def generate_or_check(manifest, args, path, func):
"""Generate/check a file with a single generator
Return True if successful; False if a comparison failed.
"""
outfile = io.StringIO()
func(manifest, args, outfile)
generated = outfile.getvalue()
existing = path.read_text()
if generated != existing:
if args.generate:
path.write_text(generated)
else:
print(f'File {path} differs from expected!')
diff = difflib.unified_diff(
generated.splitlines(),
existing.splitlines(),
str(path),
'<expected>',
lineterm='',
)
for line in diff:
print(line)
return False
return True
def write_yaml(dictionary, filename, logger=None):
"""Write YAML file.
Parameters
----------
dictionary : dict
Python dictionary
filename : `~pathlib.Path`
Filename
logger : `~logging.Logger`
Logger
"""
text = yaml.safe_dump(dictionary, default_flow_style=False)
path = make_path(filename)
path.parent.mkdir(exist_ok=True)
if logger is not None:
logger.info("Writing {}".format(path))
path.write_text(text)
def run(language: str, struct_file, destination_path: pathlib.Path):
template = structy_generator.templates.template_for(language)
if not destination_path.exists():
if sys.stdout.isatty():
create = input(
f"Hey, {destination_path} doesn't exist, do want me to create it? (y/n)"
)
if create == "y":
destination_path.mkdir(parents=True)
else:
raise StructyError(
f"Well, fine, {destination_path} doesn't exist and you don't want me to make it so I give up."
)
else:
raise StructyError(f"C'mon, {destination_path} doesn't exist!")
if not destination_path.is_dir():
raise StructyError(
f"Hey, {destination_path} isn't a path. I can't put files into another file."
)
source_file_name = pathlib.Path(struct_file.name).name
source_file_stem = pathlib.Path(struct_file.name).stem
struct = structy_generator.parser.parse(struct_file.read())
outputs = template.render(
source_file_stem,
date=datetime.datetime.utcnow(),
source=source_file_name,
source_stem=source_file_stem,
struct=struct,
kinds=structy_generator.kinds.get_kinds(),
)
for output_name, output_contents in outputs.items():
path = destination_path / output_name
path.write_text(output_contents)
print(f"Generated {path}.")
def write_yaml(dictionary, filename, logger=None, sort_keys=True):
"""Write YAML file.
Parameters
----------
dictionary : dict
Python dictionary
filename : `~pathlib.Path`
Filename
logger : `~logging.Logger`
Logger
sort_keys : bool
Whether to sort keys.
"""
text = yaml.safe_dump(dictionary, default_flow_style=False, sort_keys=sort_keys)
path = make_path(filename)
path.parent.mkdir(exist_ok=True)
if logger is not None:
logger.info(f"Writing {path}")
path.write_text(text)
def copy_pub(self):
htm_dir = self.get_htm_dir()
if htm_dir:
src = self.home / 'bld' / htm_dir
if src.exists():
ignore = shutil.ignore_patterns('.*')
dst = self.home / 'pub'
for child in src.iterdir():
if child.name.startswith('.'):
continue
if child.is_dir():
shutil.copytree(child, dst / child.name, ignore=ignore)
else:
shutil.copy2(child, dst / child.name)
# create empty files
for name in ['.nojekyll']:
path = dst / name
if not path.exists():
path.write_text('')
# create CNAME
if self.cname:
(dst / 'CNAME').write_text(self.cname)
def cacheDict(filePath, dictionary):
path = Path(filePath)
path.write_text( json.dumps(dictionary) )
def main():
if (len(sys.argv) < 2):
print(
"Error: missing xlsx file - correct usage is:\n\tpython3 R4CapStatement_Maker.py [xlsx file]"
)
return
xls = sys.argv[1]
print('....creating CapabilityStatement.....')
# Read the config sheet from the spreadsheet
# use the index_col = 0 for setting the first row as the index
config_df = read_excel(xls, 'config', na_filter=False, index_col=0)
# --------- ig specific variable -------------------
pre = config_df.Value.pre # for Titles - not sure this is actually used
canon = config_df.Value.canon # don't forget the slash - fix using os.join or path
publisher = config_df.Value.publisher
restinteraction = config_df.Value.rest
publisher_endpoint = dict(
system=config_df.Value.publishersystem,
value=config_df.Value.publishervalue,
)
definitions_file = config_df.Value.definitions_file #source of spec.internal file manually extracted from downloaded spec
# Read the meta sheet from the spreadsheet
meta_df = read_excel(xls, 'meta', na_filter=False)
meta_dict = dict(zip(meta_df.Element, meta_df.Value))
meta = namedtuple("Meta", meta_dict.keys())(*meta_dict.values())
# Create the CapabilityStatement
cs = create_capabilitystatement(meta, canon, publisher, publisher_endpoint,
xls)
rest = CS.CapabilityStatementRest(
dict(mode=meta.mode,
documentation=meta.documentation,
security=dict(
description=meta.security) if meta.security else None,
interaction=get_rest_ints(xls) if restinteraction else None,
operation=get_sys_op(xls)))
cs.rest = [rest]
df_profiles = read_excel(xls, 'profiles', na_filter=False)
df_profiles = df_profiles[df_profiles.Profile.str[0] != '!']
resources_df = read_excel(xls, 'resources', na_filter=False)
resources_df = resources_df[resources_df.type.str[0] != '!']
df_i = read_excel(xls, 'interactions', na_filter=False)
df_sp = read_excel(xls, 'sps', na_filter=False)
df_combos = read_excel(xls, 'sp_combos', na_filter=False)
df_op = read_excel(xls, 'ops', na_filter=False)
rest.resource = []
for r in resources_df.itertuples(index=True):
supported_profile = [
p.Profile for p in df_profiles.itertuples(index=True)
if p.Type == r.type
]
res = CS.CapabilityStatementRestResource(
dict(type=r.type,
documentation=r.documentation
if r.documentation not in none_list else None,
versioning=r.versioning
if r.versioning not in none_list else None,
readHistory=r.readHistory
if r.readHistory not in none_list else None,
updateCreate=r.updateCreate
if r.updateCreate not in none_list else None,
conditionalCreate=r.conditionalCreate
if r.conditionalCreate not in none_list else None,
conditionalRead=r.conditionalRead
if r.conditionalRead not in none_list else None,
conditionalUpdate=r.conditionalUpdate
if r.conditionalUpdate not in none_list else None,
conditionalDelete=r.conditionalDelete
if r.conditionalDelete not in none_list else None,
referencePolicy=[
re.sub('\s+', '', x) for x in r.referencePolicy.split(",")
if x
],
searchInclude=[
re.sub('\s+', '', x) for x in r.shall_include.split(",") +
r.should_include.split(",") if x
],
searchRevInclude=[
re.sub('\s+', '', x)
for x in r.shall_revinclude.split(",") +
r.should_revinclude.split(",") if x
],
interaction=get_i(r.type, df_i),
searchParam=get_sp(r.type, df_sp, pre, canon),
operation=get_op(r.type, df_op),
supportedProfile=supported_profile))
res.extension = get_conf(r.conformance)
combos = {(i.combo, i.combo_conf)
for i in df_combos.itertuples(index=True)
if i.base == r.type}
# convert list to lst of combo extension
res.extension = res.extension + get_combo_ext(r.type, combos)
rest.resource.append(res)
rest.resource = sorted(rest.resource,
key=lambda x: x.type) # sort resources
cs.rest = [rest]
# add in conformance expectations for primitives
# convert to dict since model can't handle primitive extensions
resttype_dict = res.as_json()
for i in ['Include', 'RevInclude']:
element = f'_search{i}'
resttype_dict[element] = []
for expectation in ['should',
'shall']: # list all should includes first
sp_attr = f'{expectation}_{i.lower()}'
includes = getattr(r, sp_attr).split(',')
for include in includes:
if include not in none_list:
conf = get_conf(expectation.upper(), as_dict=True)
resttype_dict[element].append(conf)
if not resttype_dict[element]:
del (resttype_dict[element])
print(resttype_dict)
print(dumps(cs.as_json(), indent=3)) # %% [markdown]
print('.............validating..............')
r = validate(cs)
if (r.status_code != 200):
print("Error: Unable to validate - status code {}".format(
r.status_code))
path = Path.cwd() / 'validation.html'
path.write_text(
f'<h1>Validation output</h1><h3>Status Code = {r.status_code}</h3> {r.json()["text"]["div"]}'
)
print(f"HTML webpage of validation saved to:\n\t {path}")
# get from package (json) file in local .fhir directory
si = get_si2(definitions_file)
path_map = si['paths']
path_map
in_path = ''
in_file = 'R4capabilitystatement-server.j2'
env = Environment(loader=FileSystemLoader(searchpath=in_path),
autoescape=select_autoescape(
['html', 'xml', 'xhtml', 'j2', 'md']))
env.filters['markdown'] = markdown
template = env.get_template(in_file)
sp_map = {sp.code: sp.type for sp in df_sp.itertuples(index=True)}
pname_map = {p.Profile: p.Name for p in df_profiles.itertuples(index=True)}
sp_url_map = {sp.code: sp.rel_url for sp in df_sp.itertuples(index=True)}
purl_map = {
p.Profile: p.url if p.url not in none_list else p.Profile
for p in df_profiles.itertuples(index=True)
}
# below taken from source code. Not clear what these are, perhaps from an updated spreadsheet source.
#igname_map = {ig.canonical:ig.name for ig in df_igs.itertuples(index=True)}
#igurl_map = {ig.canonical:ig.url if ig.url not in none_list else ig.canonical for ig in df_igs.itertuples(index=True)}
#csname_map = {cs.canonical:cs.name for cs in df_capstatements.itertuples(index=True)}
#csurl_map = {cs.canonical:cs.url if cs.url not in none_list else cs.canonical for cs in df_capstatements.itertuples(index=True)
print(pname_map)
rendered = template.render(cs=cs,
path_map=path_map,
pname_map=pname_map,
purl_map=purl_map,
sp_map=sp_map,
sp_url_map=sp_url_map)
# print(HTML(rendered))
parser = etree.XMLParser(remove_blank_text=True)
root = etree.fromstring(rendered, parser=parser)
div = (etree.tostring(root[1][0], encoding='unicode', method='html'))
narr = N.Narrative()
narr.status = 'generated'
narr.div = div
cs.text = narr
# save to file
print('...........saving to file............')
# path = Path.cwd() / f'capabilitystatement-{cs.id.lower()}.json'
path = Path.cwd() / f'capabilitystatement-{meta.title.lower()}.json'
path.write_text(dumps(cs.as_json(), indent=4))
print(f"CapabilityStatement saved to:\n\t {path}")
def main():
if (len(sys.argv) < 2):
print(
"Error: missing json file - correct usage is:\n\tpython3 R4CapStatement_NarrativeMaker.py [json file] {[Artifacts Folder]}")
return
xls = sys.argv[1]
in_json_file = sys.argv[1]
artifacts_folder = ""
if len(sys.argv) > 2:
artifacts_folder = sys.argv[2]
print('....Generating CapabilityStatement Narrative.....')
with open(in_json_file, 'r') as h:
pjs = json.load(h)
capStatement = CS.CapabilityStatement(pjs)
#print(dumps(capStatement.as_json(), indent=3)) # %% [markdown]
# CapabilityStatement loaded
in_path = ''
in_file = 'R4capabilitystatement-server.j2'
env = Environment(
loader=FileSystemLoader(searchpath=in_path),
autoescape=select_autoescape(['html', 'xml', 'xhtml', 'j2', 'md'])
)
env.filters['markdown'] = markdown
template = env.get_template(in_file)
pname_map = {}
igname_map = {}
csname_map = {}
# Load name maps
if artifacts_folder != "":
print('....Retrieving Artifact Names .....')
artifacts_folder = os.path.abspath(artifacts_folder)
struct_def_files = glob.glob(artifacts_folder + "/StructureDefinition-*.json")
imp_guide_files = glob.glob(artifacts_folder + "/ImplementationGuide-*.json")
cap_stmt_files = glob.glob(artifacts_folder + "/CapabilityStatement-*.json")
pname_map = get_pname_map(struct_def_files)
igname_map = get_igname_map(imp_guide_files)
csname_map = get_csname_map(cap_stmt_files)
# Check access to hl7.org/fhir
r = get (fhir_base_url)
if r.status_code == 200:
print('....Retrieving Online Artifact Names .....')
# Loop through all references in the CapabilityStatement and attempt to retried the artifacts to load the names into the map
# Instantiates
if capStatement.instantiates:
for url in capStatement.instantiates:
if url not in csname_map:
csname_map[url] = get_url_title(url, "instantiates CapabilityStatement")
# Imports
if capStatement.imports:
for url in capStatement.imports:
if url not in csname_map:
csname_map[url] = get_url_title(url, "imports CapabilityStatement")
# Implementation Guides
if capStatement.implementationGuide:
for url in capStatement.implementationGuide:
if url not in igname_map:
igname_map[url] = get_url_title(url, "ImplementationGuide")
# Iterate through rest resources
if capStatement.rest:
for rest in capStatement.rest:
if rest.resource:
for resource in rest.resource:
if resource.profile:
url = resource.profile
if url not in pname_map:
pname_map[url] = get_url_title(url, resource.type + " profile")
if resource.supportedProfile:
for url in resource.supportedProfile:
if url not in pname_map:
pname_map[url] = get_url_title(url, resource.type + " supported profile")
else:
print("Unable to connect to " + fhir_base_url + ". Will not attempt to load online artifacts to retrieve artifact names.")
rendered = template.render(cs=capStatement, path_map='', pname_map=pname_map, purl_map='', sp_map='',
csname_map=csname_map, csurl_map='', sp_url_map='', igname_map=igname_map, igurl_map='')
#template.render(cs=cs, path_map=path_map, pname_map=pname_map, purl_map=purl_map, sp_map=sp_map,
# csname_map=csname_map, csurl_map=csurl_map, igname_map=igname_map, igurl_map=igurl_map)
tempPath = Path.cwd() / "test.html"
tempPath.write_text(rendered)
#print(rendered)
parser = etree.XMLParser(remove_blank_text=True)
root = etree.fromstring(rendered, parser=parser)
div = (etree.tostring(root[1][0], encoding='unicode', method='html'))
print("\n####################################################\n")
#print(etree.tostring(root[1][0], encoding='unicode', method='html'))
print("\n####################################################\n")
narr = N.Narrative()
narr.status = 'generated'
#div = re.sub('https://paciowg.github.io/advance-directives-ig/StructureDefinition-', 'SSSSSSSSSSSSSSSSS', div)
# replace all of the supported profile urls in link text with just the profile name from inside the cononical url
#######div = re.sub('">\(https?://.*/StructureDefinition-(.*)\.html\)</a>', '">\\1</a>', div)
#div = re.sub('">\(https://paciowg.github.io/advance-directives-ig/StructureDefinition-PADI-(PersonalGoal.html)</a>', '\\1', div)
# For some reason <br /> is being replaced with <br></br>, which is wrong. Convert it back.
#div = div.replace("<br></br>", "<br />")
#print(div)
narr.div = div
#print(dumps(narr.div, indent=3)) # %% [markdown]
capStatement.text = narr
outfile = 'Narrative-' + in_json_file
path = Path.cwd() / outfile
tempOut = dumps(capStatement.as_json(), indent=4)
tempOut = tempOut.replace("<sup>+</sup>", "<sup>†</sup>")
#tempOut = tempOut.replace(“<sup>t</sup>”, “<sup>†</sup>”)
#print(tempOut)
path.write_text(tempOut)
print('.............validating..............')
r = validate(capStatement)
if (r.status_code != 200):
print("Error: Unable to validate - status code {}".format(r.status_code))
path = Path.cwd() / 'validation.html'
path.write_text(
f'<h1>Validation output</h1><h3>Status Code = {r.status_code}</h3> {r.json()["text"]["div"]}')
print(f"HTML webpage of validation saved to:\n\t {path}")
# get from package (json) file in local .fhir directory
# save to file
print('...........done............')
def test_info_path_like(tmpdir):
path = Path(tmpdir / "test_info")
path.write_text("fsspec")
fs = LocalFileSystem()
assert fs.exists(path)
def cacheDict(filePath, dictionary):
'''utility function to cache data as dictionary '''
path = Path(filePath)
path.write_text(json.dumps(dictionary))
def _process_file(path: Path, func: Callable[[str], str]):
orig_content = path.read_text()
new_content = func(orig_content)
path.write_text(new_content)
