def save_assembly_from_fasta(self, ctx, params):
"""
WARNING: has the side effect of moving the file to a temporary staging directory, because the upload
script for assemblies currently requires a working directory, not a specific file. It will attempt
to upload everything in that directory. This will move the file back to the original location, but
if you are trying to keep an open file handle or are trying to do things concurrently to that file,
this will break. So this method is certainly NOT thread safe on the input file.
:param params: instance of type "SaveAssemblyParams" (Options
supported: file / shock_id / ftp_url - mutualy exclusive
parameters pointing to file content workspace_name - target
workspace assembly_name - target object name type - should be one
of 'isolate', 'metagenome', (maybe 'transcriptome')
min_contig_length - if set and value is greater than 1, this will
only include sequences with length greater or equal to the
min_contig_length specified, discarding all other sequences
taxon_ref - sets the taxon_ref if present contig_info
- map from contig_id to a small structure that can be used to set
the is_circular and description fields for Assemblies (optional)
Uploader options not yet supported taxon_reference: The ws
reference the assembly points to. (Optional) source: The source
of the data (Ex: Refseq) date_string: Date (or date range)
associated with data. (Optional)) -> structure: parameter "file"
of type "FastaAssemblyFile" -> structure: parameter "path" of
String, parameter "assembly_name" of String, parameter "shock_id"
of type "ShockNodeId", parameter "ftp_url" of String, parameter
"workspace_name" of String, parameter "assembly_name" of String,
parameter "external_source" of String, parameter
"external_source_id" of String, parameter "taxon_ref" of String,
parameter "min_contig_length" of Long, parameter "contig_info" of
mapping from String to type "ExtraContigInfo" (Structure for
setting additional Contig information per contig is_circ - flag if
contig is circular, 0 is false, 1 is true, missing indicates
unknown description - if set, sets the description of the field in
the assembly object which may override what was in the fasta file)
-> structure: parameter "is_circ" of Long, parameter "description"
of String
:returns: instance of String
"""
# ctx is the context object
# return variables are: ref
#BEGIN save_assembly_from_fasta
print('save_assembly_from_fasta -- paramaters = ')
#pprint(params)
fta = FastaToAssembly(self.callback_url, self.sharedFolder,
self.ws_url)
assembly_info = fta.import_fasta(ctx, params)
ref = f'{assembly_info[6]}/{assembly_info[0]}/{assembly_info[4]}'
print(ref)
#END save_assembly_from_fasta
# At some point might do deeper type checking...
if not isinstance(ref, str):
raise ValueError('Method save_assembly_from_fasta return value ' +
'ref is not type str as required.')
# return the results
return [ref]
def save_assembly_from_fasta(self, ctx, params):
"""
WARNING: has the side effect of moving the file to a temporary staging directory, because the upload
script for assemblies currently requires a working directory, not a specific file. It will attempt
to upload everything in that directory. This will move the file back to the original location, but
if you are trying to keep an open file handle or are trying to do things concurrently to that file,
this will break. So this method is certainly NOT thread safe on the input file.
:param params: instance of type "SaveAssemblyParams" (Options
supported: file / shock_id / ftp_url - mutualy exclusive
parameters pointing to file content workspace_name - target
workspace assembly_name - target object name type - should be one
of 'isolate', 'metagenome', (maybe 'transcriptome')
min_contig_length - if set and value is greater than 1, this will
only include sequences with length greater or equal to the
min_contig_length specified, discarding all other sequences
taxon_ref - sets the taxon_ref if present contig_info
- map from contig_id to a small structure that can be used to set
the is_circular and description fields for Assemblies (optional)
Uploader options not yet supported taxon_reference: The ws
reference the assembly points to. (Optional) source: The source
of the data (Ex: Refseq) date_string: Date (or date range)
associated with data. (Optional)) -> structure: parameter "file"
of type "FastaAssemblyFile" -> structure: parameter "path" of
String, parameter "assembly_name" of String, parameter "shock_id"
of type "ShockNodeId", parameter "ftp_url" of String, parameter
"workspace_name" of String, parameter "assembly_name" of String,
parameter "external_source" of String, parameter
"external_source_id" of String, parameter "taxon_ref" of String,
parameter "min_contig_length" of Long, parameter "contig_info" of
mapping from String to type "ExtraContigInfo" (Structure for
setting additional Contig information per contig is_circ - flag if
contig is circular, 0 is false, 1 is true, missing indicates
unknown) -> structure: parameter "is_circ" of Long, parameter
"description" of String
:returns: instance of String
"""
# ctx is the context object
# return variables are: ref
#BEGIN save_assembly_from_fasta
print('save_assembly_from_fasta -- paramaters = ')
pprint(params)
fta = FastaToAssembly(self.callback_url, self.sharedFolder)
assembly_info = fta.import_fasta(ctx, params)
ref = str(assembly_info[6]) + '/' + str(assembly_info[0]) + '/' + str(assembly_info[4])
#END save_assembly_from_fasta
# At some point might do deeper type checking...
if not isinstance(ref, basestring):
raise ValueError('Method save_assembly_from_fasta return value ' +
'ref is not type basestring as required.')
# return the results
return [ref]