def __init__(self, spec, resource):
assert 'content' in resource
self.spec = spec
self.definition = resource
self.url = resource.get('url')
if self.url in self.spec.settings.enum_namemap:
self.name = self.spec.settings.enum_namemap[self.url]
else:
self.name = self.spec.safe_enum_name(resource.get('name'),
ucfirst=True)
self.codes = None
self.generate_enum = False
concepts = self.definition.get('concept', [])
if resource.get('experimental'):
return
self.generate_enum = 'complete' == resource['content']
if not self.generate_enum:
logger.debug(
"Will not generate enum for CodeSystem \"{}\" whose content is {}"
.format(self.url, resource['content']))
return
assert concepts, "Expecting at least one code for \"complete\" CodeSystem"
if len(concepts) > 200:
self.generate_enum = False
logger.info(
"Will not generate enum for CodeSystem \"{}\" because it has > 200 ({}) concepts"
.format(self.url, len(concepts)))
return
self.codes = self.parsed_codes(concepts)
def render(self):
if self.spec.unit_tests is None:
return
# render all unit test collections
for coll in self.spec.unit_tests:
data = {
'info': self.spec.info,
'class': coll.klass,
'tests': coll.tests,
}
file_pattern = coll.klass.name
if self.settings.resource_modules_lowercase:
file_pattern = file_pattern.lower()
file_name = self.settings.tpl_unittest_target_ptrn.format(file_pattern)
file_path = os.path.join(self.settings.tpl_unittest_target, file_name)
self.do_render(data, self.settings.tpl_unittest_source, file_path)
# copy unit test files, if any
if self.settings.unittest_copyfiles is not None:
for origfile in self.settings.unittest_copyfiles:
utfile = os.path.join(*origfile.split('/'))
if os.path.exists(utfile):
target = os.path.join(self.settings.tpl_unittest_target, os.path.basename(utfile))
logger.info('Copying unittest file {} to {}'.format(os.path.basename(utfile), target))
shutil.copyfile(utfile, target)
else:
logger.warning("Unit test file \"{}\" configured in `unittest_copyfiles` does not exist"
.format(utfile))
def read_profiles(self):
""" Find all (JSON) profiles and instantiate into FHIRStructureDefinition.
"""
resources = []
for filename in ['profiles-types.json', 'profiles-resources.json'
]: #, 'profiles-others.json']:
bundle_res = self.read_bundle_resources(filename)
for resource in bundle_res:
if 'StructureDefinition' == resource['resourceType']:
resources.append(resource)
else:
logger.debug('Not handling resource of type {}'.format(
resource['resourceType']))
# create profile instances
for resource in resources:
profile = FHIRStructureDefinition(self, resource,
self.settings.sort_resources)
for pattern in skip_because_unsupported:
if re.search(pattern, profile.url) is not None:
logger.info('Skipping "{}"'.format(resource['url']))
profile = None
break
if profile is not None and self.found_profile(profile):
profile.process_profile()
def render(self):
for profile in self.spec.writable_profiles():
classes = profile.writable_classes()
if self.settings.sort_resources:
classes = sorted(classes, key=lambda x: x.name)
if 0 == len(classes):
if profile.url is not None: # manual profiles have no url and usually write no classes
logger.info('Profile "{}" returns zero writable classes, skipping'.format(profile.url))
continue
imports = profile.needed_external_classes()
self.set_forwards(imports, classes)
data = {
'profile': profile,
'info': self.spec.info,
'imports': imports,
'classes': classes
}
ptrn = profile.targetname.lower() if self.settings.resource_modules_lowercase else profile.targetname
source_path = self.settings.tpl_resource_source
target_name = self.settings.tpl_resource_target_ptrn.format(ptrn)
target_path = os.path.join(self.settings.tpl_resource_target, target_name)
self.do_render(data, source_path, target_path)
self.copy_files(self.settings.tpl_resource_target)
def parse_profile(self, profile):
""" Parse a JSON profile into a structure.
"""
assert profile
assert 'StructureDefinition' == profile['resourceType']
# parse structure
self.url = profile.get('url')
logger.info('Parsing profile "{}"'.format(profile.get('name')))
self.structure = FHIRStructureDefinitionStructure(self, profile)
def render(self):
if not self.settings.tpl_codesystems_source:
logger.info("Not rendering value sets and code systems since `tpl_codesystems_source` is not set")
return
systems = [v for k,v in self.spec.codesystems.items()]
data = {
'info': self.spec.info,
'systems': sorted(systems, key=lambda x: x.name) if self.settings.sort_resources else systems,
}
target_name = self.settings.tpl_codesystems_target_name
target_path = os.path.join(self.settings.tpl_resource_target, target_name)
self.do_render(data, self.settings.tpl_codesystems_source, target_path)
def copy_files(self, target_dir):
""" Copy base resources to the target location, according to settings.
"""
for origpath, module, contains in self.settings.manual_profiles:
if not origpath:
continue
origpath = self.rel_to_settings_path(self.settings, self.clean_it(origpath))
if os.path.exists(origpath):
tgt = os.path.join(target_dir, os.path.basename(origpath))
logger.info("Copying manual profiles in {} to {}".format(os.path.basename(origpath), tgt))
os.makedirs(os.path.dirname(tgt), exist_ok=True)
shutil.copyfile(origpath, tgt)
else:
logger.error(f"Manual profile {origpath} does not exits")
def read_valuesets(self):
resources = self.read_bundle_resources('valuesets.json')
for resource in resources:
if 'ValueSet' == resource['resourceType']:
assert 'url' in resource
self.valuesets[resource['url']] = FHIRValueSet(self, resource)
elif 'CodeSystem' == resource['resourceType']:
assert 'url' in resource
if 'content' in resource and 'concept' in resource:
self.codesystems[resource['url']] = FHIRCodeSystem(
self, resource)
else:
logger.warning("CodeSystem with no concepts: {}".format(
resource['url']))
logger.info("Found {} ValueSets and {} CodeSystems".format(
len(self.valuesets), len(self.codesystems)))
def content(self):
""" Process the unit test file, determining class structure
from the given classes dict.
:returns: A tuple with (top-class-name, [test-dictionaries])
"""
if self._content is None:
logger.info('Parsing unit test {}'.format(
os.path.basename(self.filepath)))
utest = None
assert os.path.exists(self.filepath)
with io.open(self.filepath, 'r', encoding='utf-8') as handle:
utest = json.load(handle)
assert utest
self._content = utest
return self._content
def load(self):
""" Makes sure all the files needed have been downloaded.
:returns: The path to the directory with all our files.
"""
if self.force_download: assert not self.force_cache
# If we're not forcing anything, see whether our cached version matches what is on the server
version_path = os.path.join(self.cache, 'version.info')
if not (self.force_download or self.force_cache):
from fhirparser.fhirspec import FHIRVersionInfo
cached_version = FHIRVersionInfo(None, self.cache) \
if not self.force_cache and os.path.exists(version_path) else None
self.download('version.info')
server_version = FHIRVersionInfo(None, self.cache)
if cached_version.version != server_version.version:
logger.info(f"Server version ({server_version.version}) "
f"doesn't match cache ({cached_version.version}) - Reloading cache")
self.force_download = True
if os.path.isdir(self.cache) and self.force_download:
import shutil
shutil.rmtree(self.cache)
if not os.path.isdir(self.cache):
os.mkdir(self.cache)
# check all files and download if missing
uses_cache = False
for local, remote in self.__class__.needs.items():
path = os.path.join(self.cache, local)
if not os.path.exists(path):
if self.force_cache:
raise Exception('Resource missing from cache: {}'.format(local))
logger.info('Downloading {}'.format(remote))
filename = self.download(remote)
# unzip
if '.zip' == filename[-4:]:
logger.info('Extracting {}'.format(filename))
self.expand(filename)
else:
if local == 'version.info':
uses_cache = True
if uses_cache:
logger.info('Using cached resources, supply "-f" to re-download')
return self.cache
def read_bundle_resources(self, filename):
""" Return an array of the Bundle's entry's "resource" elements.
"""
logger.info("Reading {}".format(filename))
filepath = os.path.join(self.directory, filename)
if not os.path.exists(filepath) and not self.loader.force_cache:
self.loader.download(filename)
if not os.path.exists(filepath):
raise Exception('Resource missing from cache: {}'.format(filename))
with io.open(filepath, encoding='utf-8') as handle:
parsed = json.load(handle)
if 'resourceType' not in parsed:
raise Exception(
"Expecting \"resourceType\" to be present, but is not in {}"
.format(filepath))
if 'Bundle' != parsed['resourceType']:
raise Exception("Can only process \"Bundle\" resources")
if 'entry' not in parsed:
raise Exception(
"There are no entries in the Bundle at {}".format(
filepath))
return [e['resource'] for e in parsed['entry']]
def parsed_codes(self, codes, prefix=None):
found = []
for c in codes:
if re.match(r'\d', c['code'][:1]):
self.generate_enum = False
logger.info(
"Will not generate enum for CodeSystem \"{}\" because at least one concept code starts with a number"
.format(self.url))
return None
cd = c['code']
name = '{}-{}'.format(
prefix, cd) if prefix and not cd.startswith(prefix) else cd
c['name'] = self.spec.safe_enum_name(cd)
c['definition'] = c.get('definition') or c['name']
found.append(c)
# nested concepts?
if 'concept' in c:
fnd = self.parsed_codes(c['concept'])
if fnd is None:
return None
found.extend(fnd)
return found
def do_render(self, data, template_name, target_path):
""" Render the given data using a Jinja2 template, writing to the file
at the target path.
:param template_name: The Jinja2 template to render, located in settings.tpl_base
:param target_path: Output path
"""
try:
template = self.jinjaenv.get_template(os.path.basename(template_name))
except TemplateNotFound as e:
logger.error("Template \"{}\" not found in «{}», cannot render"
.format(template_name, self.settings.tpl_base))
return
if not target_path:
raise Exception("No target filepath provided")
dirpath = os.path.dirname(target_path)
if not os.path.isdir(dirpath):
os.makedirs(dirpath)
with io.open(target_path, 'w', encoding='utf-8') as handle:
logger.info('Writing {}'.format(target_path))
rendered = template.render(data)
handle.write(rendered)
def generator(args: List[str]) -> Optional[int]:
cwd = os.getcwd()
opts = genargs().parse_args(args)
if opts.force and opts.cached:
raise ArgumentError('force and cached options cannot both be true')
# Load the settings
if os.path.isdir(opts.settings):
opts.settings = os.path.join(opts.settings, 'settings.py')
opts.settings_dir = os.path.abspath(os.path.dirname(opts.settings))
logger.info(f"Loading settings from {opts.settings}")
with open(opts.settings) as f:
settings_py = f.read()
settings = ModuleType('settings')
exec(settings_py, settings.__dict__)
settings.settings_dir = opts.settings_dir
# Sort option -- default if not in the settings directory
if opts.nosort:
settings.sort_resources = False
elif getattr(settings, "sort_resources", None) is None:
settings.sort_resources = True
if settings.sort_resources:
logger.info("Sorting resource properties")
else:
logger.info("Resource properties are not sorted")
if opts.fhirurl:
settings.specification_url = opts.fhirurl
adjust_source_target_paths(settings, opts)
logger.info(f"Specification: {settings.specification_url}")
logger.info(f"Template directory: {os.path.relpath(settings.tpl_base, cwd)}")
logger.info(f"Output directory: {os.path.relpath(settings.tpl_resource_target, cwd)}")
if settings.write_unittests:
logger.info(f"Unit test directory: {os.path.relpath(settings.tpl_unittest_target, cwd)}")
logger.info(f"Cache directory: {opts.cachedir}")
loader = fhirloader.FHIRLoader(settings, opts.cachedir, force_download=opts.force, force_cache= opts.cached)
spec_source = loader.load()
if not opts.loadonly:
spec = fhirspec.FHIRSpec(spec_source, settings, loader)
if not opts.parseonly:
spec.write()
return 0
