usage: alexandria3k [-h] [-a ATTACH_DATABASES [ATTACH_DATABASES ...]]
                    [-c COLUMNS [COLUMNS ...]] [-D DEBUG [DEBUG ...]]
                    [-d DATA_SOURCE [DATA_SOURCE ...]] [-E OUTPUT_ENCODING]
                    [-F FIELD_SEPARATOR] [-H] [-i [INDEX ...]]
                    [-L LIST_SCHEMA] [-l LINKED_RECORDS] [-o OUTPUT] [-P]
                    [-p POPULATE_DB_PATH] [-Q QUERY_FILE] [-q QUERY]
                    [-R ROW_SELECTION_FILE] [-r ROW_SELECTION] [-s SAMPLE]
                    [-v] [-x EXECUTE]

alexandria3k: Relational interface to publication metadata

optional arguments:
  -h, --help            show this help message and exit
  -a ATTACH_DATABASES [ATTACH_DATABASES ...], --attach-databases ATTACH_DATABASES [ATTACH_DATABASES ...]
                        Databases to attach for the row selection query
  -c COLUMNS [COLUMNS ...], --columns COLUMNS [COLUMNS ...]
                        Columns to populate using table.column or table.*
  -D DEBUG [DEBUG ...], --debug DEBUG [DEBUG ...]
                        Output debuggging information as specfied by the
                        arguments. files-read: Counts of Crossref data files
                        read; link: Record linking operations; sql: Executed
                        SQL statements; perf: Performance timings; populated-
                        counts: Counts of the populated database; populated-
                        data: Data of the populated database; populated-
                        reports: Query results from the populated database;
                        progress: Report population progress; sorted-tables:
                        Topologically ordered Crossref query tables; stderr:
                        Log to standard error; virtual-counts: Counts of the
                        virtual database; virtual-data: Data of the virtual
                        database.
  -d DATA_SOURCE [DATA_SOURCE ...], --data-source DATA_SOURCE [DATA_SOURCE ...]
                        Specify data set to be processed and its source. The
                        following data sets are supported: ASJC [<CSV-file> |
                        <URL>] (defaults to internal table); Crossref
                        <container-directory>; DOAJ [<CSV-file> | <URL>]
                        (defaults to https://doaj.org/csv); funder-names
                        [<CSV-file> | <URL>] (defaults to
                        https://doi.crossref.org/funderNames?mode=list);
                        journal-names [<CSV-file> | <URL>] (defaults to
                        http://ftp.crossref.org/titlelist/titleFile.csv);
                        ORCID <summaries.tar.gz-file> ROR <zip-file>;
  -E OUTPUT_ENCODING, --output-encoding OUTPUT_ENCODING
                        Query output character encoding (use utf-8-sig for
                        Excel)
  -F FIELD_SEPARATOR, --field-separator FIELD_SEPARATOR
                        Character to use for separating query output fields
  -H, --header          Include a header in the query output
  -i [INDEX ...], --index [INDEX ...]
                        SQL expressions that select the populated rows
  -L LIST_SCHEMA, --list-schema LIST_SCHEMA
                        List the schema of the specified database. The
                        following names are supported: Crossref, ORCID, ROR,
                        other, all
  -l LINKED_RECORDS, --linked-records LINKED_RECORDS
                        Only add ORCID records that link to existing <persons>
                        or <works>
  -o OUTPUT, --output OUTPUT
                        Output file for query results
  -P, --partition       Run the query over partitioned data slices. (Warning:
                        arguments are run per partition.)
  -p POPULATE_DB_PATH, --populate-db-path POPULATE_DB_PATH
                        Populate the SQLite database in the specified path
  -Q QUERY_FILE, --query-file QUERY_FILE
                        File containing query to run on the virtual tables
  -q QUERY, --query QUERY
                        Query to run on the virtual tables
  -R ROW_SELECTION_FILE, --row-selection-file ROW_SELECTION_FILE
                        File containing SQL expression that selects the
                        populated rows
  -r ROW_SELECTION, --row-selection ROW_SELECTION
                        SQL expression that selects the populated rows
  -s SAMPLE, --sample SAMPLE
                        Python expression to sample the Crossref tables (e.g.
                        random.random() < 0.0002)
  -v, --version         Report program version and exit
  -x EXECUTE, --execute EXECUTE
                        Operation to execute on the data. This can be one of:
                        link-aa-base-ror (link author affiliations to base-
                        level research organizations); link-aa-top-ror (link
                        author affiliations to top-level research
                        organizations); link-works-asjcs (link works with
                        Scopus All Science Journal Classification Codes —
                        ASJCs).
