blob: 9990e58a4d92809497b364499c49d69882dbe0e3 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
|
TODAY ?= $(shell date --iso --utc)
SNAPSHOTITEM ?= $(shell grep ia_item sources.toml | cut -f2 -d'"')
.PHONY: help
help: ## Print info about all commands
@echo "Commands:"
@echo
@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf " \033[01;32m%-20s\033[0m %s\n", $$1, $$2}'
.PHONY: dep
dep: ## Create local virtualenv using pipenv
pipenv install --dev
.PHONY: lint
lint: ## Run lints (eg, flake8, mypy)
pipenv run flake8 *.py chocula/*.py chocula/*/*.py tests/ --exit-zero
pipenv run mypy *.py chocula/*.py chocula/*/*.py --ignore-missing-imports
.PHONY: fmt
fmt: ## Run code formating on all source code
pipenv run black *.py chocula/ tests/
.PHONY: test
test: ## Run all tests
pipenv run pytest
.PHONY: coverage
coverage: ## Run all tests with coverage
pipenv run pytest --cov
.PHONY: container-stats
container-stats: data/$(TODAY)/container_stats.json ## Summarize fatcat container counts
wc -l data/$(TODAY)/container_stats.json
@echo
@echo Done
.PHONY: homepage-status
homepage-status: data/$(TODAY)/homepage_status.json ## Check homepage "live"/"archive" existance for current database
wc -l data/$(TODAY)/homepage_status.json
@echo
@echo Done
.PHONY: export-fatcat
export-fatcat: ## Output compressed JSON for fatcat journal metadata importer
pipenv run python -m chocula export_fatcat | gzip > chocula_fatcat_export.$(TODAY).json.gz
.PHONY: fetch-sources
fetch-sources: ## Download existing snapshot versions of all sources from archive.org
mkdir -p data
ia download --checksum --no-directories $(SNAPSHOTITEM) --destdir data/
rm data/$(SNAPSHOTITEM)_*
data/$(TODAY)/kbart_JSTOR.txt:
mkdir -p data/$(TODAY)
wget -c "https://www.jstor.org/kbart/collections/all-archive-titles?contentType=journals" -O $@.wip
mv $@.wip $@
data/$(TODAY)/kbart_CLOCKSS.txt:
wget -c "https://reports.clockss.org/kbart/kbart_CLOCKSS.txt" -O $@.wip
mv $@.wip $@
data/$(TODAY)/kbart_CLOCKSS-triggered.txt:
wget -c "https://reports.clockss.org/kbart/kbart_CLOCKSS-triggered.txt" -O $@.wip
mv $@.wip $@
data/$(TODAY)/kbart_LOCKSS.txt:
wget -c "https://reports.lockss.org/kbart/kbart_LOCKSS.txt" -O $@.wip
mv $@.wip $@
data/$(TODAY)/kbart_Portico.txt:
wget -c "http://api.portico.org/kbart/Portico_Holding_KBart.txt" -O $@.wip
mv $@.wip $@
data/$(TODAY)/ISSN-to-ISSN-L.txt:
wget -c "https://www.issn.org/wp-content/uploads/2014/03/issnltables.zip" -O /tmp/issnltables.$(TODAY).zip
unzip -p /tmp/issnltables.$(TODAY).zip "*.ISSN-to-ISSN-L.txt" > $@.wip
mv $@.wip $@
data/$(TODAY)/entrez.txt:
wget -c "ftp://ftp.ncbi.nlm.nih.gov/pubmed/J_Entrez.txt" -O $@.wip
mv $@.wip $@
data/$(TODAY)/doaj.csv:
wget -c "https://doaj.org/csv" -O $@.wip
mv $@.wip $@
data/$(TODAY)/crossref_titles.csv:
wget -c "https://wwwold.crossref.org/titlelist/titleFile.csv" -O $@.wip
mv $@.wip $@
data/$(TODAY)/onix_pkp_pln.csv:
wget -c "http://pkp.sfu.ca/files/pkppn/onix.csv" -O $@.wip
mv $@.wip $@
.PHONY: update-sources
update-sources: data/$(TODAY)/kbart_JSTOR.txt data/$(TODAY)/kbart_CLOCKSS.txt data/$(TODAY)/kbart_CLOCKSS-triggered.txt data/$(TODAY)/kbart_LOCKSS.txt data/$(TODAY)/kbart_Portico.txt data/$(TODAY)/ISSN-to-ISSN-L.txt data/$(TODAY)/entrez.txt data/$(TODAY)/doaj.csv data/$(TODAY)/crossref_titles.csv data/$(TODAY)/onix_pkp_pln.csv ## Download new versions of updatable sources
@echo
@echo "Successfully updated for date (UTC): $(TODAY)"
data/$(TODAY)/homepage_status.json:
pipenv run python -m chocula export_urls | shuf | pv -l > /tmp/chocula_urls.tsv
pipenv run parallel -j10 --pipepart --line-buffer -a /tmp/chocula_urls.tsv ./check_issn_urls.py | pv -l > /tmp/homepage_status.json
mv /tmp/homepage_status.json $@
data/$(TODAY)/container_stats.json: data/container_export.json
cat data/container_export.json | jq .ident -r | sort -u > /tmp/container_ident.tsv
cat /tmp/container_ident.tsv | parallel -j10 curl --max-time 30 --fail -s 'https://fatcat.wiki/container/{}/stats.json' | jq -c . | pv -l > /tmp/container_stats.json
mv /tmp/container_stats.json $@
.PHONY: upload-sources
upload-sources: update-sources ## Upload most recent update-able sources to a new IA item
ia upload --checksum -m collection:ia_biblio_metadata chocula-sources-snapshot-$(TODAY) data/*.tsv data/*.json data/*.txt data/*.csv
.PHONY: upload-database
upload-database: ## Upload an sqlite snapshot to archive.org
ia upload --checksum --no-derive -m collection:ia_biblio_metadata chocula-database-snapshot-$(TODAY) chocula.sqlite sources.toml README.md extra/count_chocula.jpg
.PHONY: database
database: ## Build database from sources
@if [ ! -f data/ISSN-to-ISSN-L.txt ]; then echo "You must run 'make fetch-sources' first"; exit -1; fi
pipenv run python -m chocula everything
|
