def export_pdb_structures(self, ctx, params):
"""
:param params: instance of type "ExportParams" (Input/output of the
export_pdb_structures function obj_ref: generics object reference)
-> structure: parameter "input_ref" of type "obj_ref" (An X/Y/Z
style reference @id ws)
:returns: instance of type "ExportStructOutput" -> structure:
parameter "shock_id" of list of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_pdb_structures
logging.info(
'Starting export_pdb_structures with params:\n{}'.format(params))
self.config['USER_ID'] = ctx['user_id']
self.pdb_util = PDBUtil(self.config)
result = self.pdb_util.export_pdb_structures(params)
#END export_pdb_structures
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_pdb_structures return value ' +
'result is not type dict as required.')
# return the results
return [result]
def batch_import_pdbs_from_metafile(self, ctx, params):
"""
batch_import_pdbs_from_metafile: import a batch of ProteinStructures from PDB files
:param params: instance of type "BatchPDBImportParams" (Input/Output
of the batch_import_pdbs_from_metafile structures_name:
Proteinstructures object name workspace_name: workspace name for
object to be saved to metadata_staging_file_path: path to a
spreadsheet file that lists the metadata of PDB files and their
KBase metadata) -> structure: parameter
"metadata_staging_file_path" of String, parameter
"structures_name" of String, parameter "workspace_name" of type
"workspace_name" (workspace name of the object)
:returns: instance of type "BatchPDBImportOutput" -> structure:
parameter "structures_ref" of String, parameter "report_name" of
String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN batch_import_pdbs_from_metafile
logging.info(
'Starting batch_import_pdbs_from_metafile with params:\n{}'.format(
params))
self.config['USER_ID'] = ctx['user_id']
self.pdb_util = PDBUtil(self.config)
result = self.pdb_util.batch_import_pdbs(params)
#END batch_import_pdbs_from_metafile
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method batch_import_pdbs_from_metafile return value ' +
'result is not type dict as required.')
# return the results
return [result]
def __init__(self, config):
#BEGIN_CONSTRUCTOR
self.config = config
self.config['SDK_CALLBACK_URL'] = os.environ['SDK_CALLBACK_URL']
self.config['KB_AUTH_TOKEN'] = os.environ['KB_AUTH_TOKEN']
self.scratch = config['scratch']
self.pdb_util = PDBUtil(self.config)
#END_CONSTRUCTOR
pass
class ProteinStructureUtils:
'''
Module Name:
ProteinStructureUtils
Module Description:
A KBase module: ProteinStructureUtils
'''
######## WARNING FOR GEVENT USERS ####### noqa
# Since asynchronous IO can lead to methods - even the same method -
# interrupting each other, you must be *very* careful when using global
# state. A method could easily clobber the state set by another while
# the latter method is running.
######################################### noqa
VERSION = "0.0.2"
GIT_URL = "https://github.com/Tianhao-Gu/ProteinStructureUtils.git"
GIT_COMMIT_HASH = "7fb3a1f471f5f5832cbb415fadda86ff878fc0f7"
#BEGIN_CLASS_HEADER
logging.basicConfig(format='%(asctime)s %(levelname)-8s %(message)s',
level=logging.INFO,
datefmt='%Y-%m-%d %H:%M:%S')
#END_CLASS_HEADER
# config contains contents of config file in a hash or None if it couldn't
# be found
def __init__(self, config):
#BEGIN_CONSTRUCTOR
self.config = config
self.config['SDK_CALLBACK_URL'] = os.environ['SDK_CALLBACK_URL']
self.config['KB_AUTH_TOKEN'] = os.environ['KB_AUTH_TOKEN']
self.scratch = config['scratch']
self.pdb_util = PDBUtil(self.config)
#END_CONSTRUCTOR
pass
def structure_to_pdb_file(self, ctx, params):
"""
:param params: instance of type "StructureToPDBFileParams" ->
structure: parameter "input_ref" of type "obj_ref" (An X/Y/Z style
reference @id ws), parameter "destination_dir" of String
:returns: instance of type "StructureToPDBFileOutput" -> structure:
parameter "file_path" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN structure_to_pdb_file
logging.info(
'Starting structure_to_pdb_file with params:\n{}'.format(params))
result = self.pdb_util.structure_to_pdb_file(params)
#END structure_to_pdb_file
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method structure_to_pdb_file return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_pdb(self, ctx, params):
"""
:param params: instance of type "ExportParams" (Input of the
export_pdb function obj_ref: generics object reference) ->
structure: parameter "obj_ref" of type "obj_ref" (An X/Y/Z style
reference @id ws)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_pdb
logging.info('Starting export_pdb with params:\n{}'.format(params))
result = self.pdb_util.export_pdb(params)
#END export_pdb
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_pdb return value ' +
'result is not type dict as required.')
# return the results
return [result]
def import_model_pdb_file(self, ctx, params):
"""
import_model_pdb_file: import a ProteinStructure from PDB
:param params: instance of type "ImportPDBParams" (Input of the
import_matrix_from_excel function input_shock_id: file shock id
input_file_path: absolute file path input_staging_file_path:
staging area file path structure_name: structure object name
workspace_name: workspace name for object to be saved to) ->
structure: parameter "input_shock_id" of String, parameter
"input_file_path" of String, parameter "input_staging_file_path"
of String, parameter "structure_name" of String, parameter
"description" of String, parameter "workspace_name" of type
"workspace_name" (workspace name of the object)
:returns: instance of type "ImportPDBOutput" -> structure: parameter
"report_name" of String, parameter "report_ref" of String,
parameter "structure_obj_ref" of type "obj_ref" (An X/Y/Z style
reference @id ws)
"""
# ctx is the context object
# return variables are: result
#BEGIN import_model_pdb_file
logging.info(
'Starting import_pdb_file with params:\n{}'.format(params))
result = self.pdb_util.import_model_pdb_file(params)
#END import_model_pdb_file
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method import_model_pdb_file return value ' +
'result is not type dict as required.')
# return the results
return [result]
def status(self, ctx):
#BEGIN_STATUS
returnVal = {
'state': "OK",
'message': "",
'version': self.VERSION,
'git_url': self.GIT_URL,
'git_commit_hash': self.GIT_COMMIT_HASH
}
#END_STATUS
return [returnVal]
class ProteinStructureUtils:
'''
Module Name:
ProteinStructureUtils
Module Description:
A KBase module: ProteinStructureUtils
'''
######## WARNING FOR GEVENT USERS ####### noqa
# Since asynchronous IO can lead to methods - even the same method -
# interrupting each other, you must be *very* careful when using global
# state. A method could easily clobber the state set by another while
# the latter method is running.
######################################### noqa
VERSION = "0.0.2"
GIT_URL = ""
GIT_COMMIT_HASH = "e3fa454e548690312f32e34f0b865fce65b4547c"
#BEGIN_CLASS_HEADER
logging.basicConfig(format='%(asctime)s %(levelname)-8s %(message)s',
level=logging.INFO,
datefmt='%Y-%m-%d %H:%M:%S')
#END_CLASS_HEADER
# config contains contents of config file in a hash or None if it couldn't
# be found
def __init__(self, config):
#BEGIN_CONSTRUCTOR
self.config = config
self.config['SDK_CALLBACK_URL'] = os.environ['SDK_CALLBACK_URL']
self.config['KB_AUTH_TOKEN'] = os.environ['KB_AUTH_TOKEN']
self.scratch = config['scratch']
#END_CONSTRUCTOR
pass
def batch_import_pdbs_from_metafile(self, ctx, params):
"""
batch_import_pdbs_from_metafile: import a batch of ProteinStructures from PDB files
:param params: instance of type "BatchPDBImportParams" (Input/Output
of the batch_import_pdbs_from_metafile structures_name:
Proteinstructures object name workspace_name: workspace name for
object to be saved to metadata_staging_file_path: path to a
spreadsheet file that lists the metadata of PDB files and their
KBase metadata) -> structure: parameter
"metadata_staging_file_path" of String, parameter
"structures_name" of String, parameter "workspace_name" of type
"workspace_name" (workspace name of the object)
:returns: instance of type "BatchPDBImportOutput" -> structure:
parameter "structures_ref" of String, parameter "report_name" of
String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN batch_import_pdbs_from_metafile
logging.info(
'Starting batch_import_pdbs_from_metafile with params:\n{}'.format(
params))
self.config['USER_ID'] = ctx['user_id']
self.pdb_util = PDBUtil(self.config)
result = self.pdb_util.batch_import_pdbs(params)
#END batch_import_pdbs_from_metafile
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method batch_import_pdbs_from_metafile return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_pdb_structures(self, ctx, params):
"""
:param params: instance of type "ExportParams" (Input/output of the
export_pdb_structures function obj_ref: generics object reference)
-> structure: parameter "input_ref" of type "obj_ref" (An X/Y/Z
style reference @id ws)
:returns: instance of type "ExportStructOutput" -> structure:
parameter "shock_id" of list of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_pdb_structures
logging.info(
'Starting export_pdb_structures with params:\n{}'.format(params))
self.config['USER_ID'] = ctx['user_id']
self.pdb_util = PDBUtil(self.config)
result = self.pdb_util.export_pdb_structures(params)
#END export_pdb_structures
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_pdb_structures return value ' +
'result is not type dict as required.')
# return the results
return [result]
def status(self, ctx):
#BEGIN_STATUS
returnVal = {
'state': "OK",
'message': "",
'version': self.VERSION,
'git_url': self.GIT_URL,
'git_commit_hash': self.GIT_COMMIT_HASH
}
#END_STATUS
return [returnVal]