Checking empty descriptions

In this example, we use fastobo to create a small validation script which will report empty definitions in an OBO file. We also use requests in order to connect to the OBO library.

import fastobo
import requests

fastobo.load takes a file-handle, which can be accessed using the raw property of the Response object returned by requests.get:

res = requests.get("http://purl.obolibrary.org/obo/ms.obo", stream=True)
doc = fastobo.load(res.raw)

Header

Now, we can check the header for empty descriptions in definition clauses:

for clause in doc.header:
    if isinstance(clause, fastobo.header.SynonymTypedefClause) and not clause.description:
        print("Empty description in definition of", clause.typedef)
    elif isinstance(clause, fastobo.header.SubsetdefClause) and not clause.description:
        print("Empty description in definition of", clause.subset)

Note that we are using isinstance a lot compared to what you may be used to in other Python library: this is because fastobo is based on a Rust library which is strongly-typed, so that is reflected in the Python library that wraps it. We could use the strong typing to write the same snippet using type-specific callback wrapped in a dict:

def check_synonym_typedef(clause):
    if not clause.description:
        print("Empty description in definition of", clause.typedef, "in header")

def check_subsetdef(clause):
    if not clause.description:
        print("Empty description in definition of", clause.subset, "in header")

CALLBACKS = {
    fastobo.header.SynonymTypedefClause: check_synonym_typedef,
    fastobo.header.SynonymTypedefClause: check_subsetdef,
}

for clause in doc.header:
    callback = CALLBACKS.get(type(clause))
    if callback is not None:
        callback(clause)

Such a construct can be used to process all possible clauses while reducing the number of if/elif branches, in particular when many different clauses are processed at the same time.

Entities

Checking for definitions in entity frames is straightforward: all definition clauses have a definition property that returns the textual definition of the entity. We can use duck-typing here to check for empty definitions:

for frame in doc:
    for clause in frame:
        try:
            if not clause.definition:
                print("Empty definition of", frame.id)
        except AttributeError:
            pass