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Rearrange handling of input args in order to support a new policy for…
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… the names of output files
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@aozalevsky
aozalevsky committed Jul 29, 2024
1 parent 86c5267 commit 48c8415
Showing 1 changed file with 60 additions and 55 deletions.
115 changes: 60 additions & 55 deletions ihm_validation/ihm_validator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,16 +87,6 @@
parser.add_argument('--enable-cx', default=False, type=lambda x: bool(strtobool(x)),
help="Run crosslinking-MS validation")

args = parser.parse_args()
if args.p.upper() == 'YES':
physics = [
'Sequence connectivity',
'Excluded volume'
]
else:
physics = ['Information about physical principles was not provided']

logging.basicConfig(level=logging.INFO if args.verbose else logging.WARNING)

#############################################################################################################################
# Input for Jinja
Expand Down Expand Up @@ -150,35 +140,6 @@
d_format = d.astimezone(timezone)
timestamp = d_format.strftime("%B %d, %Y - %I:%M %p %Z")


output_root = args.output_root

output_prefix = Path(args.f).stem
if args.output_prefix is not None:
output_prefix = args.output_prefix

output_path = Path(output_root, output_prefix)

dirNames = {
'root': str(output_path),
'root_html': str(Path(output_path, output_prefix)),
}

dirNames.update(
{
'html': str(Path(dirNames['root_html'], 'htmls')),
}
)

dirNames.update(
{
'images': str(Path(dirNames['root_html'], 'images')),
'csv': str(Path(dirNames['root_html'], 'csv')),
'pdf': str(Path(dirNames['root_html'], 'pdf')),
# 'json': str(Path(output_path, 'json')),
}
)

# This is a temporary hack for ../templates
template_path = Path(Path(__file__).parent.parent.resolve(), 'templates')
templateLoader = jinja2.FileSystemLoader(searchpath=template_path)
Expand Down Expand Up @@ -254,9 +215,58 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
#################################################

if __name__ == "__main__":
logging.info("Clean up and create output directories")
args = parser.parse_args()

if args.p.upper() == 'YES':
physics = [
'Sequence connectivity',
'Excluded volume'
]
else:
physics = ['Information about physical principles was not provided']

logging.basicConfig(level=logging.INFO if args.verbose else logging.WARNING)

logging.info("Clean up temporary files")
utility.clean_all()

report = WriteReport(args.f,
db=args.databases_root,
cache=args.cache_root,
nocache=args.nocache)

logging.info("Entry composition")
template_dict = report.run_entry_composition(Template_Dict)

output_root = args.output_root

output_prefix = Path(args.f).stem
if args.output_prefix is not None:
output_prefix = args.output_prefix

output_path = Path(output_root, output_prefix)

dirNames = {
'root': str(output_path),
'root_html': str(Path(output_path, template_dict['ID_f'])),
}

dirNames.update(
{
'html': str(Path(dirNames['root_html'], 'htmls')),
}
)

dirNames.update(
{
'images': str(Path(dirNames['root_html'], 'images')),
'csv': str(Path(dirNames['root_html'], 'csv')),
'pdf': str(Path(dirNames['root_html'], 'pdf')),
# 'json': str(Path(output_path, 'json')),
}
)

logging.info("Creating output directories")
if Path(output_path).is_dir():
if args.force:
logging.info(f'Overwriting output directory {output_path}')
Expand All @@ -273,13 +283,6 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
createdirs(dirNames)
manager = Manager() # create only 1 mgr
d = manager.dict() # create only 1 dict
report = WriteReport(args.f,
db=args.databases_root,
cache=args.cache_root,
nocache=args.nocache)

logging.info("Entry composition")
template_dict = report.run_entry_composition(Template_Dict)

logging.info("Model quality")
template_dict, molprobity_dict, exv_data = report.run_model_quality(
Expand Down Expand Up @@ -317,9 +320,10 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
molprobity_dict, exv_data, sas_data, sas_fit, cx_fit, imageDirName=dirNames['images'])

logging.info("Write PDF")
output_pdf = write_pdf(output_prefix, template_dict, template_pdf,
output_pdf = write_pdf(template_dict['ID_f'], template_dict, template_pdf,
dirNames['pdf'], dirNames['pdf'])
shutil.copy(output_pdf, str(output_path))
output_pdf_ext = Path(str(output_path), utility.get_output_file_pdf(output_prefix))
shutil.copy(output_pdf, str(output_pdf_ext))

template_dict['validation_pdf'] = Path(output_pdf).name

Expand All @@ -335,8 +339,9 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
clustering=None,
)
output_pdf = write_supplementary_table(
output_prefix, template_dict, template_file_supp, dirNames['pdf'], dirNames['pdf'])
shutil.copy(output_pdf, str(output_path))
template_dict['ID_f'], template_dict, template_file_supp, dirNames['pdf'], dirNames['pdf'])
output_pdf_ext = Path(str(output_path), utility.get_supp_file_pdf(output_prefix))
shutil.copy(output_pdf, str(output_pdf_ext))

template_dict['supplementary_pdf'] = Path(output_pdf).name

Expand All @@ -346,20 +351,20 @@ def write_json(mmcif_file: str, template_dict: dict, dirName: str, dirName_Outpu
logging.info("Write HTML")
# set html mode
template_dict['html_mode'] = args.html_mode
write_html(output_prefix, template_dict, template_flask, dirNames['html'])
write_html(template_dict['ID_f'], template_dict, template_flask, dirNames['html'])
if args.html_mode == 'local':
shutil.copytree(
args.html_resources,
str(Path(dirNames['html'], Path(args.html_resources).stem))
)
# Compress html output to one file
logging.info('Compressing html archive')
shutil.make_archive(
root_dir=output_path,
base_dir=output_prefix,
base_name=f'{dirNames["root_html"]}_html',
base_dir=template_dict['ID_f'],
base_name=str(Path(output_path, f'{output_prefix}_html')),
format='gztar')


# Keep uncompressed html output for convience
# otherwise delete
if args.keep_html:
Expand Down

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