Command line interface¶
The a3k command can be invoked from the shell as follows.
a3k: Relational interface to publication metadata
usage: a3k [-h] [-d DEBUG] [-v]
{help,populate,process,query,list-processes,list-complete-schema,list-source-schema,list-process-schema,list-sources,version}
...
Positional Arguments¶
- command
Possible choices: help, populate, process, query, list-processes, list-complete-schema, list-source-schema, list-process-schema, list-sources, version
Name of the a3k operation to perform.
Named Arguments¶
- -d, --debug
- Output debuggging information according to the comma-separated 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; progress_bar: Display a progress bar; sorted-tables: Topologically ordered Crossref query tables; stacktrace: Produce a stack trace when an error occurs; stderr: Log to standard error;
Default: []
- -v, --version
Report program version and exit
Default: False
Sub-commands¶
populate¶
Populate an SQLite database.
a3k populate [-h] [-a ATTACH_DATABASES [ATTACH_DATABASES ...]]
[-c COLUMNS [COLUMNS ...]] [-R ROW_SELECTION_FILE]
[-r ROW_SELECTION] [-s SAMPLE]
database
{asjcs,ror,uspto,crossref,funder-names,pubmed,doaj,journal-names,orcid}
[data_location]
Positional Arguments¶
- database
File path of the database to populate
- data_name
Possible choices: asjcs, ror, uspto, crossref, funder-names, pubmed, doaj, journal-names, orcid
Name of the data source to use
- data_location
Path or URL of the source’s data
Named Arguments¶
- -a, --attach-databases
Databases to attach for the row selection expression
- -c, --columns
Columns to populate using table.column or table.*
- -R, --row-selection-file
File containing SQL expression that selects the populated rows
- -r, --row-selection
SQL expression that selects the populated rows
- -s, --sample
Python expression to sample the data (e.g. random.random() < 0.0002). The expression can also use a variable named data whose value is documented in the constructor API of each data source.
Default: “True”
process¶
Run a processing step on the specified database.
a3k process [-h]
database
{link-uspto-doi,link-aa-top-ror,link-aa-base-ror,link-works-asjcs}
Positional Arguments¶
- database
file path of the database to run the process on
- process
Possible choices: link-uspto-doi, link-aa-top-ror, link-aa-base-ror, link-works-asjcs
Name of the process to perform;see the data processing operations in the Alexandria3k Python user API documentation for more details
query¶
Run a query directly on a data source.
a3k query [-h] [-a ATTACH_DATABASES [ATTACH_DATABASES ...]]
[-E OUTPUT_ENCODING] [-F FIELD_SEPARATOR] [-H] [-o OUTPUT] [-P]
(-Q QUERY_FILE | -q QUERY) [-s SAMPLE]
{asjcs,ror,uspto,crossref,funder-names,pubmed,doaj,journal-names,orcid}
[data_location]
Positional Arguments¶
- data_name
Possible choices: asjcs, ror, uspto, crossref, funder-names, pubmed, doaj, journal-names, orcid
Name of the data source to use
- data_location
Path or URL of the source’s data
Named Arguments¶
- -a, --attach-databases
Databases to attach making them available to the query
- -E, --output-encoding
Query output character encoding (use utf-8-sig for Excel)
Default: “utf-8”
- -F, --field-separator
Character to use for separating query output fields
Default: “,”
- -H, --header
Include a header in the query output
Default: False
- -o, --output
Output file for query results
- -P, --partition
Run the query over partitioned data slices. (Warning: arguments are run per partition.)
Default: False
- -Q, --query-file
File containing query to run on the virtual tables
- -q, --query
Query to run on the virtual tables
- -s, --sample
Python expression to sample the data (e.g. random.random() < 0.0002). The expression can also use a variable named data whose value is documented in the constructor API of each data source.
Default: “True”
list-source-schema¶
List all data source schemas (default) or the specified one.
a3k list-source-schema [-h]
[{asjcs,ror,uspto,crossref,funder-names,pubmed,doaj,journal-names,orcid}]
Positional Arguments¶
- facility
Possible choices: asjcs, ror, uspto, crossref, funder-names, pubmed, doaj, journal-names, orcid
list-process-schema¶
List the schema of all processes (default) or of the specified one.
a3k list-process-schema [-h]
[{link-uspto-doi,link-aa-top-ror,link-aa-base-ror,link-works-asjcs}]
Positional Arguments¶
- facility
Possible choices: link-uspto-doi, link-aa-top-ror, link-aa-base-ror, link-works-asjcs