIV
+ 17887 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW
+ 5255 Status.DIFFERENT Reason.TITLE_FILENAME
+ 2451 Status.AMBIGUOUS Reason.APPENDIX
+ 1946 Status.STRONG Reason.FIGSHARE_VERSION
+ 1263 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN
+ 798 Status.DIFFERENT Reason.NUM_DIFF
+ 463 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916
+ 125 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT
+ 18 Status.STRONG Reason.CUSTOM_BSI_UNDATED
+ 18 Status.DIFFERENT Reason.CUSTOM_PREFIX_10_14288
+ 7 Status.STRONG Reason.CUSTOM_BSI_SUBDOC
+
+```
+
+286M positive links.
+
+```
+$ grep -E "Status.STRONG|Status.EXACT" version_1_fuzzy_stats.txt | awk '{print $1}' | paste -sd+ | bc
+286008492
+```
+
+Or 175M, if we exclude DOI and work matches.
+
+```
+$ grep -E "Status.STRONG|Status.EXACT" version_1_fuzzy_stats.txt | grep -Ev "Reason.DOI|Reason.WORK_ID" | awk '{print $1}' | paste -sd+ | bc
+175547235
+```
+
+----
+
+The final derivation dep tree looks like:
+
+```
+ $ ./tasks.py -d BiblioRef
+ \_ BiblioRef(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ BiblioRefFuzzy(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsFatcatClusterVerify(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsFatcatClusters(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsFatcatSortedKeys(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsReleasesMerged(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ ReleaseExportExpanded()
+ \_ RefsToRelease(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ Input()
+ \_ BiblioRefFromJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsFatcatGroupJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsFatcatPMCIDJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsPMCID(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ Input()
+ \_ FatcatPMCID(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ ReleaseExportExpanded()
+ \_ RefsFatcatArxivJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ FatcatArxiv(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ ReleaseExportExpanded()
+ \_ RefsArxiv(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ Input()
+ \_ RefsFatcatPMIDJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ FatcatPMID(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ ReleaseExportExpanded()
+ \_ RefsPMID(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ Input()
+ \_ RefsFatcatDOIJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ FatcatDOIsLower(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ FatcatDOIs(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ ReleaseExportExpanded()
+ \_ RefsDOIsLower(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ RefsDOIs(sha1=ef1756a5856085807742966f48d95b4cb00299a0)
+ \_ Input()
+```
diff --git a/python/notes/version_1_fuzzy_stats.txt b/python/notes/version_1_fuzzy_stats.txt
new file mode 100644
index 0000000..210fc0b
--- /dev/null
+++ b/python/notes/version_1_fuzzy_stats.txt
@@ -0,0 +1,30 @@
+146095427 Status.DIFFERENT Reason.YEAR
+110052214 Status.EXACT Reason.DOI
+94300998 Status.STRONG Reason.JACCARD_AUTHORS
+68986574 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY
+55199653 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH
+21545821 Status.STRONG Reason.TOKENIZED_AUTHORS
+7746937 Status.AMBIGUOUS Reason.UNKNOWN
+3626713 Status.EXACT Reason.TITLE_AUTHOR_MATCH
+1265506 Status.DIFFERENT Reason.PAGE_COUNT
+1171178 Status.AMBIGUOUS Reason.SHORT_TITLE
+ 409043 Status.EXACT Reason.WORK_ID
+ 374051 Status.DIFFERENT Reason.COMPONENT
+ 356772 Status.AMBIGUOUS Reason.BLACKLISTED
+ 336588 Status.STRONG Reason.VERSIONED_DOI
+ 249723 Status.STRONG Reason.PREPRINT_PUBLISHED
+ 177547 Status.STRONG Reason.PMID_DOI_PAIR
+ 56445 Status.STRONG Reason.ARXIV_VERSION
+ 51776 Status.STRONG Reason.CUSTOM_IEEE_ARXIV
+ 17887 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW
+ 5255 Status.DIFFERENT Reason.TITLE_FILENAME
+ 2451 Status.AMBIGUOUS Reason.APPENDIX
+ 1946 Status.STRONG Reason.FIGSHARE_VERSION
+ 1263 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN
+ 798 Status.DIFFERENT Reason.NUM_DIFF
+ 463 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916
+ 125 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT
+ 18 Status.STRONG Reason.CUSTOM_BSI_UNDATED
+ 18 Status.DIFFERENT Reason.CUSTOM_PREFIX_10_14288
+ 7 Status.STRONG Reason.CUSTOM_BSI_SUBDOC
+
diff --git a/python/notes/version_2.md b/python/notes/version_2.md
new file mode 100644
index 0000000..873b5bf
--- /dev/null
+++ b/python/notes/version_2.md
@@ -0,0 +1,219 @@
+# Version 2 (2021-02-18)
+
+As target document we want, as per `proposals/2021-01-29_citation_api.md` the following:
+
+```
+BiblioRef ("bibliographic reference")
+ _key: Optional[str] elasticsearch doc key
+ ("release", source_release_ident, ref_index)
+ ("wikipedia", source_wikipedia_article, ref_index)
+ update_ts: Optional[datetime] elasticsearch doc timestamp
+
+ # metadata about source of reference
+ source_release_ident: Optional[str]
+ source_work_ident: Optional[str]
+ source_wikipedia_article: Optional[str]
+ with lang prefix like "en:Superglue"
+ # skipped: source_openlibrary_work
+ # skipped: source_url_surt
+ source_release_stage: Optional[str]
+ source_year: Optional[int]
+
+ # context of the reference itself
+ ref_index: int
+ 1-indexed, not 0-indexed
+ ref_key: Optional[str]
+ eg, "Lee86", "BIB23"
+ ref_locator: Optional[str]
+ eg, page number
+
+ # target of reference (identifiers)
+ target_release_ident: Optional[str]
+ target_work_ident: Optional[str]
+ target_openlibrary_work: Optional[str]
+ target_url_surt: Optional[str]
+ target_url: Optional[str]
+ would not be stored in elasticsearch, but would be auto-generated
+ by all "get" methods from the SURT, so calling code does not need
+ to do SURT transform
+ # skipped: target_wikipedia_article
+
+ match_provenance: str
+ crossref, pubmed, grobid, etc
+ match_status: Optional[str]
+ strong, weak, etc
+ TODO: "match_strength"?
+ match_reason: Optional[str]
+ "doi", "isbn", "fuzzy title, author", etc
+ maybe "fuzzy-title-author"?
+
+ target_unstructured: string (only if no release_ident link/match)
+ target_csl: free-form JSON (only if no release_ident link/match)
+ CSL-JSON schema (similar to ReleaseEntity schema, but not exactly)
+ generated from unstructured by a GROBID parse, if needed
+```
+
+This resulting docs/index will be generated from various pipelines:
+
+* various identifier joins (doi, pmid, pmcid, arxiv, ...)
+* a fuzzy matching pipeline
+* a wikipedia "scan" over publications, by DOI, title, direct link
+* an open library "scan", matching possibly ISBN or book titles against the catalog
+* relating a source document to all its referenced web pages (as `target_url`)
+
+The raw inputs:
+
+* release export (expanded or minimized)
+* an aggregated list of references
+* wikipedia dumps, e.g. en, de, fr, es, ...
+* an openlibrary dump
+* auxiliary data structures, e.g. journal name lookup database (abbreviations), etc.
+* MAG, base, aminer, and other datasets to run comparisons against
+
+# Setup and deployment
+
+* [-] clone this repo
+* [x] copy "zipapp"
+* [x] setup raw inputs in settings.ini
+* [x] run task
+
+Using shiv for creating single-file deployment. Single config file. Handle to
+list and inspect files. Keep it minimal. External tools in skate.
+
+----
+
+# Match with more complete data
+
+* [x] more sensible changing between inputs (e.g. sample, full, etc.)
+
+For joins.
+
+* [x] reduce release entities to minimum (ReleaseEntityReduced)
+
+Reduced 120G to 48G, big win (stipping files, refs, and container extra); 154203375 docs (12min to count)
+
+* [ ] extract not to (ident, value), but (ident, value, doc) or the like
+* [ ] the joined row should contain both md blobs to generate fuller schema
+
+Zipped Merge
+
+We need:
+
+* refs to releases, derive key, sort
+* reduced releases, derive key, sort
+
+* [ ] sort fatcat and refs by key
+* [ ] zipped iteration over both docs (and run verify)
+
+----
+
+# Other datasets
+
+* [ ] https://archive.org/details/enwiki-20210120, example: https://archive.org/download/enwiki-20210120/enwiki-20210120-pages-articles-multistream11.xml-p6899367p7054859.bz2
+
+----
+
+## Zipped Verification
+
+* beside a one blob per line model, we can run a "comm" like procedure to verify group (or run any other routine on groups)
+
+Advantages of zip mode:
+
+* only need to generate any sorted dataset; we can save the "group by" transform
+* easier to carry the whole doc around, which is what we want, to generate a
+ more complete result document
+
+```
+$ skate-verify -m zip -R <(zstdcat -T0 /bigger/.cache/refcat/FatcatSortedKeys/dataset-full-date-2021-02-20.json.zst) \
+ -F <(zstdcat -T0 /bigger/.cache/refcat/RefsSortedKeys/dataset-full-date-2021-02-20.json.zst)
+```
+
+A basic framework in Go for doing zipped iteration.
+
+* we need the generic (id, key, doc) format, maybe just a jq tweak
+
+----
+
+Example size increase by carrying data to the key matching step; about 10x (3 to 30G compressed).
+
+----
+
+* Putting pieces together:
+
+* 620,626,126 DOI "join"
+* 23,280,469 fuzzy
+* 76,382,408 pmid
+* 49,479 pmcid
+* 3,011,747 arxiv
+
+COCI/crossref has currently:
+
+* 759,516,507 citation links.
+* we: ~723,350,228
+
+```
+$ zstdcat -T0 /bigger/.cache/refcat/BiblioRefV1/dataset-full-date-2021-02-20.json.zst|LC_ALL=C wc
+717435777 717462400 281422956549
+```
+
+----
+
+Some notes on unparsed data:
+
+```
+ "unstructured": "S. F. Fischer and A. Laubereau, Chem. Phys. Lett. 55, 189 (1978).CHPLBC0009-2614"
+
+$ zstdcat -T0 /bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst| jq
+-rc 'select(.biblio.title == null and .biblio.doi == null and .biblio.pmid ==
+null and .biblio.unstructured != null) | .biblio.unstructured' | head -1000000
+| grep -c -E ' [0-9]{1,3}-[0-9]{1,3}'
+```
+
+* 4400/100000; 5% of 500M would still be 25M?
+
+
+
+* pattern matching?
+
+```
+$ zstdcat -T0 /bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst | jq -rc 'select(.biblio.title == null and .biblio.doi == null and .biblio.pmid == null and .biblio.unstructured != null) | .biblio.unstructured'
+```
+
+Data lineage for "v2":
+
+```
+$ refcat.pyz deps BiblioRefV2
+ \_ BiblioRefV2(dataset=full, date=2021-02-20)
+ \_ BiblioRefZippyPMID(dataset=full, date=2021-02-20)
+ \_ FatcatPMID(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsPMID(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ BiblioRefFromFuzzyClusters(dataset=full, date=2021-02-20)
+ \_ RefsFatcatClusters(dataset=full, date=2021-02-20)
+ \_ RefsFatcatSortedKeys(dataset=full, date=2021-02-20)
+ \_ RefsReleasesMerged(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsToRelease(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ BiblioRefZippyPMCID(dataset=full, date=2021-02-20)
+ \_ RefsPMCID(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ FatcatPMCID(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ BiblioRefZippyDOI(dataset=full, date=2021-02-20)
+ \_ FatcatDOI(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsDOI(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ BiblioRefZippyArxiv(dataset=full, date=2021-02-20)
+ \_ RefsArxiv(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ FatcatArxiv(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+```
diff --git a/python/notes/version_3.md b/python/notes/version_3.md
new file mode 100644
index 0000000..8074214
--- /dev/null
+++ b/python/notes/version_3.md
@@ -0,0 +1,187 @@
+# V3
+
+V2 plus:
+
+* [ ] wikipedia
+* [ ] some unstrucutured refs
+* [ ] OL
+* [ ] weblinks
+
+## Unstructured
+
+* about 300M w/o title, etc.
+* some docs mention a "doi" in "unstructured"
+
+Possible extractable information:
+
+* pages ranges with regex
+* doi, isbn, issn
+* author names with some NER?
+* journal abbreviation
+
+Numbers:
+
+$ time zstdcat -T0 dataset-full-date-2021-02-20.json.zst | LC_ALL=C pv -l | LC_ALL=C grep -c -i "doi"
+2772622
+
+Sometimes, the key contains an ISBN:
+
+```
+"key":"9781108604222#EMT-rl-1_BIBe-r-213"
+```
+
+key with doi:
+
+```
+"index":63,"key":"10.1002/9781118960608.gbm01177-BIB6970|gbm01177-cit-6970","locator":"7
+```
+
+ISBN format:
+
+* 978-9279113639
+* 9781566773362
+* 978-80-7357-299-0
+
+URLs may be broken:
+
+```
+http://www. unaids.org/hivaidsinfo/statistics/fact_sheets/pdfs/Thailand_en.pdf
+```
+
+* 2030021 DOI
+* 36376 arxiv
+
+Some cases only contain authors and year, e.g.
+
+```
+{
+ "biblio": {
+ "contrib_raw_names": [
+ "W H Hartmann",
+ "B H Hahn",
+ "H Abbey",
+ "L E Shulman"
+ ],
+ "unstructured": "Hartmann, W. H., Hahn, B. H., Abbey, H., and Shulman, L. E., Lancer, 1965, 1, 123.",
+ "year": 1965
+ },
+```
+
+Here, we could run a query, e.g.
+https://fatcat.wiki/release/search?q=hahn+shulman+abbey+hartmann, and check for
+result set size, year, etc.
+
+Other example:
+
+* https://fatcat.wiki/release/search?q=Goudie+Anderson+Gray+boyle+buchanan+year%3A1965
+
+```
+{
+ "biblio": {
+ "contrib_raw_names": [
+ "R B Goudie",
+ "J R Anderson",
+ "K G Gray",
+ "J A Boyle",
+ "W W Buchanar"
+ ],
+ "unstructured": "Goudie, R. B., Anderson, J. R., Gray, K. G., Boyle, J. A., and Buchanar, W. W., ibid., 1965, 1, 322.",
+ "year": 1965
+ },
+```
+
+----
+
+With `skate-from-unstructured` we get some more doi and arxiv identifiers from
+unstructured refs (unstructured, key). How many?
+
+```
+$ time zstdcat -T0 dataset-full-date-2021-02-20.json.zst | pv -l | \
+ skate-from-unstructured | jq -rc 'select(.biblio.doi != null or .biblio.arxiv_id != null)' | wc -l
+```
+
+The https://anystyle.io/ CRF implementation seems really useful to parse out
+the rest of the unstructured data.
+
+* [ ] parse fields with some containerized anystyle (create an oci container
+ and somehow get it running w/ or w/o docker; maybe podman allows to run as
+library?)
+
+Example:
+
+```
+$ anystyle -f json parse xxxx.txt
+[
+ {
+ "citation-number": [
+ "3. "
+ ],
+ "author": [
+ {
+ "family": "JP",
+ "given": "Morgan"
+ },
+ {
+ "family": "CS",
+ "given": "Bailey"
+ }
+ ],
+ "title": [
+ "Cauda equina syndrome in the dog: radiographical evaluation"
+ ],
+ "volume": [
+ "21"
+ ],
+ "pages": [
+ "45 – 58"
+ ],
+ "type": "article-journal",
+ "container-title": [
+ "J Small Anim Practice"
+ ],
+ "date": [
+ "1980"
+ ]
+ }
+]
+```
+
+Can dump the whole unstructured list in to a single file (one per line).
+
+* 10K lines take: 32s
+* 100M would take probably ~100h to parse.
+
+----
+
+* from 308 "UnmatchedRefs" we would extract doi/arxiv for 47696153.
+
+Stats:
+
+* 759,516,507 citation links.
+* ~723,350,228 + 47,696,153
+* 771046381 edges
+
+----
+
+* aitio has docker installed
+
+```
+Client:
+ Version: 17.06.0-ce
+ API version: 1.30
+ Go version: go1.8.3
+ Git commit: 02c1d87
+ Built: Fri Jun 23 21:23:31 2017
+ OS/Arch: linux/amd64
+
+Server:
+ Version: 17.06.0-ce
+ API version: 1.30 (minimum version 1.12)
+ Go version: go1.8.3
+ Git commit: 02c1d87
+ Built: Fri Jun 23 21:19:04 2017
+ OS/Arch: linux/amd64
+ Experimental: false
+```
+
+Maybe build an alpine based image?
diff --git a/python/notes/wikipedia_citations_2020-07-14.md b/python/notes/wikipedia_citations_2020-07-14.md
new file mode 100644
index 0000000..d079312
--- /dev/null
+++ b/python/notes/wikipedia_citations_2020-07-14.md
@@ -0,0 +1,51 @@
+# Notes on wikipedia_citations_2020-07-14
+
+* https://archive.org/details/wikipedia_citations_2020-07-14
+* https://zenodo.org/record/3940692
+* https://github.com/Harshdeep1996/cite-classifications-wiki
+
+```
+.
+├── [6.6G] citations_from_wikipedia.zip
+├── [819M] lookup_data.zip
+├── [1.4G] minimal_dataset.zip
+├── [ 91K] wikipedia_citations_2020-07-14_archive.torrent
+├── [2.0K] wikipedia_citations_2020-07-14_files.xml
+├── [ 20K] wikipedia_citations_2020-07-14_meta.sqlite
+└── [1.3K] wikipedia_citations_2020-07-14_meta.xml
+```
+
+Using `parquet-tools cat --json`
+(https://stackoverflow.com/questions/36140264/inspect-parquet-from-command-line)
+to convert to json.
+
+About 1442176 DOI, 1027006 unique.
+
+Most referenced on WP:
+
+```
+ 4393 10.1073/pnas.242603899
+ 3182 10.1101/gr.2596504
+ 2307 10.24436/2
+ 2079 10.1038/ng1285
+ 1447 10.1007/BF00171763
+ 1357 10.1051/0004-6361:20078357
+ 1346 10.1038/nature04209
+ 1293 10.1016/0378-1119(94)90802-8
+ 1246 10.1016/S0378-1119(97)00411-3
+ 927 10.1111/j.1096-3642.2005.00153.x
+ 738 10.1016/j.cell.2006.09.026
+ 657 10.1101/gr.4039406
+ 631 10.1101/gr.6.9.791
+ 607 10.1038/msb4100134
+ 602 10.1101/gr.143000
+ 591 10.5194/hess-11-1633-2007
+ 531 10.1101/gr.GR1547R
+ 492 10.1080/002229300299282
+ 480 10.1101/gr.2576704
+ 460 10.1093/nar/gkj139
+```
+
+* https://git.archive.org/webgroup/fatcat/-/blob/10eb30251f89806cb7a0f147f427c5ea7e5f9941/proposals/2021-01-29_citation_api.md
+* `source_wikipedia_article: Optional[str]`
+
diff --git a/python/refcat/__init__.py b/python/refcat/__init__.py
new file mode 100644
index 0000000..b794fd4
--- /dev/null
+++ b/python/refcat/__init__.py
@@ -0,0 +1 @@
+__version__ = '0.1.0'
diff --git a/python/refcat/cli.py b/python/refcat/cli.py
new file mode 100644
index 0000000..ca1cab7
--- /dev/null
+++ b/python/refcat/cli.py
@@ -0,0 +1,251 @@
+"""
+ ____ __
+ ________ / __/________ _/ /_
+ / ___/ _ \/ /_/ ___/ __ `/ __/
+ / / / __/ __/ /__/ /_/ / /_
+/_/ \___/_/ \___/\__,_/\__/
+
+Command line entry point for running various data tasks.
+
+ $ refcat.pyz [COMMAND | TASK] [OPTIONS]
+
+Commands: ls, ll, deps, tasks, files, config, cat, completion
+
+To install completion run:
+
+ $ source <(refcat.pyz completion)
+"""
+
+import logging
+import subprocess
+import sys
+import tempfile
+
+import gluish
+import luigi
+from luigi.parameter import MissingParameterException
+from luigi.task import Register
+from luigi.task_register import TaskClassNotFoundException
+
+from refcat import __version__
+from refcat.settings import LOGGING_CONF_FILE, settings
+from refcat.deps import dump_deps
+from refcat.tasks import *
+from refcat.utils import columnize
+
+# XXX: get rid of gluish dep, include them in refcat
+suppress_task_names = [
+ "Available",
+ "BaseTask",
+ "Config",
+ "Executable",
+ "ExternalTask",
+ "FillSolrIndex",
+ "GitCloneRepository",
+ "GitUpdateRepository",
+ "MockTask",
+ "RangeBase",
+ "RangeByMinutes",
+ "RangeByMinutesBase",
+ "RangeDaily",
+ "RangeDailyBase",
+ "RangeHourly",
+ "RangeHourlyBase",
+ "RangeMonthly",
+ "Task",
+ "TestNotificationsTask",
+ "WrapperTask",
+]
+
+
+def tasks():
+ """
+ Print task name.
+ """
+ names = [name for name in sorted(Register.task_names()) if name not in suppress_task_names and not name.islower()]
+ for name in names:
+ print(name)
+
+
+def files():
+ """
+ Print task name and file.
+ """
+ names = [name for name in sorted(Register.task_names()) if name not in suppress_task_names and not name.islower()]
+ for name in names:
+ klass = Register.get_task_cls(name)
+ try:
+ print("{:30s}{}".format(name, klass().output().path))
+ except AttributeError:
+ print("{:30s}".format(name))
+
+
+def cat(*args):
+ """
+ Inspect file.
+ """
+ if len(args) == 0:
+ raise ValueError("ls failed: task name required")
+ task = find_task(args[0])
+ try:
+ filename = task().output().path
+ if filename.endswith(".zst"):
+ subprocess.run(["zstdcat", "-T0", filename])
+ elif filename.endswith(".gz"):
+ subprocess.run(["zcat", filename])
+ else:
+ subprocess.run(["cat", filename])
+ except FileNotFoundError:
+ print("file not found: {}".format(filename), file=sys.stderr)
+ except AttributeError:
+ print("{} is most likely not a task object".format(name), file=sys.stderr)
+
+
+def ls(*args):
+ """
+ Print output filename for task.
+ """
+ if len(args) == 0:
+ raise ValueError("ls failed: task name required")
+ task = find_task(args[0])
+ print(task().output().path)
+
+
+def ll(*args):
+ """
+ Long output.
+ """
+ if len(args) == 0:
+ raise ValueError("ls failed: task name required")
+ task = find_task(args[0])
+ try:
+ filename = task().output().path
+ subprocess.run(["ls", "-lah", filename])
+ except FileNotFoundError:
+ print("file not found: {}".format(filename), file=sys.stderr)
+ except AttributeError:
+ print("{} is most likely not a task object".format(name), file=sys.stderr)
+
+
+def deps(*args):
+ """
+ Render task dependencies.
+ """
+ if len(args) == 0:
+ raise ValueError("deps failed: task name required")
+ task = find_task(args[0])
+ dump_deps(task())
+
+
+def config():
+ """
+ Dump config to stdout.
+ """
+ with open(settings.settings_file) as f:
+ print(f.read())
+
+
+def completion():
+ snippet = """
+_refcat_completion()
+{
+ local cur prev
+ COMPREPLY=()
+ cur=${COMP_WORDS[COMP_CWORD]}
+ prev=${COMP_WORDS[COMP_CWORD-1]}
+
+ if [ $COMP_CWORD -eq 1 ]; then
+ COMPREPLY=( $(compgen -W "cat completion config deps files ll ls tasks" -- $cur) )
+ elif [ $COMP_CWORD -eq 2 ]; then
+ case "$prev" in
+ "cat")
+ COMPREPLY=( $(compgen -W "$(refcat.pyz tasks)" -- $cur) )
+ ;;
+ "ll")
+ COMPREPLY=( $(compgen -W "$(refcat.pyz tasks)" -- $cur) )
+ ;;
+ "ls")
+ COMPREPLY=( $(compgen -W "$(refcat.pyz tasks)" -- $cur) )
+ ;;
+ *)
+ ;;
+ esac
+ fi
+ return 0
+}
+
+complete -F _refcat_completion "refcat.pyz"
+complete -F _refcat_completion "refcat"
+ """
+ print(snippet)
+
+
+def find_task(name):
+ """
+ Note: return task class, not instance.
+ """
+ task = globals().get(name)
+ if task is None:
+ raise RuntimeError("no such task: {}".format(name))
+ if not isinstance(task(), luigi.Task):
+ raise RuntimeError("not a task: {}".format(name))
+ return task
+
+
+def main():
+ """
+ The main command line entry point.
+ """
+ if os.path.exists(LOGGING_CONF_FILE):
+ logging.config.fileConfig(LOGGING_CONF_FILE)
+
+ if settings.TMPDIR:
+ # This might not be passed on to subprocesses.
+ tempfile.tempdir = settings.TMPDIR
+
+ # Explicitly name valid subcommands.
+ sub_commands = [
+ "cat",
+ "completion",
+ "config",
+ "deps",
+ "files",
+ "ll",
+ "ls",
+ "tasks",
+ ]
+
+ if len(sys.argv) >= 2 and sys.argv[1] in sub_commands:
+ try:
+ func = globals()[sys.argv[1]]
+ if callable(func):
+ func(*sys.argv[2:])
+ else:
+ print("not implemented: {}".format(sys.argv[1]))
+ except KeyError:
+ print("sub-command not implemented: {}".format(sys.argv[1]), file=sys.stderr)
+ except (AttributeError, ValueError, RuntimeError) as exc:
+ print(exc, file=sys.stderr)
+ sys.exit(1)
+ else:
+ sys.exit(0)
+ elif len(sys.argv) == 1:
+ print(__doc__)
+ print("VERSION {}".format(__version__))
+ print("SETTINGS {}".format(settings.settings_file))
+ print("BASE {}".format(settings.BASE))
+ print("TMPDIR {}".format(settings.TMPDIR))
+ print()
+ names = [name for name in sorted(Register.task_names()) if name not in suppress_task_names and not name.islower()]
+ print(columnize(names))
+ sys.exit(0)
+
+ # If we found not subcommand, assume task name.
+ try:
+ luigi.run(local_scheduler=True) # XXX: add logging_conf_file
+ except MissingParameterException as err:
+ print('missing parameter: %s' % err, file=sys.stderr)
+ sys.exit(1)
+ except TaskClassNotFoundException as err:
+ print(err, file=sys.stderr)
+ sys.exit(1)
diff --git a/python/refcat/deps.py b/python/refcat/deps.py
new file mode 100644
index 0000000..4d9a49b
--- /dev/null
+++ b/python/refcat/deps.py
@@ -0,0 +1,29 @@
+# Utilities, e.g. for printing dependency tree.
+
+import collections
+
+
+def dump_deps(task=None, indent=0):
+ """
+ Print dependency graph for a given task to stdout.
+ """
+ if task is None:
+ return
+ g = build_dep_graph(task)
+ print('%s \_ %s' % (' ' * indent, task))
+ for dep in g[task]:
+ dump_deps(task=dep, indent=indent + 1)
+
+
+def build_dep_graph(task=None):
+ """
+ Return the task graph as dict mapping nodes to children.
+ """
+ g = collections.defaultdict(set)
+ queue = [task]
+ while len(queue) > 0:
+ task = queue.pop()
+ for dep in task.deps():
+ g[task].add(dep)
+ queue.append(dep)
+ return g
diff --git a/python/refcat/settings.py b/python/refcat/settings.py
new file mode 100644
index 0000000..699e31c
--- /dev/null
+++ b/python/refcat/settings.py
@@ -0,0 +1,16 @@
+from pathlib import Path
+
+from dynaconf import Dynaconf
+
+# logging configuration
+LOGGING_CONF_FILE = str(Path.home().joinpath(".config/refcat/logging.ini"))
+
+# application settings
+CONFIG_FILE = str(Path.home().joinpath(".config/refcat/settings.ini"))
+ENVVAR_PREFIX_FOR_DYNACONF = "REFCAT"
+ENV_FOR_DYNACONF = "default"
+
+settings = Dynaconf(ENVIRONMENTS=True,
+ ENV_FOR_DYNACONF=ENV_FOR_DYNACONF,
+ ENVVAR_PREFIX_FOR_DYNACONF=ENVVAR_PREFIX_FOR_DYNACONF,
+ SETTINGS_FILE_FOR_DYNACONF=CONFIG_FILE)
diff --git a/python/refcat/tasks.py b/python/refcat/tasks.py
new file mode 100644
index 0000000..4fcf97a
--- /dev/null
+++ b/python/refcat/tasks.py
@@ -0,0 +1,1366 @@
+#!/usr/bin/env python3
+"""
+Set of luigi tasks to extract and build various derivations from fatcat
+reference data. Reference data can come from metadata or ML extraction
+(grobid).
+
+Rationale is that we successively want to build a derived dataset (citation
+graph and various reports) and we expect the data to be messy and partial. We
+want to cache intermediate results for quicker feature development.
+
+Notes.
+
+We use a single zstd-compressed input file for easier handling (albeit splits
+would be run in parallel by luigi). A sha1sum takes 67 minutes.
+
+Outputs should be compressed as well to save space.
+
+Use TMPDIR=... to adjust temporary directory.
+
+To list available tasks, there is a convenience "run.sh" in the repo:
+
+ $ refcat.pyz
+
+ ____ __
+ ________ / __/________ _/ /_
+ / ___/ _ \/ /_/ ___/ __ `/ __/
+ / / / __/ __/ /__/ /_/ / /_
+ /_/ \___/_/ \___/\__,_/\__/
+
+ Command line entry point for running various data tasks.
+
+ $ refcat [COMMAND | TASK] [OPTIONS]
+
+ Commands: ls, ll, deps
+
+ VERSION 0.1.0
+ SETTINGS /home/tir/.config/refcat/settings.ini
+ BASE /magna/.cache
+ TMPDIR /magna/tmp
+
+ BiblioRef RGSitemapToRelease RefsKeyStats
+ BiblioRefFromJoin Refcat RefsPMCID
+ BiblioRefFuzzy Refs RefsPMID
+ CommonDOI RefsArxiv RefsReleasesMerged
+ CommonTitles RefsCounter RefsSortedKeys
+ CommonTitlesLower RefsDOI RefsTitleFrequency
+ FatcatArxiv RefsFatcatArxivJoin RefsTitles
+ FatcatDOI RefsFatcatClusterVerify RefsTitlesLower
+ FatcatPMCID RefsFatcatClusters RefsToRelease
+ FatcatPMID RefsFatcatDOIJoin ReleaseExportExpanded
+ FatcatSortedKeys RefsFatcatGroupJoin ReleaseExportReduced
+ FatcatTitles RefsFatcatPMCIDJoin ReleaseExportTitleOnly
+ FatcatTitlesLower RefsFatcatPMIDJoin URLList
+ KeyDistribution RefsFatcatRanked URLTabs
+ RGSitemapFatcatMerged RefsFatcatSortedKeys
+ RGSitemapFatcatSortedKeys RefsFatcatTitleLowerJoin
+
+Config (e.g. raw input data) taken from $HOME/.config/refcat/settings.ini.
+
+--------
+
+TODO and report notes
+
+* [ ] how many of these links point to DOI?
+* [ ] how many DOI refs do we have, which DOI do we miss?
+* [ ] exact title matches?
+* [ ] lowercase title matches?
+* [ ] fuzzy title matches?
+* [ ] lowercase DOI lists; common dois, dois only in references
+
+Derive release entity schema from refs, join with release export then run
+clustering and verify.
+
+Task BiblioRef is a current artifact:
+
+ \_ BiblioRef(dataset=full, date=2021-02-20)
+ \_ BiblioRefFromJoin(dataset=full, date=2021-02-20)
+ \_ RefsFatcatGroupJoin(dataset=full, date=2021-02-20)
+ \_ RefsFatcatPMIDJoin(dataset=full, date=2021-02-20)
+ \_ RefsPMID(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ FatcatPMID(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsFatcatDOIJoin(dataset=full, date=2021-02-20)
+ \_ RefsDOI(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ FatcatDOI(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsFatcatArxivJoin(dataset=full, date=2021-02-20)
+ \_ FatcatArxiv(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsArxiv(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ RefsFatcatPMCIDJoin(dataset=full, date=2021-02-20)
+ \_ FatcatPMCID(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+ \_ RefsPMCID(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ BiblioRefFuzzy(dataset=full, date=2021-02-20)
+ \_ RefsFatcatClusterVerify(dataset=full, date=2021-02-20)
+ \_ RefsFatcatClusters(dataset=full, date=2021-02-20)
+ \_ RefsFatcatSortedKeys(dataset=full, date=2021-02-20)
+ \_ RefsReleasesMerged(dataset=full, date=2021-02-20)
+ \_ RefsToRelease(dataset=full, date=2021-02-20)
+ \_ Refs(dataset=full, date=2021-02-20)
+ \_ ReleaseExportReduced(dataset=full, date=2021-02-20)
+ \_ ReleaseExportExpanded(dataset=full, date=2021-02-20)
+
+"""
+
+import argparse
+import collections
+import datetime
+import json
+import logging
+import multiprocessing
+import os
+import sys
+import tempfile
+
+import luigi
+from fuzzycat.cluster import Cluster, release_key_title_sandcrawler
+from gluish.format import Zstd
+from gluish.task import BaseTask
+from gluish.utils import shellout
+
+from refcat.settings import settings
+from refcat.docstats import SetEncoder, docstats
+from refcat.utils import extract_dois, extract_urls, ref_to_release
+
+
+class Refcat(BaseTask):
+ """
+ A base tasks for all refcat related tasks.
+ """
+ BASE = settings.BASE
+ TAG = 'refcat'
+
+ date = luigi.DateParameter(default=datetime.date(2021, 2, 20), description="a versioning help, change this manually")
+ tmpdir = luigi.Parameter(default="/magna/tmp", description="set tempdir", significant=False)
+ n = luigi.IntParameter(default=multiprocessing.cpu_count(), significant=False)
+
+ @property
+ def logger(self):
+ """
+ Return the logger. Module logging uses singleton internally, so no worries.
+ """
+ return logging.getLogger('refcat')
+
+
+# ----8< Raw inputs; XXX: add wikipedia dump, mag, OCI, ...
+
+
+class Refs(luigi.ExternalTask, Refcat):
+ """
+ Compressed (zstd) references, as of 01/2021 containing ~1.8B docs.
+ """
+ def output(self):
+ return luigi.LocalTarget(path=settings.REFS_FILE, format=Zstd)
+
+
+class ReleaseExportExpanded(luigi.ExternalTask, Refcat):
+ """
+ Release export, zstd version.
+ """
+ def output(self):
+ return luigi.LocalTarget(path=settings.RELEASE_EXPORT_EXPANDED_FILE, format=Zstd)
+
+
+# ----8< Derivations
+
+
+class ReleaseExportReduced(Refcat):
+ """
+ Reduce dataset size, stripping fields.
+ """
+ def requires(self):
+ return ReleaseExportExpanded()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ parallel --block 10M -j 16 --pipe "jq -rc 'del(.files) | del(.refs) | del(.container.extra)'" |
+ zstd -T0 -c9 > {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 ReleaseExportTitleOnly(Refcat):
+ """
+ Reduce dataset size, only keep title.
+ """
+ def requires(self):
+ return ReleaseExportReduced()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ parallel --block 10M -j 16 --pipe "jq -rc '{{\"title\": .title}}'" |
+ zstd -T0 -c9 > {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 URLTabs(Refcat):
+ """
+ Tabular URLs, note: URL can contain artifacts from parsing.
+
+ Performance data point:
+
+ real 70m6.309s
+ user 757m4.317s
+ sys 85m54.710s
+ """
+ def requires(self):
+ return Refs()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ parallel -j {n} --block 100M --pipe "jq -rc '[.work_ident, .release_ident, .biblio.url?] | @tsv'" |
+ zstd -T0 -c > {output}
+ """,
+ 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 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 Refs()
+
+ 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 Refs()
+
+ 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 Refs()
+
+ 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 Refs()
+
+ 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 Refs()
+
+ 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 Refs()
+
+ 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 Refs()
+
+ 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 Refs()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ skate-ref-to-release -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)
+
+
+class RefsFatcatClusterVerify(Refcat):
+ """
+ Verification; took 50h+, ran manually, documenting here (not running,
+ fuzzycat needs pipenv currently).
+
+ Output like:
+
+ https://fatcat.wiki/release/a6xucdggk5h7bcmbxidvqt7hxe https://fatcat.wiki/release/amnpvj5ma5dxlc2a3x2bm2zbnq Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH
+ https://fatcat.wiki/release/vyppsuuh2bhapdwcqzln5momta https://fatcat.wiki/release/6gd53yl5yzakrlr72xeojamchi Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY
+ https://fatcat.wiki/release/hazousx6wna5bn5e27s5mrljzq https://fatcat.wiki/release/iajt2xam5nbc3ichkxxuhqaqw4 Status.DIFFERENT Reason.YEAR
+
+ XXX: can we get rid of this?
+ """
+ def requires(self):
+ return RefsFatcatClusters()
+
+ def run(self):
+ # As ran in 2021-02-12 on aitio
+ #
+ # $ time zstdcat -T0
+ # sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | parallel
+ # --tmpdir /bigger/tmp --blocksize 4M --pipe -j 16 'python -m fuzzycat
+ # verify_ref' > cluster_ref_verify.tsv
+ print(""" zstdcat -T0 {input} | parallel --tmpdir {tmpdir}
+ --blocksize 4M --pipe -j 16 'python -m fuzzycat verify_ref' |
+ zstd -c -T0 > {output} """.format(input=self.input().path, tmpdir=self.tmpdir, output=self.output().path))
+
+ def output(self):
+ return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd)
+
+
+class BiblioRefFuzzy(Refcat):
+ """
+ A biblioref document from fuzzy match results. 12min.
+ """
+ def requires(self):
+ return RefsFatcatClusterVerify()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ LC_ALL=C grep -E "(EXACT|STRONG)" |
+ LC_ALL=C grep -E -v "(Reason.DOI|Reason.WORK_ID)" |
+ skate-biblioref |
+ zstd -T0 -c9 > {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 BiblioRefFromJoin(Refcat):
+ """
+ Biblio ref from join.
+ """
+ def requires(self):
+ return RefsFatcatGroupJoin()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ skate-biblioref |
+ zstd -T0 -c9 > {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 BiblioRef(Refcat):
+ """
+ Generate proposed biblioref docs from various pipelines.
+ """
+ def requires(self):
+ return [BiblioRefFromJoin(), BiblioRefFuzzy()]
+
+ def run(self):
+ _, tmpf = tempfile.mkstemp(prefix="refcat-")
+ for target in self.input():
+ output = shellout("cat {input} >> {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)
+
+
+# ==== 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
+
+
+class UnmatchedRefs(Refcat):
+ """
+ File with not yet considered refs (e.g. no title, doi, ...)
+ """
+ def requires(self):
+ return Refs()
+
+ def run(self):
+ output = shellout("""
+ zstdcat -T0 {input} |
+ parallel -j {n} --block 10M --pipe "jq -rc 'select(.biblio.doi == null and .biblio.title == null and .biblio.pmid == null and .biblio.pmcid == null and .biblio.arxiv_id == null)'" |
+ zstd -T0 -c > {output}""",
+ n=self.n,
+ 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)
+
+
+# ==== 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)
diff --git a/python/refcat/utils.py b/python/refcat/utils.py
new file mode 100644
index 0000000..2fbaec5
--- /dev/null
+++ b/python/refcat/utils.py
@@ -0,0 +1,268 @@
+"""
+Assorted utilities.
+"""
+
+import collections
+import io
+import re
+
+DOI_PATTERN = re.compile(r"10.[0-9]{1,6}/[^ ]*[\w]")
+
+# via: https://gist.github.com/gruber/8891611
+URL_PATTERN = re.compile(r"""(?xi)
+\b
+( # Capture 1: entire matched URL
+ (?:
+ https?: # URL protocol and colon
+ (?:
+ /{1,3} # 1-3 slashes
+ | # or
+ [a-z0-9%] # Single letter or digit or '%'
+ # (Trying not to match e.g. "URI::Escape")
+ )
+ | # or
+ # looks like domain name followed by a slash:
+ [a-z0-9.\-]+[.]
+ (?:com|net|org|edu|gov|mil|aero|asia|biz|cat|coop|info|int|jobs|mobi|museum|name|post|pro|tel|travel|xxx|ac|ad|ae|af|ag|ai|al|am|an|ao|aq|ar|as|at|au|aw|ax|az|ba|bb|bd|be|bf|bg|bh|bi|bj|bm|bn|bo|br|bs|bt|bv|bw|by|bz|ca|cc|cd|cf|cg|ch|ci|ck|cl|cm|cn|co|cr|cs|cu|cv|cx|cy|cz|dd|de|dj|dk|dm|do|dz|ec|ee|eg|eh|er|es|et|eu|fi|fj|fk|fm|fo|fr|ga|gb|gd|ge|gf|gg|gh|gi|gl|gm|gn|gp|gq|gr|gs|gt|gu|gw|gy|hk|hm|hn|hr|ht|hu|id|ie|il|im|in|io|iq|ir|is|it|je|jm|jo|jp|ke|kg|kh|ki|km|kn|kp|kr|kw|ky|kz|la|lb|lc|li|lk|lr|ls|lt|lu|lv|ly|ma|mc|md|me|mg|mh|mk|ml|mm|mn|mo|mp|mq|mr|ms|mt|mu|mv|mw|mx|my|mz|na|nc|ne|nf|ng|ni|nl|no|np|nr|nu|nz|om|pa|pe|pf|pg|ph|pk|pl|pm|pn|pr|ps|pt|pw|py|qa|re|ro|rs|ru|rw|sa|sb|sc|sd|se|sg|sh|si|sj| Ja|sk|sl|sm|sn|so|sr|ss|st|su|sv|sx|sy|sz|tc|td|tf|tg|th|tj|tk|tl|tm|tn|to|tp|tr|tt|tv|tw|tz|ua|ug|uk|us|uy|uz|va|vc|ve|vg|vi|vn|vu|wf|ws|ye|yt|yu|za|zm|zw)
+ /
+ )
+ (?: # One or more:
+ [^\s()<>{}\[\]]+ # Run of non-space, non-()<>{}[]
+ | # or
+ \([^\s()]*?\([^\s()]+\)[^\s()]*?\) # balanced parens, one level deep: (…(…)…)
+ |
+ \([^\s]+?\) # balanced parens, non-recursive: (…)
+ )+
+ (?: # End with:
+ \([^\s()]*?\([^\s()]+\)[^\s()]*?\) # balanced parens, one level deep: (…(…)…)
+ |
+ \([^\s]+?\) # balanced parens, non-recursive: (…)
+ | # or
+ [^\s`!()\[\]{};:'".,<>?«»“”‘’] # not a space or one of these punct chars
+ )
+ | # OR, the following to match naked domains:
+ (?:
+ (?<!@) # not preceded by a @, avoid matching foo@_gmail.com_
+ [a-z0-9]+
+ (?:[.\-][a-z0-9]+)*
+ [.]
+ (?:com|net|org|edu|gov|mil|aero|asia|biz|cat|coop|info|int|jobs|mobi|museum|name|post|pro|tel|travel|xxx|ac|ad|ae|af|ag|ai|al|am|an|ao|aq|ar|as|at|au|aw|ax|az|ba|bb|bd|be|bf|bg|bh|bi|bj|bm|bn|bo|br|bs|bt|bv|bw|by|bz|ca|cc|cd|cf|cg|ch|ci|ck|cl|cm|cn|co|cr|cs|cu|cv|cx|cy|cz|dd|de|dj|dk|dm|do|dz|ec|ee|eg|eh|er|es|et|eu|fi|fj|fk|fm|fo|fr|ga|gb|gd|ge|gf|gg|gh|gi|gl|gm|gn|gp|gq|gr|gs|gt|gu|gw|gy|hk|hm|hn|hr|ht|hu|id|ie|il|im|in|io|iq|ir|is|it|je|jm|jo|jp|ke|kg|kh|ki|km|kn|kp|kr|kw|ky|kz|la|lb|lc|li|lk|lr|ls|lt|lu|lv|ly|ma|mc|md|me|mg|mh|mk|ml|mm|mn|mo|mp|mq|mr|ms|mt|mu|mv|mw|mx|my|mz|na|nc|ne|nf|ng|ni|nl|no|np|nr|nu|nz|om|pa|pe|pf|pg|ph|pk|pl|pm|pn|pr|ps|pt|pw|py|qa|re|ro|rs|ru|rw|sa|sb|sc|sd|se|sg|sh|si|sj| Ja|sk|sl|sm|sn|so|sr|ss|st|su|sv|sx|sy|sz|tc|td|tf|tg|th|tj|tk|tl|tm|tn|to|tp|tr|tt|tv|tw|tz|ua|ug|uk|us|uy|uz|va|vc|ve|vg|vi|vn|vu|wf|ws|ye|yt|yu|za|zm|zw)
+ \b
+ /?
+ (?!@) # not succeeded by a @, avoid matching "foo.na" in "foo.na@example.com"
+ )
+)
+""")
+
+
+def derive_from_ref(doc):
+ """
+ Given a ref document, return an extended document.
+
+ * biblio might have doi, or url with doi
+
+ Sometimes the doi is not the doi, e.g.
+
+ ... "doi": "https:/www.atsjournals.org/doi/10.1513/AnnalsATS.201602-127OC",
+
+ Do less expensive lookups first:
+
+ * is there a doi? we need a (sorted) doi release ident table for quick
+ lookups, e.g. shelve
+ * is there some doi hidden in a url or elsewhere?
+ * is there a QID?
+ * derive a number of keys (from fuzzycat) from title and authors
+ * find the key in a prepared key-value store or do some binary search over a sorted cache file
+ * run verification between a pseudo-release and a release document
+ * run verification between a pseudo-release and a release document
+
+ """
+ raise NotImplementedError
+
+
+def extract_urls(s):
+ return URL_PATTERN.findall(s)
+
+
+def extract_dois(s):
+ return DOI_PATTERN.findall(s)
+
+
+def cleanup_url(url):
+ """
+ Given a URL string, check if it yields a 200.
+
+ http://www.ces.clemson.edu/~ahoover/stare/[14
+ http://rsbweb.nih.gov/ij/(accessed
+ http://www.construction-chanvre.asso.fr.
+ http://dx
+ USDA/RM/SARH/INIFAPGeneral
+ ...
+
+ """
+ raise NotImplementedError
+
+
+def ref_to_release(ref, require_title=False):
+ """
+ Turn ref into a release.
+
+ {
+ "biblio": {
+ "container_name": "Leisure in Contemporary Society",
+ "contrib_raw_names": [
+ "K Roberts"
+ ],
+ "unstructured": "Roberts, K. (1999) Leisure in Contemporary Society. Oxford: CABI Publishing.",
+ "year": 1999
+ },
+ "index": 10,
+ "key": "8_CR11",
+ "ref_source": "crossref",
+ "release_ident": "k7jnyix375blxffr4llcc7gfaa",
+ "release_year": 2007,
+ "work_ident": "aaaonixgi5b6ziulq4odznf5fa"
+ }
+
+ Sample (1M) keys:
+
+ {
+ "has_any_extid": 393409,
+ "has_container_volume_issue_pages": 58133,
+ "has_title_contrib_year": 467613,
+ "has_contrib_container_year": 562049,
+ "has_title_container_year": 357526,
+ "total": 1000000,
+ "has_key": 917486,
+ "source_grobid": 457224,
+ "has_release_ident": 1000000,
+ "has_release_year": 965173,
+ "has_work_ident": 1000000,
+ "has_container_name": 590519,
+ "has_contrib_raw_names": 729729,
+ "has_issue": 77384,
+ "has_pages": 339494,
+ "has_title": 524288,
+ "has_unstructured": 651102,
+ "has_volume": 533352,
+ "has_year": 721823,
+ "has_index": 969778,
+ "has_publisher": 40750,
+ "source_crossref": 425789,
+ "has_doi": 344885,
+ "has_locator": 246106,
+ "has_url": 25284,
+ "source_datacite": 34855,
+ "source_pubmed": 66027,
+ "has_target_release_id": 44076,
+ "has_pmid": 49144,
+ "source_fatcat": 16105,
+ "has_arxiv_id": 2018,
+ "has_pmcid": 45
+ }
+
+ Report from indigo (10M):
+
+ {
+ "biblio": 10000000,
+ "biblio.arxiv_id": 23227,
+ "biblio.container_name": 5760760,
+ "biblio.contrib_raw_names": 7156385,
+ "biblio.doi": 3584451,
+ "biblio.issue": 763784,
+ "biblio.pages": 3331911,
+ "biblio.pmcid": 776,
+ "biblio.pmid": 471338,
+ "biblio.publisher": 398305,
+ "biblio.title": 5164864,
+ "biblio.unstructured": 6304402,
+ "biblio.url": 256771,
+ "biblio.volume": 5202508,
+ "biblio.year": 7055442,
+ "index": 10000000,
+ "key": 8986307,
+ "locator": 2390436,
+ "ref_source": 10000000,
+ "release_ident": 10000000,
+ "release_year": 9629380,
+ "target_release_id": 419033,
+ "work_ident": 10000000
+ }
+
+ TODO: reduce footprint in the "_" meta section.
+
+ """
+ if not "biblio" in ref:
+ return None
+
+ biblio = ref["biblio"]
+ result = collections.defaultdict(collections.defaultdict)
+
+ # we need this for clustering
+ result["ident"] = ref["release_ident"]
+
+ result["_"]["release_ident"] = ref["release_ident"]
+ result["_"]["work_ident"] = ref["work_ident"]
+ if "target_release_id" in ref:
+ # via pmid?
+ result["_"]["target_release_id"] = ref["target_release_id"]
+
+ if "arxiv_id" in biblio:
+ result["ext_ids"]["arxiv"] = biblio["arxiv_id"]
+ if "doi" in biblio:
+ result["ext_ids"]["doi"] = biblio["doi"]
+ if "pmid" in biblio:
+ result["ext_ids"]["pmid"] = biblio["pmid"]
+ if "pmcid" in biblio:
+ result["ext_ids"]["pmcid"] = biblio["pmcid"]
+
+ if "title" in biblio:
+ result["title"] = biblio["title"]
+ elif require_title:
+ if "ext_ids" in result:
+ return result
+ else:
+ return None
+
+ if "publisher" in biblio:
+ result["publisher"] = biblio["publisher"]
+ if "container_name" in biblio:
+ result["container"]["name"] = biblio["container_name"]
+ if "volume" in biblio:
+ result["volume"] = biblio["volume"]
+ if "issue" in biblio:
+ result["issue"] = biblio["issue"]
+ if "pages" in biblio:
+ result["pages"] = biblio["pages"]
+ if "release_year" in biblio:
+ result["release_year"] = biblio["release_year"]
+ if "contrib_raw_names" in biblio:
+ result["contribs"] = [{"raw_name": name} for name in biblio["contrib_raw_names"]]
+
+ return result
+
+
+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()
diff --git a/python/setup.py b/python/setup.py
new file mode 100644
index 0000000..6645545
--- /dev/null
+++ b/python/setup.py
@@ -0,0 +1,42 @@
+import setuptools
+
+from refcat import __version__
+
+with open("README.md", "r") as fh:
+ long_description = fh.read()
+
+ setuptools.setup(
+ name="refcat",
+ version=__version__,
+ author="Martin Czygan",
+ author_email="martin@archive.org",
+ description="Reference data munging utilities",
+ long_description=long_description,
+ long_description_content_type="text/markdown",
+ url="https://git.archive.org/martin/cgraph",
+ packages=setuptools.find_packages(),
+ classifiers=[
+ "Programming Language :: Python :: 3",
+ "License :: OSI Approved :: MIT License",
+ "Operating System :: OS Independent",
+ ],
+ python_requires=">=3.6",
+ entry_points={"console_scripts": [
+ "refcat=refcat.cli:main"
+ ]},
+ install_requires=[
+ "dynaconf[ini]",
+ "fuzzycat",
+ "gluish",
+ ],
+ extras_require={"dev": [
+ "ipython",
+ "isort",
+ "mypy",
+ "pylint",
+ "pytest",
+ "pytest-cov",
+ "twine",
+ "yapf",
+ ],},
+ )
diff --git a/python/tests/test_utils.py b/python/tests/test_utils.py
new file mode 100644
index 0000000..79c8919
--- /dev/null
+++ b/python/tests/test_utils.py
@@ -0,0 +1,41 @@
+from refcat.utils import extract_urls, extract_dois
+
+
+def test_extract_urls():
+ assert extract_urls("") == []
+ assert extract_urls("abc") == []
+ assert extract_urls("httP//abc") == []
+ assert extract_urls("http//a.com") == ["a.com"]
+ assert extract_urls("http://a.com") == ["http://a.com"]
+ assert extract_urls("http://a.com/b") == ["http://a.com/b"]
+ assert extract_urls("https://a.com/b") == ["https://a.com/b"]
+ assert extract_urls("http=://a.com/b") == ["a.com/"]
+ assert extract_urls("http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") == ["http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"]
+ assert extract_urls(
+ "CertificaçãoDigitalNº1311532/CA40/005129/2012Apensadoao40/006810/2011-1ºTermoAditivonº52/2012aoContratonº282/2011-Celebradoem08/08/2012") == []
+ assert extract_urls("http://www.brookings.edu/~/media/Research/Files/Papers/2015/04/global-drug-policy/Caulkinsfinal.pdf?la=en") == [
+ "http://www.brookings.edu/~/media/Research/Files/Papers/2015/04/global-drug-policy/Caulkinsfinal.pdf?la=en"
+ ]
+ assert extract_urls("DOI:10.1093/forestry/cpr048") == []
+ assert extract_urls("www.dtic.mil/cgi-bin/GetTRDoc?Location=U2&doc=GetTRDoc.pdf&AD=ADA475228") == [
+ "www.dtic.mil/cgi-bin/GetTRDoc?Location=U2&doc=GetTRDoc.pdf&AD=ADA475228"
+ ]
+ assert extract_urls("http://bit.ly/cJbkv") == ["http://bit.ly/cJbkv"]
+ assert extract_urls("hello http://bit.ly/cJbkv") == ["http://bit.ly/cJbkv"]
+ assert extract_urls("hello http://bit.ly/cJbkv http://bit.ly/cJbkv") == ["http://bit.ly/cJbkv", "http://bit.ly/cJbkv"]
+ assert extract_urls("jul./set.de") == ["set.de"]
+
+
+def test_extract_doi():
+ assert extract_dois("https://doi.org/10.1016/j.jsr.2003.05.009") == ["10.1016/j.jsr.2003.05.009"]
+ assert extract_dois("http://dx.doi.org/10.1002/elps.200500338") == ["10.1002/elps.200500338"]
+
+ assert extract_dois("!!10.1016/j.chiabu.2013.09.002") == ['10.1016/j.chiabu.2013.09.002']
+ assert extract_dois("!!10.1049/joe.2014.0134.!") == ["10.1049/joe.2014.0134"]
+ assert extract_dois("!!10.1080/00335630.2012.714899") == ["10.1080/00335630.2012.714899"]
+ assert extract_dois("!!10.1177/1075547007306508.!") == ["10.1177/1075547007306508"]
+ assert extract_dois("!!445!!10.3390/nu6114822") == ["10.3390/nu6114822"]
+ assert extract_dois("!0141-9889,!pp.!448-464!doi:!10.1111/j.1467J9566.2010.01286.!") == ["10.1111/j.1467J9566.2010.01286"]
+ assert extract_dois("!10.1002/(SICI)1097-4679(200004)56:4<519::AID-JCLP6>3.0.CO") == ["10.1002/(SICI)1097-4679(200004)56:4<519::AID-JCLP6>3.0.CO"]
+ assert extract_dois("!10.1002/ajpa.20674.!") == ["10.1002/ajpa.20674"]
+ assert extract_dois("!10.1002/chem.201700953.!") == ["10.1002/chem.201700953"]
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-24 10:09:01 +0000