gizmos

Utilities for ontology development

Installation

You can install gizmos by running:

python3 -m pip install ontodev-gizmos

This will include all requirements for using gizmos with SQLite databases. If you plan to use a PostgreSQL database, you must also install the psycopg2 module:

python3 -m pip install psycopg2

Testing

For development, we recommend installing and testing using:

python3 -m pip install -e .
python3 setup.py pytest

For running the PostgreSQL tests in Docker, you must set up postgres:

docker run --rm -e POSTGRES_PASSWORD=postgres -p 5432:5432 postgres

There are some dependencies that are test-only (e.g., will not be listed in the project requirements). If you try and run pytest alone, it may fail due to missing dependencies.

Databases

Each gizmos module uses a SQL database version of an RDF or OWL ontology to create outputs. SQL database inputs should be created from OWL using rdftab to ensure they are in the right format. RDFTab creates SQLite databases, but we also support PostgreSQL. The database is specified by -d/--database.

When loading from a SQLite database, use the path to the database (foo.db). When loading a PostgreSQL database, use a path to a configuration file ending in .ini (e.g., conf.ini) with a [postgresql] section. We recommend that the configuration file contain at least database, user, and password fields. An example configuration file with all optional fields looks like:

[postgresql]
host = 127.0.0.1
database = my_ontology
user = postgres
password = secret_password
port = 5432

The following prefixes are required to be defined in the prefix table for the gizmos commands to work:

owl: http://www.w3.org/2002/07/owl#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#

After loading the OWL into the database, we highly recommend creating an index on the stanza column to speed up operations. Other indexes are optional.

sqlite3 [path-to-database] "CREATE INDEX stanza_idx ON statements(stanza);"

When using gizmos as a Python module, all operations accept a sqlalchemy Connection object. For details on the Connection, see Working with Engines and Connections. We currently support SQLite and PostgreSQL. Using other connections may result in unanticipated errors due to slight variations in syntax. Note that if you use a PostgreSQL database, you must install or include psycopg2 in your requirements.

Modules

`gizmos.check`

The check module validates a SQLite database for use with other gizmos modules. We recommend running your database through gizmos.check before using the other commands.

python3 -m gizmos.check [path-to-database]

This command will check that both the prefix and statements tables exist with valid columns as defined by rdftab. If those tables are valid, it checks the contents of prefix and statements to make sure that:

required prefixes are defined (see Databases)
all CURIEs use valid prefixes
stanza is never a blank node
stanza, subject, and predicate are never NULL

check will also warn on the following:

missing index on stanza column
full IRIs that use a base defined in prefix

All errors are logged, and if errors are found, the command will exit with status code 1. Only the first 10 messages about specific rows in the statements table are logged to save time. If you wish to override this, use the --limit <int>/-l <int> option. To print all messages, include --limit none.

`gizmos.export`

The export module creates a table (default TSV) output containing the terms and their predicates written to stdout.

python3 -m gizmos.export -d [path-to-database] > [output-tsv]

Terms

If you know the term or set of terms you wish to include in the export, you can use the --term/--terms options. The term (-t or --term) should be the CURIE or label of your desired term, and you can include more than one -t option. Mulitple terms can be specified with -T <file>/--terms <file> with each CURIE or label on one line.

If a term or terms are not included, all terms in the database will be returned. The set of all terms returned can be narrowed using the -w/--where option (note that this option will not do anything when you are using --term or --terms). The argument to --where should be a SQL-like statement to append after the WHERE clause, excluding the WHERE. For example:

python3 -m gizmos.export -d ont.db -w "subject LIKE 'EX:%'" > out.tsv

For information on the structure of the statements table, please see RDFTab.

Output Formats

You can specify a format other than TSV by using the -f <format>/--format <format> option. The following formats are supported:

TSV
CSV
HTML *

* This is full HTML page. If you just want the content without <html> and <body> tags, include -c/--content-only.

Headers and Values

By default, headers are included. The headers are the predicate labels. If you wish to not include headers, include -n/--no-headers.

You can also specify the subset of predicates you wish to include using the -p <term>/--predicate <term> option. The term should be the term CURIE or the term label. Whatever you input will be used as the header for that column. The values in the column will be string values (for literal annotations) or IRIs (for objects and IRI annotations). If you want to use CURIEs instead of full IRIs, include -V CURIE/--values CURIE or, for labels, -V label/--values label.

For more fine grained control of how objects are output, you can include value formats in the predicate label as such: label [format] (e.g., rdfs:subClassOf [CURIE]). The following formats are supported:

label: label when available, or the CURIE otherwise
CURIE: the CURIE
IRI: the full IRI

Any time the predicate doesn't have a value format, the value format will be the -V value format (IRI when not included). Note that the value formats above can also be used in -p and -P.

If an ontology term has more than one value for a given predicate, it will be returned as a pipe-separated list. You can specify a different character to split multiple values on with -s <char>/--split <char>, for example -s ", " for a comma-separated list.

If you have many predicates to include, you can use -P <file>/--predicates <file> for a list of predicates (CURIE or label), each on one line.

`gizmos.extract`

The extract module creates a TTL or JSON-LD file containing the term, predicates, and ancestors written to stdout.

python3 -m gizmos.extract -d [path-to-database] -t [term] > [output-ttl]

For JSON-LD, you must include -f JSON-LD/--format JSON-LD.

The term or terms as CURIEs or labels are specified with -t <term>/--term <term>. You may also specify multiple terms to extract with -T <file>/--terms <file> where the file contains a list of CURIEs to extract.

The output contains the specified term and all its ancestors up to owl:Thing. If you don't wish to include the ancestors of the term/terms, include the -n/--no-hierarchy flag.

You may also specify which predicates you would like to include with -p <term>/--predicate <term> or -P <file>/--predicates <file>, where the file contains a list of predicate CURIEs or labels. Otherwise, the output includes all predicates. Since this extracts a hierarchy, unless you include the -n flag, rdfs:subClassOf will always be included.

By default, all intermediate terms are included between the term to extract and the highest-level term. If you don't want to include any intermediates, you can run extract with --i none/--intermediates none. This maintains the hierarchy between extracted terms, but removes intermediate terms that are not in the set of input terms to extract.

Finally, if you want to annotate all extracted terms with a source ontology IRI, you can use the -m <IRI>/--imported-from <IRI> option. This expects the full ontology IRI. The annotation added to each term, by default, will use the IAO 'imported from' property (note that this means IAO must be defined in your prefixes table as well). You can override this property with -M <term_id>/--import-from-property <term_id>.

Creating Import Modules

gizmos.extract can also be used with import configuration files (-i <file>/--imports <file>):

python3 -m gizmos.extract -d [path-to-database] -i [path-to-imports] > [output-ttl]

These files contain the terms you wish to include in your import module, along with some other details. The required headers are:

ID: The term ID to include
Label: optional; the term's label for documentation
Parent ID: optional; a term ID of a parent to assert
Parent Label: optional; the parent's label for documentation
Related: optional; related entities to include
Source: optional; a short ontology ID that specifies the source

Including the source can be useful when you have one file that you are using to create more than one import module. When you specify the Source column, you can use the -s <source>/--source <source> option in the command line. For example, if one of the sources in your import config is obi:

python3 -m gizmos.extract -d obi.db -i imports.tsv -s obi > out.ttl

The Related column should be a space-separated list that can use zero or more of the following. When included, all terms that match the relationship from the input database will be included in the output:

ancestors: Get all intermediate terms between the given term and it's first ancestor that is included in the input terms. If --intermediates none, get the first included ancestor OR the top-level ancestor if an ancestor is not included in the input terms.
children: Include the direct children of the term, regardless of if they are included in the input terms or not.
descendants: Get all intermediate terms between the given term and the lowest-level term (terms that do not have children). If --intermediates none, get all bottom-level terms only.
parents: Include the direct parents of the term, regardless of if they are included in the input terms or not.

You can also pass a source configuration file that contains the options for each source ontology used in your imports file using -c <file>/--config <file>. Note that with this option, a --source is always required:

python3 -m gizmos.extract -d obi.db -i imports.tsv -c config.tsv -s obi > out.ttl

This is a TSV or CSV with the following headers:

Source: a short ontology ID that specifies the source; matches a source in the imports file
IRI: optional; the IRI of the ontology to be added to each term as the value of an 'imported from' statement
Intermediates: optional; an --intermediates option: all or none
Predicates: optional; a space-separated list of predicate IDs to include from the import

The config file can be useful for handling multiple imports with different options in a Makefile. If your imports all use the same --intermediates option and the same predicates, there is no need to specify a config file.

`gizmos.search`

The search module returns a list of JSON objects for use with the tree browser search bar.

Usage in the command line:

python3 -m gizmos.search [path-to-database] [search-text] > [output-json]

Usage in Python (with defaults for optional parameters):

json = gizmos.search(     # returns: JSON string
    database_connection,  # Connection: database connection object
    search_text,          # string: text to search
    label="rdfs:label",   # string: term ID for label
    short_label=None,     # string: term ID for short label
    synonyms=None,        # list: term IDs for synonyms
    limit=30              # int: max results to return
)

Each returned object has the following attributes:

id: The term ID
label: The term rdfs:label (or other property if specified)
short_label: The term's short label property value, if provided
synonym: The term's synonym property value, if provided
property: The term ID of the matched property (e.g., rdfs:label)
order: The order in which the term will appear in the search results, from shortest to longest match

By default, the label will use the rdfs:label property. You can override this with --label <term>/-L <term>.

A short label is only included if you include a property with --short-label <term>/-S <term>. To set the short label to the term's ID, use --short-label ID. The same goes for synonyms, which are only included if --synonym/-s <term> is specified. You may include more than one synonym property with multiple -s options. Synonyms are only shown in the search result if they match the search text, whereas a short label is always shown (if the term has one).

When both short label and synonym(s) are provided and the matching term has both properties, the search result is shown as:

short label - label - synonym

Search is run over all three properties, so even if a term's label does not match the text, it may still be returned if the synonym matches.

Finally, the search only returns the first 30 results by default. If you wish to return less or more, you can specify this with --limit <int>/-l <int>.

`gizmos.tree`

The tree module produces a CGI tree browser for a given term contained in a SQL database.

Usage in the command line:

python3 -m gizmos.tree [path-to-database] [term] > [output-html]

Usage in Python (with defaults for optional parameters):

html = gizmos.tree(        # returns: HTML string
    database_connection,   # Connection: database connection object
    term_id,               # string: term ID to show or None
    href="?id={curie}",    # string: format for hrefs
    title=None,            # string: title to display
    predicate_ids=None,    # list: IDs of predicates to include
    include_search=False,  # boolean: if True, include search bar
    standalone=True        # boolean: if False, do not include HTML headers
)

The term should be a CURIE with a prefix already defined in the prefix table of the database. If the term is not included, the output will show a tree starting at owl:Thing.

This can be useful when writing scripts that return trees from different databases.

If you provide the -s/--include-search flag, a search bar will be included in the page. This search bar uses typeahead.js and expects the output of gizmos.search. The URL for the fetching the data for Bloodhound is ?text=[search-text]&format=json, or ?db=[db]&text=[search-text]&format=json if the -d flag is also provided. The format=json is provided as a flag for use in scripts. See the CGI Example below for details on implementation.

The title displayed in the HTML output is the database file name. If you'd like to override this, you can use the -t <title>/--title <title> option. This is full HTML page. If you just want the content without <html> and <body> tags, include -c/--content-only.

Tree Links

The links in the tree return query strings with the ID of the term to browse all the terms in the tree:

?id=FOO:123

If you provide the -d/--include-db flag, you will also get the db parameter in the query string. The value of this parameter is the base name of the database file.

?db=bar&id=FOO:123

Alternatively, if your script expects a different format than query strings (or different parameter names), you can use the -H/--href option and pass a python-esqe formatting string, e.g. -H "./{curie}" or -H "?curie={curie}". When you click on the FOO:123 term, the link will direct to ./FOO:123 or ?curie=FOO:123, respectively, instead of ?id=FOO:123.

The formatting string must contain {curie}, and optionally contain {db}. Any other text enclosed in curly brackets will be ignored. This should not be used with the -d flag.

Predicates

When displaying a term, gizmos.tree will display all predicate-value pairs listed in alphabetical order by predicate label on the right-hand side of the window. You can define which predicates to include with the -p/--predicate and -P/--predicates options.

You can pass one or more predicate CURIEs in the command line using -p/--predicate. These will appear in the order that you pass:

python3 -m gizmos.tree foo.db foo:123 -p rdfs:label -p rdfs:comment > bar.html

You can also pass a text file containing a list of predicate CURIEs (one per line) using -P/--predicates:

python3 -m gizmos.tree foo.db foo:123 -P predicates.txt > bar.html

You can specify to include the remaining predicates with *. The * can appear anywhere in the list, so you can choose to include certain predicates last:

rdfs:label
*
rdfs:comment

The * character also works on the command line, but must be enclosed in quotes:

python3 -m gizmos.tree foo.db foo:123 -p rdfs:label -p "*" > bar.html

CGI Script Example

A simple, single-database setup. Note that foo.db must exist.

# Create a phony URL from QUERY_STRING env variable
URL="http://example.com?${QUERY_STRING}"

# Retrieve the ID using urlp
ID=$(urlp --query --query_field=id "${URL}")

# Generate the tree view
if [[ ${ID} ]]; then
    python3 -m gizmos.tree foo.db ${ID}
else
    python3 -m gizmos.tree foo.db
fi

A more complex example with multiple databases and a search bar. Note that the build/ directory containing all database files must exist.

# Create a phony URL from QUERY_STRING env variable
URL="http://example.com?${QUERY_STRING}"

# Retrieve values using urlp
ID=$(urlp --query --query_field=id "${URL}")
DB=$(urlp --query --query_field=db "${URL}")

# These parameters are used exclusively for gizmos.search
FORMAT=$(urlp --query --query_field=format "${URL}")
TEXT=$(urlp --query --query_field=text "${URL}")

if [ ${FORMAT} == "json" ]; then
    # Call gizmos.search to return names JSON for typeahead search
    if [[ ${TEXT} ]]; then
        python3 -m gizmos.search build/${DB}.db ${TEXT}
    else
        python3 -m gizmos.search build/${DB}.db
    fi
else
    # Generate the tree view with database query parameter and search bar
    if [[ ${ID} ]]; then
        python3 -m gizmos.tree build/${DB}.db ${ID} -d -s
    else
        python3 -m gizmos.tree build/${DB}.db -d -s
    fi
fi

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README.md

README.md

gizmos

Installation

Testing

Databases

Modules

`gizmos.check`

`gizmos.export`

Terms

Output Formats

Headers and Values

`gizmos.extract`

Creating Import Modules

`gizmos.search`

`gizmos.tree`

Tree Links

Predicates

CGI Script Example

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README.md

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gizmos

Installation

Testing

Databases

Modules

gizmos.check

gizmos.export

Terms

Output Formats

Headers and Values

gizmos.extract

Creating Import Modules

gizmos.search

gizmos.tree

Tree Links

Predicates

CGI Script Example

`gizmos.check`

`gizmos.export`

`gizmos.extract`

`gizmos.search`

`gizmos.tree`