def generate_index_page(self):
"""Generates the index page for help where all programs and artifacts are listed"""
# let's add the 'path' for each artifact to simplify
# access from the template:
for artifact in self.artifacts_info:
self.artifacts_info[artifact]['path'] = f"artifacts/{artifact}"
# please note that artifacts get a fancy dictionary with everything, while programs get a crappy tuples list.
# if we need to improve the functionality of the help index page, we may need to update programs
# to a fancy dictionary, too.
d = {
'programs': [(p, 'programs/%s' % p,
self.programs[p].meta_info['description']['value'])
for p in self.programs],
'artifacts':
self.artifacts_info,
'artifact_types':
self.artifact_types,
'meta': {
'summary_type': 'programs_and_artifacts_index',
'version':
'%s (%s)' % (anvio.anvio_version, anvio.anvio_codename),
'date': utils.get_date()
}
}
d['program_provides_requires'] = self.get_program_requires_provides_dict(
prefix='')
output_file_path = os.path.join(self.output_directory_path, 'index.md')
open(output_file_path,
'w').write(SummaryHTMLOutput(d, r=run, p=progress).render())
def generate_pages_for_artifacts(self):
"""Generates static pages for artifacts in the output directory"""
self.progress.new("Rendering artifact pages",
progress_total_items=len(ANVIO_ARTIFACTS))
self.progress.update('...')
for artifact in ANVIO_ARTIFACTS:
self.progress.update(f"'{artifact}' ...", increment=True)
d = {
'artifact': ANVIO_ARTIFACTS[artifact],
'meta': {
'summary_type':
'artifact',
'version':
'\n'.join([
'|%s|%s|' % (t[0], t[1])
for t in anvio.get_version_tuples()
]),
'date':
utils.get_date(),
'version_short_identifier':
self.version_short_identifier
}
}
d['artifact']['name'] = artifact
d['artifact']['required_by'] = [
(r, '../../programs/%s' % r)
for r in self.artifacts_info[artifact]['required_by']
]
d['artifact']['provided_by'] = [
(r, '../../programs/%s' % r)
for r in self.artifacts_info[artifact]['provided_by']
]
d['artifact']['description'] = self.artifacts_info[artifact][
'description']
d['artifact'][
'icon'] = '../../images/icons/%s.png' % ANVIO_ARTIFACTS[
artifact]['type']
if anvio.DEBUG:
self.progress.reset()
run.warning(None, 'THE OUTPUT DICT')
import json
print(json.dumps(d, indent=2))
self.progress.update(f"'{artifact}' ... rendering ...",
increment=False)
artifact_output_dir = filesnpaths.gen_output_directory(
os.path.join(self.artifacts_output_dir, artifact))
output_file_path = os.path.join(artifact_output_dir, 'index.md')
open(output_file_path,
'w').write(SummaryHTMLOutput(d, r=run, p=progress).render())
self.progress.end()
def generate(self):
d = {}
log_file = filesnpaths.get_temp_file_path()
num_all_programs = len(self.all_programs)
for i in range(0, num_all_programs):
program_path = self.all_programs[i]
program_name = os.path.basename(program_path)
if program_name in self.programs_to_skip:
run.warning("Someone doesn't want %s to be in the output :/ Fine. Skipping." % (program_name))
progress.new('Bleep bloop')
progress.update('%s (%d of %d)' % (program_name, i+1, num_all_programs))
output = utils.run_command_STDIN('%s --help' % (program_path), log_file, '').split('\n')
if anvio.DEBUG:
usage, description, params, output = parse_help_output(output)
else:
try:
usage, description, params, output = parse_help_output(output)
except Exception as e:
progress.end()
run.warning("The program '%s' does not seem to have the expected help menu output. Skipping to the next.\
For the curious, this was the error message: '%s'" % (program_name, str(e).strip()))
continue
d[program_name] = {'usage': usage,
'description': description,
'params': params,
'tags': get_meta_information_from_file(program_path, '__tags__'),
'resources': get_meta_information_from_file(program_path, '__resources__')}
progress.end()
os.remove(log_file)
# generate output
program_names = sorted([p for p in d if not p.startswith('anvi-script-')])
script_names = sorted([p for p in d if p.startswith('anvi-script-')])
vignette = {'vignette': d,
'program_names': program_names,
'script_names': script_names,
'all_names': program_names + script_names,
'meta': {'summary_type': 'vignette',
'version': '\n'.join(['|%s|%s|' % (t[0], t[1]) for t in anvio.get_version_tuples()]),
'date': utils.get_date()}}
if anvio.DEBUG:
run.warning(None, 'THE OUTPUT DICT')
import json
print(json.dumps(d, indent=2))
open(self.output_file_path, 'w').write(SummaryHTMLOutput(vignette, r=run, p=progress).render())
run.info('Output file', os.path.abspath(self.output_file_path))
def generate_pages_for_programs(self):
"""Generates static pages for programs in the output directory"""
program_provides_requires_dict = self.get_program_requires_provides_dict(
)
for program_name in self.programs:
program = self.programs[program_name]
d = {
'program': {},
'meta': {
'summary_type':
'program',
'version':
'\n'.join([
'|%s|%s|' % (t[0], t[1])
for t in anvio.get_version_tuples()
]),
'date':
utils.get_date()
}
}
d['program']['name'] = program_name
d['program']['usage'] = program.usage
d['program']['description'] = program.meta_info['description'][
'value']
d['program']['resources'] = program.meta_info['resources']['value']
d['program']['requires'] = program_provides_requires_dict[
program_name]['requires']
d['program']['provides'] = program_provides_requires_dict[
program_name]['provides']
d['program']['icon'] = '../../images/icons/%s.png' % 'PROGRAM'
d['artifacts'] = self.artifacts_info
if anvio.DEBUG:
run.warning(None, 'THE OUTPUT DICT')
import json
print(json.dumps(d, indent=2))
program_output_dir = filesnpaths.gen_output_directory(
os.path.join(self.programs_output_dir, program_name))
output_file_path = os.path.join(program_output_dir, 'index.md')
open(output_file_path,
'w').write(SummaryHTMLOutput(d, r=run, p=progress).render())
# create the program network, too
program_network = ProgramsNetwork(argparse.Namespace(
output_file=os.path.join(program_output_dir, "network.json"),
program_names_to_focus=program_name),
r=terminal.Run(verbose=False))
program_network.generate()
def generate_pages_for_artifacts(self):
"""Generates static pages for artifacts in the output directory"""
for artifact in ANVIO_ARTIFACTS:
d = {
'artifact': ANVIO_ARTIFACTS[artifact],
'meta': {
'summary_type':
'artifact',
'version':
'\n'.join([
'|%s|%s|' % (t[0], t[1])
for t in anvio.get_version_tuples()
]),
'date':
utils.get_date()
}
}
d['artifact']['name'] = artifact
d['artifact']['required_by'] = [
(r, '../../programs/%s' % r)
for r in self.artifacts_info[artifact]['required_by']
]
d['artifact']['provided_by'] = [
(r, '../../programs/%s' % r)
for r in self.artifacts_info[artifact]['provided_by']
]
d['artifact']['description'] = self.artifacts_info[artifact][
'description']
d['artifact'][
'icon'] = '../../images/icons/%s.png' % ANVIO_ARTIFACTS[
artifact]['type']
if anvio.DEBUG:
run.warning(None, 'THE OUTPUT DICT')
import json
print(json.dumps(d, indent=2))
artifact_output_dir = filesnpaths.gen_output_directory(
os.path.join(self.artifacts_output_dir, artifact))
output_file_path = os.path.join(artifact_output_dir, 'index.md')
open(output_file_path,
'w').write(SummaryHTMLOutput(d, r=run, p=progress).render())
def generate_index_page(self):
d = {
'programs': [(p, 'programs/%s' % p,
self.programs[p].meta_info['description']['value'])
for p in self.programs],
'artifacts':
[(a, 'artifacts/%s' % a) for a in self.artifacts_info],
'meta': {
'summary_type': 'programs_and_artifacts_index',
'version':
'%s (%s)' % (anvio.anvio_version, anvio.anvio_codename),
'date': utils.get_date()
}
}
d['program_provides_requires'] = self.get_program_requires_provides_dict(
prefix='')
output_file_path = os.path.join(self.output_directory_path, 'index.md')
open(output_file_path,
'w').write(SummaryHTMLOutput(d, r=run, p=progress).render())