scripts doc updated

opencitations · Mar 25, 2024 · f3edd7e · f3edd7e
1 parent e46cef1
commit f3edd7e
Show file tree

Hide file tree

Showing 149 changed files with 12 additions and 4 deletions.
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
diff --git a/.gitignore b/.gitignore
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/LICENSE b/LICENSE
diff --git a/Makefile b/Makefile
diff --git a/README.md b/README.md
diff --git a/USAGE.md b/USAGE.md
diff --git a/config.ini b/config.ini
diff --git a/index/cpp/.gitignore b/index/cpp/.gitignore
diff --git a/index/cpp/include/StringHasher.hpp b/index/cpp/include/StringHasher.hpp
diff --git a/index/cpp/lib/BooPHF.h b/index/cpp/lib/BooPHF.h
diff --git a/index/cpp/src/build.cpp b/index/cpp/src/build.cpp
diff --git a/index/cpp/src/lookup.cpp b/index/cpp/src/lookup.cpp
diff --git a/index/python/.gitignore b/index/python/.gitignore
diff --git a/index/python/requirements.txt b/index/python/requirements.txt
diff --git a/index/python/src/__init__.py b/index/python/src/__init__.py
diff --git a/index/python/src/finder/__init__.py b/index/python/src/finder/__init__.py
diff --git a/index/python/src/finder/base.py b/index/python/src/finder/base.py
diff --git a/index/python/src/finder/crossref.py b/index/python/src/finder/crossref.py
diff --git a/index/python/src/finder/datacite.py b/index/python/src/finder/datacite.py
diff --git a/index/python/src/finder/nih.py b/index/python/src/finder/nih.py
diff --git a/index/python/src/finder/ocmeta.py b/index/python/src/finder/ocmeta.py
diff --git a/index/python/src/finder/orcid.py b/index/python/src/finder/orcid.py
diff --git a/index/python/src/glob/__init__.py b/index/python/src/glob/__init__.py
diff --git a/index/python/src/glob/csv.py b/index/python/src/glob/csv.py
diff --git a/index/python/src/glob/datasource.py b/index/python/src/glob/datasource.py
diff --git a/index/python/src/glob/redis.py b/index/python/src/glob/redis.py
diff --git a/index/python/src/identifier/__init__.py b/index/python/src/identifier/__init__.py
diff --git a/index/python/src/identifier/base.py b/index/python/src/identifier/base.py
diff --git a/index/python/src/identifier/doi.py b/index/python/src/identifier/doi.py
diff --git a/index/python/src/identifier/issn.py b/index/python/src/identifier/issn.py
diff --git a/index/python/src/identifier/omid.py b/index/python/src/identifier/omid.py
diff --git a/index/python/src/identifier/orcid.py b/index/python/src/identifier/orcid.py
diff --git a/index/python/src/identifier/pmid.py b/index/python/src/identifier/pmid.py
diff --git a/index/python/src/legacy/__init__.py b/index/python/src/legacy/__init__.py
diff --git a/index/python/src/legacy/csv.py b/index/python/src/legacy/csv.py
diff --git a/index/python/src/oci/__init__.py b/index/python/src/oci/__init__.py
diff --git a/index/python/src/oci/citation.py b/index/python/src/oci/citation.py
diff --git a/index/python/src/oci/storer.py b/index/python/src/oci/storer.py
diff --git a/index/python/src/oci/update.py b/index/python/src/oci/update.py
diff --git a/index/python/src/parsing/__init__.py b/index/python/src/parsing/__init__.py
diff --git a/index/python/src/parsing/base.py b/index/python/src/parsing/base.py
diff --git a/index/python/src/parsing/crossref.py b/index/python/src/parsing/crossref.py
diff --git a/index/python/src/parsing/crowdsourced.py b/index/python/src/parsing/crowdsourced.py
diff --git a/index/python/src/parsing/datacite.py b/index/python/src/parsing/datacite.py
diff --git a/index/python/src/parsing/index.py b/index/python/src/parsing/index.py
diff --git a/index/python/src/parsing/nih.py b/index/python/src/parsing/nih.py
diff --git a/index/python/src/parsing/scholix.py b/index/python/src/parsing/scholix.py
diff --git a/index/python/src/preprocessing/__init__.py b/index/python/src/preprocessing/__init__.py
diff --git a/index/python/src/preprocessing/base.py b/index/python/src/preprocessing/base.py
diff --git a/index/python/src/preprocessing/datacite.py b/index/python/src/preprocessing/datacite.py
diff --git a/index/python/src/preprocessing/pubmed.py b/index/python/src/preprocessing/pubmed.py
diff --git a/index/python/src/utils/__init__.py b/index/python/src/utils/__init__.py
diff --git a/index/python/src/utils/config.py b/index/python/src/utils/config.py
diff --git a/index/python/src/utils/dictionary.py b/index/python/src/utils/dictionary.py
diff --git a/index/python/src/utils/logging.py b/index/python/src/utils/logging.py
diff --git a/index/python/src/validate/__init__.py b/index/python/src/validate/__init__.py
diff --git a/index/python/src/validate/base.py b/index/python/src/validate/base.py
diff --git a/index/python/src/validate/crossref.py b/index/python/src/validate/crossref.py
diff --git a/index/python/src/validate/datacite.py b/index/python/src/validate/datacite.py
diff --git a/index/python/src/validate/index.py b/index/python/src/validate/index.py
diff --git a/index/python/src/validate/nih.py b/index/python/src/validate/nih.py
diff --git a/index/python/test/__init__.py b/index/python/test/__init__.py
diff --git a/index/python/test/data/citations_data.csv b/index/python/test/data/citations_data.csv
diff --git a/index/python/test/data/citations_data.ttl b/index/python/test/data/citations_data.ttl
diff --git a/index/python/test/data/citations_data_prov.scholix b/index/python/test/data/citations_data_prov.scholix
diff --git a/index/python/test/data/citations_prov.csv b/index/python/test/data/citations_prov.csv
diff --git a/index/python/test/data/citations_prov.ttl b/index/python/test/data/citations_prov.ttl
diff --git a/index/python/test/data/coci_validate/0.json b/index/python/test/data/coci_validate/0.json
diff --git a/index/python/test/data/croci_citations.csv b/index/python/test/data/croci_citations.csv
diff --git a/index/python/test/data/croci_dump.csv b/index/python/test/data/croci_dump.csv
diff --git a/index/python/test/data/crossref_citations.csv b/index/python/test/data/crossref_citations.csv
diff --git a/index/python/test/data/crossref_dump.json b/index/python/test/data/crossref_dump.json
diff --git a/index/python/test/data/crossref_glob_dump_input/crossref_dump.json b/index/python/test/data/crossref_glob_dump_input/crossref_dump.json
diff --git a/index/python/test/data/doci_citations.csv b/index/python/test/data/doci_citations.csv
diff --git a/index/python/test/data/doci_dump.csv b/index/python/test/data/doci_dump.csv
diff --git a/index/python/test/data/doci_glob_dump_input/doci_dump.json b/index/python/test/data/doci_glob_dump_input/doci_dump.json
diff --git a/index/python/test/data/doci_pp_dump_input/doci_pp_dump.json b/index/python/test/data/doci_pp_dump_input/doci_pp_dump.json
diff --git a/index/python/test/data/doci_validate/0.csv b/index/python/test/data/doci_validate/0.csv
diff --git a/index/python/test/data/glob.json b/index/python/test/data/glob.json
diff --git a/index/python/test/data/glob_test_dir/globtest_coci/__init__.py b/index/python/test/data/glob_test_dir/globtest_coci/__init__.py
diff --git a/index/python/test/data/glob_test_dir/globtest_doci/__init__.py b/index/python/test/data/glob_test_dir/globtest_doci/__init__.py
diff --git a/index/python/test/data/glob_test_dir/globtest_noci/__init__.py b/index/python/test/data/glob_test_dir/globtest_noci/__init__.py
diff --git a/index/python/test/data/initial_data.csv b/index/python/test/data/initial_data.csv
diff --git a/index/python/test/data/lookup_full.csv b/index/python/test/data/lookup_full.csv
diff --git a/index/python/test/data/lookup_new.csv b/index/python/test/data/lookup_new.csv
diff --git a/index/python/test/data/noci_citations.csv b/index/python/test/data/noci_citations.csv
diff --git a/index/python/test/data/noci_dump.csv b/index/python/test/data/noci_dump.csv
diff --git a/index/python/test/data/noci_glob_dump_input/CSVFile_1.csv b/index/python/test/data/noci_glob_dump_input/CSVFile_1.csv
diff --git a/index/python/test/data/noci_glob_dump_output_broken/CSVFile_1.csv b/index/python/test/data/noci_glob_dump_output_broken/CSVFile_1.csv
diff --git a/index/python/test/data/noci_index_dump_output_broken/CSVFile_1.csv b/index/python/test/data/noci_index_dump_output_broken/CSVFile_1.csv
diff --git a/index/python/test/data/noci_md_pp_dump_input/CSVFile_1_iCiteMD.csv b/index/python/test/data/noci_md_pp_dump_input/CSVFile_1_iCiteMD.csv
diff --git a/index/python/test/data/noci_pp_dump_input/CSVFile_1.csv b/index/python/test/data/noci_pp_dump_input/CSVFile_1.csv
diff --git a/index/python/test/data/noci_pp_dump_input_reduced/CSVFile_1.csv b/index/python/test/data/noci_pp_dump_input_reduced/CSVFile_1.csv
diff --git a/index/python/test/data/noci_validate/0.csv b/index/python/test/data/noci_validate/0.csv
diff --git a/index/python/test/data/poci_md_pp_dump_input/CSVFile_1_iCiteMD.csv b/index/python/test/data/poci_md_pp_dump_input/CSVFile_1_iCiteMD.csv
diff --git a/index/python/test/data/preprocess/data_datacite/dc_pp_input.json b/index/python/test/data/preprocess/data_datacite/dc_pp_input.json
diff --git a/index/python/test/data/preprocess/data_datacite_sample/dc_pp_input.json b/index/python/test/data/preprocess/data_datacite_sample/dc_pp_input.json
diff --git a/index/python/test/data/preprocess/data_datacite_sample/dc_pp_input2.json b/index/python/test/data/preprocess/data_datacite_sample/dc_pp_input2.json
diff --git a/index/python/test/data/preprocess/data_nih/metadata_input.csv b/index/python/test/data/preprocess/data_nih/metadata_input.csv
diff --git a/index/python/test/data/preprocess/dc_pp_input.json.zst b/index/python/test/data/preprocess/dc_pp_input.json.zst
diff --git a/index/python/test/data/preprocess/dc_pp_input_decompr_zst_dir/dc_pp_input.json b/index/python/test/data/preprocess/dc_pp_input_decompr_zst_dir/dc_pp_input.json
diff --git a/index/python/test/data/preprocess/dc_pp_inputdecompr_zst_dir/dc_pp_input.json b/index/python/test/data/preprocess/dc_pp_inputdecompr_zst_dir/dc_pp_input.json
diff --git a/index/python/test/data/preprocess/poci_csv_duplicate_check/duplicate_check.csv b/index/python/test/data/preprocess/poci_csv_duplicate_check/duplicate_check.csv
diff --git a/index/python/test/data/preprocess/poci_glob_dump_output_broken/CSVFile_1.csv b/index/python/test/data/preprocess/poci_glob_dump_output_broken/CSVFile_1.csv
diff --git a/index/python/test/data/preprocess/poci_index_dump_output_broken/CSVFile_1.csv b/index/python/test/data/preprocess/poci_index_dump_output_broken/CSVFile_1.csv
diff --git a/index/python/test/data/preprocess/poci_md_pp_dump_input/CSVFile_1_iCiteMD.csv b/index/python/test/data/preprocess/poci_md_pp_dump_input/CSVFile_1_iCiteMD.csv
diff --git a/index/python/test/data/preprocess/poci_pp_dump_input/CSVFile_1.csv b/index/python/test/data/preprocess/poci_pp_dump_input/CSVFile_1.csv
diff --git a/index/python/test/data/preprocess/poci_pp_dump_input_reduced/CSVFile_1.csv b/index/python/test/data/preprocess/poci_pp_dump_input_reduced/CSVFile_1.csv
diff --git a/index/python/test/data/preprocess/tmp_data_datacite_broken/jSonFile_1.json b/index/python/test/data/preprocess/tmp_data_datacite_broken/jSonFile_1.json
diff --git a/index/python/test/data/preprocess/tmp_data_datacite_c_broken/jSonFile_1.json b/index/python/test/data/preprocess/tmp_data_datacite_c_broken/jSonFile_1.json
diff --git a/index/python/test/data/preprocess/tmp_data_datacite_cit2_citations/duplicate_check.csv b/index/python/test/data/preprocess/tmp_data_datacite_cit2_citations/duplicate_check.csv
diff --git a/index/python/test/test_coci.py b/index/python/test/test_coci.py
diff --git a/index/python/test/test_croci.py b/index/python/test/test_croci.py
diff --git a/index/python/test/test_csv.py b/index/python/test/test_csv.py
diff --git a/index/python/test/test_doci.py b/index/python/test/test_doci.py
diff --git a/index/python/test/test_finder.py b/index/python/test/test_finder.py
diff --git a/index/python/test/test_glob.py b/index/python/test/test_glob.py
diff --git a/index/python/test/test_identifier.py b/index/python/test/test_identifier.py
diff --git a/index/python/test/test_noci.py b/index/python/test/test_noci.py
diff --git a/index/python/test/test_oci.py b/index/python/test/test_oci.py
diff --git a/index/python/test/test_preprocessing_datacite.py b/index/python/test/test_preprocessing_datacite.py
diff --git a/index/python/test/test_preprocessing_pubmed.py b/index/python/test/test_preprocessing_pubmed.py
diff --git a/index/python/test/test_storer.py b/index/python/test/test_storer.py
diff --git a/index/python/test/test_validate.py b/index/python/test/test_validate.py
diff --git a/lookup.csv b/lookup.csv
diff --git a/scripts/OLD_cnc.py b/scripts/OLD_cnc.py
diff --git a/scripts/__get_missing_cits.py b/scripts/__get_missing_cits.py
diff --git a/scripts/__init__.py b/scripts/__init__.py
diff --git a/scripts/calc_stats.py b/scripts/calc_stats.py
diff --git a/scripts/check_entities.py b/scripts/check_entities.py
diff --git a/scripts/citation_count_converter.py b/scripts/citation_count_converter.py
diff --git a/scripts/cits2redis.py b/scripts/cits2redis.py
diff --git a/scripts/cnc.py b/scripts/cnc.py
diff --git a/scripts/datasource.py b/scripts/datasource.py
diff --git a/scripts/edit_rdf.py b/scripts/edit_rdf.py
diff --git a/scripts/export_redis_db.py b/scripts/export_redis_db.py
diff --git a/scripts/fix_dump.py b/scripts/fix_dump.py
diff --git a/scripts/glob_crossref.py b/scripts/glob_crossref.py
diff --git a/scripts/glob_doci.py b/scripts/glob_doci.py
diff --git a/scripts/glob_noci.py b/scripts/glob_noci.py
diff --git a/scripts/import_redis_db.py b/scripts/import_redis_db.py
@@ -9,15 +9,23 @@
 parser.add_argument('--key', type=str, required=True,help='column (i.e. number of column) to use as key in redis')
 parser.add_argument('--value', type=str, required=True,help='column (i.e. number of column) to use as value in redis')
 
-# The following example add the names as keys and the ages aas values into the DB=0 of Redis
-# ******************
+# ****************** <CALL EXAMPLE> ******************
+
+# Having a CSV file (file.csv) containing something like this:
+# james,32
+# nicolas,44
+# david,14
+# ...
+
+# Then the following call adds the names as keys and the ages as values into DB=0 of Redis
 # --db 0
 # --in file.csv >
-#   "james,32
-#   nicolas,44"
 # --key 0
 # --value 1
 
+# ****************** </CALL EXAMPLE> ******************
+
+
 args = parser.parse_args()
 
 r_db = Redis(host="localhost", port="6379", db=args.db)

diff --git a/scripts/meta2redis.py b/scripts/meta2redis.py
diff --git a/scripts/metadata_crossref.py b/scripts/metadata_crossref.py
diff --git a/scripts/norm.py b/scripts/norm.py
diff --git a/scripts/oci.py b/scripts/oci.py
diff --git a/scripts/trim_crossref.py b/scripts/trim_crossref.py
diff --git a/scripts/validate_citations.py b/scripts/validate_citations.py
diff --git a/setup.py b/setup.py