def main_json(config_path, in_metadata_path, out_metadata_path):
"""
Main function.
This function launches the app using configuration written in two json files: defineIO.json and input_metadata.json.
:param config_path: path to a valid JSON file containing information on how the tool should be executed.
:type config_path: str
:param in_metadata_path: path to a valid JSON file containing information on tool inputs.
:type in_metadata_path: str
:param out_metadata_path: path to write the JSON file containing information on tool outputs.
:type out_metadata_path: str
:return: If result is True, execution finished successfully. False, otherwise.
:rtype: bool
"""
try:
logger.info("1. Instantiate and launch the App")
app = JSONApp()
result = app.launch(process_WF_RUNNER, config_path, in_metadata_path, out_metadata_path) # launch the app
logger.info("2. App successfully launched; see " + out_metadata_path)
return result
except Exception as error:
errstr = "App wasn't successfully launched. ERROR: {}".format(error)
logger.error(errstr)
raise Exception(errstr)
def main_json(config, in_metadata, out_metadata):
"""
Main function.
This function launches the app using configuration written in two json files: config.json and input_metadata.json.
:param config:
:param in_metadata:
:param out_metadata:
:type config:
:type in_metadata:
:type out_metadata:
:return: If result is True, execution finished successfully. False, otherwise.
:rtype: bool
"""
try:
logger.info("1. Instantiate and launch the App")
app = JSONApp()
result = app.launch(process_WF_RUNNER, config, in_metadata, out_metadata) # launch the app
logger.info("2. App successfully launched; see " + out_metadata)
return result
except Exception as error:
errstr = "App wasn't successfully launched. ERROR: {}".format(error)
logger.error(errstr)
raise Exception(errstr)
def main_wrapper(config_path, in_metadata_path, out_metadata_path):
"""
Main function.
This function launches the tool using configuration written in two json files: config.json and in_metadata.json.
:param config_path: Path to a valid VRE JSON file containing information on how the tool should be executed.
:type config_path: str
:param in_metadata_path: Path to a valid VRE JSON file containing information on tool inputs.
:type in_metadata_path: str
:param out_metadata_path: Path to write the VRE JSON file containing information on tool outputs.
:type out_metadata_path: str
:return: If result is True, execution finished successfully. False, otherwise.
:rtype: bool
"""
try:
app = JSONApp()
result = app.launch(Wrapper, config_path, in_metadata_path,
out_metadata_path)
logger.progress("DpFrEP tool successfully executed; see {}".format(
out_metadata_path))
return result
except Exception as error:
errstr = "DpFrEP tool wasn't successfully executed. ERROR: {}.".format(
error)
logger.error(errstr)
raise Exception(errstr)
def main_json(config, in_metadata, out_metadata):
"""
Main function
-------------
This function launches the app using configuration written in
two json files: config.json and input_metadata.json.
"""
# 1. Instantiate and launch the App
logger.info("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
# Fixing possible problems in the input metadata
with open(in_metadata, "r") as in_metF:
in_metaArr = json.load(in_metF)
in_fixed = False
for in_m in in_metaArr:
if in_m.get('taxon_id', 0) == 0:
in_m['taxon_id'] = -1
in_fixed = True
if in_fixed:
with open(in_metadata, "w") as in_metF:
json.dump(in_metaArr, in_metF)
result = app.launch(process_WF_RUNNER, config, in_metadata, out_metadata)
# 2. The App has finished
logger.info("2. Execution finished; see " + out_metadata)
return result
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
-------------
This function launches the app using configuration written in
two json files: config.json and input_metadata.json.
"""
# 1. Instantiate and launch the App
logger.info("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
result = app.launch(process_bamqc, config, in_metadata, out_metadata)
# 2. The App has finished
logger.info("2. Execution finished; see " + out_metadata)
return result
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
This function launch the app using the configuration written
in two json files: config_process_rmapBaitmap.json and
input_process_rmapBaitmap.json
"""
#Instantiate and lauch the app
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
results = app.launch(process_rmap, config, in_metadata, out_metadata)
#2. The App has finished
print("2. Execution finished: see " + out_metadata)
print(results)
return results
def main_json(config, in_metadata, out_metadata):
"""
Main function.
This function launches the app using configuration written in two json files: config.json and input_metadata.json.
:param config:
:param in_metadata:
:param out_metadata:
:type config:
:type in_metadata:
:type out_metadata:
:return: If result is True, execution finished successfully. False, otherwise.
:rtype: bool
"""
try:
logger.info("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
# Fixing possible problems in the input metadata
with open(in_metadata, "r") as in_metF:
in_metaArr = json.load(in_metF)
in_fixed = False
for in_m in in_metaArr:
if in_m.get('taxon_id', 0) == 0:
in_m['taxon_id'] = -1
in_fixed = True
if in_fixed:
with open(in_metadata, "w") as in_metF:
json.dump(in_metaArr, in_metF)
result = app.launch(process_WF_RUNNER, config, in_metadata,
out_metadata) # launch the app
logger.info("2. App successfully launched; see " + out_metadata)
return result
except Exception as error:
errstr = "App wasn't successfully launched. ERROR: {}".format(error)
logger.error(errstr)
raise Exception(errstr)
def main_json():
"""
Alternative main function
-------------
This function launches the app using configuration written in
two json files: config.json and input_metadata.json.
"""
# 1. Instantiate and launch the App
logger.info("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
result = app.launch(SimpleWorkflow, "tools_demos/config.json",
"tools_demos/input_metadata.json", "/tmp/results.json")
# 2. The App has finished
logger.info("2. Execution finished; see /tmp/results.json")
return result
def main_json(config, in_metadata, out_metadata):
"""
Alternative main function
This function launches the app using configuration written in
two json files: config.json and metadata.json
"""
# 1. Instantiate and launch the App
print("1. Instantiate and launch the App")
from apps.jsonapp import JSONApp
app = JSONApp()
results = app.launch(process_run_chicago, config, in_metadata,
out_metadata)
# 2. The App has finished
print("2. Execution finished; see " + out_metadata)
print(results)
return results
def main_json(config, in_metadata, out_metadata):
"""
Main function.
This function launches the app using configuration written in two json files: config.json and input_metadata.json.
:param config:
:param in_metadata:
:param out_metadata:
:type config:
:type in_metadata:
:type out_metadata:
:return: If result is True, execution finished successfully. False, otherwise.
:rtype: bool
"""
try:
logger.info("1. Instantiate and launch the App")
app = JSONApp()
# Generating output files paths for images
with open(in_metadata, "r") as in_meta:
_in = json.load(in_meta)
conf = json.load(open(config))
conf['output_files'] = []
new_file = {
"name": "ml_summary",
"required": True,
"allow_multiple": False,
"file": {
"file_type": "PDF",
"file_path": os.path.split(os.path.abspath(in_metadata[0]]['path'])),
"data_type": "tool_statistics",
"meta_data": {},
}
}
