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1.0.1
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Bugfixes
- Fixed bug where input_path_or_url could be a PosixPath and not a string

Minor updates
- Docs: Corrected some verbiage in docs / code documentaiton.
- Docs: Added prerequisite information for Python/Java
- Dependencies: Updated requests for a securiy update.
- Update: robot.jar pathing
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@joeflack4
joeflack4 committed Oct 7, 2023
1 parent 96ca67e commit d1809ff
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8 changes: 6 additions & 2 deletions README.md
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Expand Up @@ -3,6 +3,10 @@

A Python-based non-minimalistic OWL to FHIR converter.

## Prerequisite
* [Python 3.9+](https://www.python.org/downloads/)
* [Java 11+](https://www.oracle.com/java/technologies/javase/jdk11-archive-downloads.html)

## Installation
`pip install owl-on-fhir`

Expand All @@ -18,8 +22,8 @@ A Python-based non-minimalistic OWL to FHIR converter.
|:-----------|:----------|:------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| -h | --help | | Show this help message and exit. |
| -i | --input-path-or-url | True | URL or path to OWL file to convert. |
| -s | --code-system-id | True | For `fhirjson` only. The code system ID to use for identification on the server uploaded to. See: https://hl7.org/fhir/resource-definitions.html#Resource.id |
| -S | --code-system-url | True | For `fhirjson` only. Canonical URL for the code system. See: https://hl7.org/fhir/codesystem-definitions.html#CodeSystem.url |
| -s | --code-system-id | True | The code system ID to use for identification on the server uploaded to. See: https://hl7.org/fhir/resource-definitions.html#Resource.id |
| -S | --code-system-url | True | Canonical URL for the code system. See: https://hl7.org/fhir/codesystem-definitions.html#CodeSystem.url |
| -u | --native-uri-stems | True | A comma-separated list of URI stems that will be used to determine whether a concept is native to the CodeSystem. For example, for OMIM, the following URI stems are native: https://omim.org/entry/,https://omim.org/phenotypicSeries/PS". As of 2023-01-15, there is still a bug in the Obographs spec and/or `robot` where certain nodes are not being converted. This converter adds back the nodes, but to know which ones belong to the CodeSystem itself and are not foreign concepts, this parameter is necessary. OAK also makes use of this parameter. See also: https://github.com/geneontology/obographs/issues/90 |
| -o | --out-dir | False | The directory where results should be saved. |
| -n | --out-filename | False | Filename for the primary file converted, e.g. CodeSystem. |
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2 changes: 1 addition & 1 deletion makefile
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Expand Up @@ -8,7 +8,7 @@ clean:
rm -rf ./*.egg-info

build: clean
python3 setup.py sdist bdist_wheel
python setup.py sdist bdist_wheel

pypi: build
twine upload --repository-url https://upload.pypi.org/legacy/ dist/*;
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19 changes: 12 additions & 7 deletions owl_on_fhir/__main__.py
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Expand Up @@ -4,7 +4,8 @@
import shutil
import subprocess
from argparse import ArgumentParser
from typing import Dict, List
from pathlib import PosixPath
from typing import Dict, List, Union

import curies
import requests
Expand All @@ -21,7 +22,7 @@
BIN_DIR = SRC_DIR
PROJECT_DIR = os.path.join(SRC_DIR, '..')
CACHE_DIR = os.path.join(PROJECT_DIR, 'cache')
ROBOT_PATH = os.path.join(BIN_DIR, 'robot')
ROBOT_PATH = os.path.join(BIN_DIR, 'robot.jar')
INTERMEDIARY_TYPES = ['obographs', 'semsql']


Expand Down Expand Up @@ -113,7 +114,7 @@ def owl_to_obograph(inpath: str, out_dir: str, use_cache=False, cache_output=Fal
infile = os.path.basename(inpath)
cache_path = os.path.join(CACHE_DIR, infile + '.obographs.json')
outpath = os.path.join(out_dir, infile + '.obographs.json')
command = f'java -jar {ROBOT_PATH}.jar convert -i {inpath} -o {outpath} --format json'
command = f'java -jar {ROBOT_PATH} convert -i {inpath} -o {outpath} --format json'

# Convert
if not os.path.exists(out_dir):
Expand Down Expand Up @@ -194,7 +195,7 @@ def semsql_to_fhir(inpath: str, out_dir: str, out_filename: str = None, include_


def owl_to_fhir(
input_path_or_url: str, out_dir: str = None, out_filename: str = None, include_only_critical_predicates=False,
input_path_or_url: Union[str, PosixPath], out_dir: str = None, out_filename: str = None, include_only_critical_predicates=False,
retain_intermediaries=False, intermediary_type=['obographs', 'semsql'][0], use_cached_intermediaries=False,
intermediary_outdir: str = None, convert_intermediaries_only=False, native_uri_stems: List[str] = None,
code_system_id: str = None, code_system_url: str = None, dev_oak_path: str = None,
Expand All @@ -209,6 +210,7 @@ def owl_to_fhir(
# Download if necessary & determine outpaths
# todo: this section w/ urls, names, and IDs has too many possible branches and is error prone. simplify by
# updating CLI params to require url or path separately, and maybe require codesystem id
input_path_or_url = str(input_path_or_url)
input_path = input_path_or_url
url = None
maybe_url = urlparse(input_path_or_url)
Expand Down Expand Up @@ -266,17 +268,19 @@ def owl_to_fhir(
return os.path.join(out_dir, out_filename)


# TODO: some of these args said"for fhirjson only". Was this because I was going to add an option for NPM output when
# OAK supports? Either way, removed for now till I figure out if I really was parameterizing something here.
def cli():
"""Command line interface."""
parser = ArgumentParser(prog='OWL on FHIR', description='Python-based non-minimalistic OWL to FHIR converter.')
parser.add_argument('-i', '--input-path-or-url', required=True, help='URL or path to OWL file to convert.')
parser.add_argument(
'-s', '--code-system-id', required=True, default=False,
help="For `fhirjson` only. The code system ID to use for identification on the server uploaded to. "
help="The code system ID to use for identification on the server uploaded to. "
"See: https://hl7.org/fhir/resource-definitions.html#Resource.id")
parser.add_argument(
'-S', '--code-system-url', required=True, default=False,
help="For `fhirjson` only. Canonical URL for the code system. "
help="Canonical URL for the code system. "
"See: https://hl7.org/fhir/codesystem-definitions.html#CodeSystem.url")
parser.add_argument(
'-u', '--native-uri-stems', required=True, nargs='+',
Expand All @@ -288,7 +292,8 @@ def cli():
'itself and are not foreign concepts, this parameter is necessary. OAK also makes use of this parameter. '
'See also: https://github.com/geneontology/obographs/issues/90')
parser.add_argument(
'-o', '--out-dir', required=False, help='The directory where results should be saved.')
'-o', '--out-dir', required=False, default=os.getcwd(),
help='Output directory. Defaults to current working directory.')
parser.add_argument(
'-n', '--out-filename', required=False, help='Filename for the primary file converted, e.g. CodeSystem.')
parser.add_argument(
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6 changes: 4 additions & 2 deletions setup.py
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Expand Up @@ -15,13 +15,13 @@
EMAIL = '[email protected]'
AUTHOR = 'Joe Flack'
REQUIRES_PYTHON = '>=3.9.0'
VERSION = '1.0.0'
VERSION = '1.0.1'

# Requirements
REQUIRED = [
'bioontologies',
'oaklib>=0.5.1',
'requests',
'requests>2.28.2',
]

# Description
Expand Down Expand Up @@ -95,6 +95,8 @@ def run(self):
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'Programming Language :: Python :: 3.12',
'Programming Language :: Python :: Implementation :: CPython',
'Programming Language :: Python :: Implementation :: PyPy'
],
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