def edit_bins_from_binned_contig(self, ctx, params):
"""
edit_bins_from_binned_contig: merge/remove a list of bins from BinnedContig object
a wrapper method of:
merge_bins_from_binned_contig
remove_bins_from_binned_contig
input params:
old_binned_contig_ref: Original BinnedContig object reference
bins_to_remove: a list of bin ids to be removed
bin_merges: a list of bin merges dicts
new_bin_id: newly created bin id
bin_to_merge: list of bins to merge
output_binned_contig_name: Name for the output BinnedContigs object
workspace_name: the name of the workspace new object gets saved to
return params:
new_binned_contig_ref: newly created BinnedContig object referece
report_name: report name generated by KBaseReport
report_ref: report reference generated by KBaseReport
:param params: instance of type "EditBinsParams"
(old_binned_contig_ref: Original BinnedContig object reference
bins_to_remove: a list of bin ids to be removed bin_merges: a list
of bin merges dicts new_bin_id: newly created bin id bin_to_merge:
list of bins to merge output_binned_contig_name: Name for the
output BinnedContigs object workspace_name: the name of the
workspace new object gets saved to) -> structure: parameter
"old_binned_contig_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "bins_to_remove" of list of String,
parameter "bin_merges" of list of mapping from String to String,
parameter "output_binned_contig_name" of String, parameter
"workspace_name" of String
:returns: instance of type "EditBinsResult" (new_binned_contig_ref:
newly created BinnedContig object referece report_name: report
name generated by KBaseReport report_ref: report reference
generated by KBaseReport) -> structure: parameter
"new_binned_contig_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "report_name" of String, parameter
"report_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN edit_bins_from_binned_contig
logging.info(
'--->\nRunning MetagenomeUtils.edit_bins_from_binned_contig\nparams:'
+ json.dumps(params, indent=1))
for key, value in params.items():
if isinstance(value, str):
params[key] = value.strip()
binned_contig_editor = MetagenomeFileUtils(self.config)
returnVal = binned_contig_editor.edit_bins_from_binned_contig(params)
#END edit_bins_from_binned_contig
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method edit_bins_from_binned_contig return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def extract_binned_contigs_as_assembly(self, ctx, params):
"""
extract_binned_contigs_as_assembly: extract one/multiple Bins from BinnedContigs as Assembly object
input params:
binned_contig_obj_ref: BinnedContig object reference
extracted_assemblies: a list of:
bin_id: target bin id to be extracted
assembly_suffix: suffix appended to assembly object name
workspace_name: the name of the workspace it gets saved to
return params:
assembly_ref_list: list of generated result Assembly object reference
report_name: report name generated by KBaseReport
report_ref: report reference generated by KBaseReport
:param params: instance of type "ExtractBinAsAssemblyParams"
(binned_contig_obj_ref: BinnedContig object reference
extracted_assemblies: a list of dictionaries: bin_id: target bin
id to be extracted assembly_suffix: suffix appended to assembly
object name assembly_set_name: name for created assembly set
workspace_name: the name of the workspace it gets saved to) ->
structure: parameter "binned_contig_obj_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "extracted_assemblies" of
String, parameter "assembly_suffix" of String, parameter
"assembly_set_name" of String, parameter "workspace_name" of String
:returns: instance of type "ExtractBinAsAssemblyResult"
(assembly_ref_list: list of generated Assembly object reference
report_name: report name generated by KBaseReport report_ref:
report reference generated by KBaseReport) -> structure: parameter
"assembly_ref_list" of list of type "obj_ref" (An X/Y/Z style
reference), parameter "report_name" of String, parameter
"report_ref" of String, parameter "assembly_set_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN extract_binned_contigs_as_assembly
logging.info(
'--->\nRunning MetagenomeUtils.extract_binned_contigs_as_assembly\nparams:'
+ json.dumps(params, indent=1))
for key, value in params.items():
if isinstance(value, str):
params[key] = value.strip()
binned_contig_extractor = MetagenomeFileUtils(self.config)
returnVal = binned_contig_extractor.extract_binned_contigs_as_assembly(
params)
#END extract_binned_contigs_as_assembly
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method extract_binned_contigs_as_assembly return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def remove_bins_from_binned_contig(self, ctx, params):
"""
remove_bins_from_binned_contig: remove a list of bins from BinnedContig object
input params:
old_binned_contig_ref: Original BinnedContig object reference
bins_to_remove: a list of bin ids to be removed
output_binned_contig_name: Name for the output BinnedContigs object
workspace_name: the name of the workspace new object gets saved to
return params:
new_binned_contig_ref: newly created BinnedContig object referece
:param params: instance of type "RemoveBinsParams"
(old_binned_contig_ref: Original BinnedContig object reference
bins_to_remove: a list of bin ids to be removed
output_binned_contig_name: Name for the output BinnedContigs
object workspace_name: the name of the workspace new object gets
saved to) -> structure: parameter "old_binned_contig_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "bins_to_remove"
of list of String, parameter "output_binned_contig_name" of
String, parameter "workspace_name" of String
:returns: instance of type "RemoveBinsResult" (new_binned_contig_ref:
newly created BinnedContig object referece report_name: report
name generated by KBaseReport report_ref: report reference
generated by KBaseReport) -> structure: parameter
"new_binned_contig_ref" of type "obj_ref" (An X/Y/Z style
reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN remove_bins_from_binned_contig
print '--->\nRunning MetagenomeUtils.remove_bins_from_binned_contig\nparams:'
print json.dumps(params, indent=1)
for key, value in params.iteritems():
if isinstance(value, basestring):
params[key] = value.strip()
binned_contig_remover = MetagenomeFileUtils(self.config)
returnVal = binned_contig_remover.remove_bins_from_binned_contig(
params)
#END remove_bins_from_binned_contig
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method remove_bins_from_binned_contig return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def file_to_binned_contigs(self, ctx, params):
"""
file_to_binned_contigs: Generating BinnedContigs ojbect from files
input params:
file_directory: file directory containing compressed/unpacked contig file(s) to build BinnedContig object
assembly_ref: Metagenome assembly object reference
binned_contig_name: BinnedContig object name
workspace_name: the name/id of the workspace it gets saved to
return params:
binned_contig_obj_ref: generated result BinnedContig object reference
:param params: instance of type "FileToBinnedContigParams"
(file_directory: file directory containing compressed/unpacked
contig file(s) to build BinnedContig object assembly_ref:
Metagenome assembly object reference binned_contig_name:
BinnedContig object name workspace_name: the name/id of the
workspace it gets saved to) -> structure: parameter
"file_directory" of String, parameter "assembly_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter
"binned_contig_name" of String, parameter "workspace_name" of
String
:returns: instance of type "FileToBinnedContigResult" -> structure:
parameter "binned_contig_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN file_to_binned_contigs
logging.info(
'--->\nRunning MetagenomeUtils.file_to_binned_contigs\nparams:' +
json.dumps(params, indent=1))
for key, value in params.items():
if isinstance(value, str):
params[key] = value.strip()
binned_contig_builder = MetagenomeFileUtils(self.config)
returnVal = binned_contig_builder.file_to_binned_contigs(params)
#END file_to_binned_contigs
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method file_to_binned_contigs return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def export_binned_contigs_as_excel(self, ctx, params):
"""
export_binned_contigs_as_excel: Convert BinnedContig object to an excel file and pack it to shock
required params:
input_ref: BinnedContig object reference
optional params:
save_to_shock: saving result bin files to shock. default to True
return params:
shock_id: saved packed file shock id (None if save_to_shock is set to False)
bin_file_directory: directory that contains all bin files
:param params: instance of type "ExportParams" (input_ref:
BinnedContig object reference optional params: save_to_shock:
saving result bin files to shock. default to True) -> structure:
parameter "input_ref" of String, parameter "save_to_shock" of type
"boolean" (A boolean - 0 for false, 1 for true. @range (0, 1))
:returns: instance of type "ExportOutput" (shock_id: saved packed
file shock id bin_file_directory: directory that contains all bin
files) -> structure: parameter "shock_id" of String, parameter
"bin_file_directory" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN export_binned_contigs_as_excel
logging.info(
'--->\nRunning MetagenomeUtils.export_binned_contigs_as_excel\nparams:'
+ json.dumps(params, indent=1))
for key, value in params.items():
if isinstance(value, str):
params[key] = value.strip()
binned_contig_downloader = MetagenomeFileUtils(self.config)
returnVal = binned_contig_downloader.export_binned_contigs_as_excel(
params)
#END export_binned_contigs_as_excel
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method export_binned_contigs_as_excel return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def import_excel_as_binned_contigs(self, ctx, params):
"""
import_excel_as_binned_contigs: Import an excel file as BinnedContigs
required params:
shock_id: Excel file stored in shock
workspace_name: the name of the workspace object gets saved to
optional params:
binned_contigs_name: saved BinnedContig name.
Auto append timestamp from excel if not given.
:param params: instance of type "ImportExcelParams" -> structure:
parameter "shock_id" of String, parameter "workspace_name" of
String, parameter "binned_contigs_name" of String
:returns: instance of type "ImportExcelOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "binned_contigs_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN import_excel_as_binned_contigs
logging.info(
'--->\nRunning MetagenomeUtils.import_excel_as_binned_contigs\nparams:'
+ json.dumps(params, indent=1))
for key, value in params.items():
if isinstance(value, str):
params[key] = value.strip()
binned_contig_importer = MetagenomeFileUtils(self.config)
returnVal = binned_contig_importer.import_excel_as_binned_contigs(
params)
#END import_excel_as_binned_contigs
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method import_excel_as_binned_contigs return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def setUpClass(cls):
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('MetagenomeUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
token,
'user_id':
user_id,
'provenance': [{
'service': 'MetagenomeUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = MetagenomeUtils(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
suffix = int(time.time() * 1000)
wsName = "test_kb_maxbin_" + str(suffix)
cls.ws_info = cls.wsClient.create_workspace({'workspace': wsName})
cls.dfu = DataFileUtil(os.environ['SDK_CALLBACK_URL'], token=token)
cls.au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'], token=token)
cls.binned_contig_builder = MetagenomeFileUtils(cls.cfg)
cls.prepare_data()