def setUpClass(cls):
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenericsAPI'):
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': 'GenericsAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = GenericsAPI(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
cls.pca_util = PCAUtil(cls.cfg)
suffix = int(time.time() * 1000)
cls.wsName = "test_pca_util_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.wsId = ret[0]
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.attr_util = AttributesUtil(self.config)
self.matrix_util = MatrixUtil(self.config)
self.corr_util = CorrelationUtil(self.config)
self.data_util = DataUtil(self.config)
self.network_util = NetworkUtil(self.config)
self.biom_util = BiomUtil(self.config)
self.pca_util = PCAUtil(self.config)
self.data_table_util = DataTableUtil(self.config)
logging.basicConfig(format='%(created)s %(levelname)s: %(message)s',
level=logging.INFO)
#END_CONSTRUCTOR
pass
def setUpClass(cls):
cls.token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenericsAPI'):
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(cls.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':
cls.token,
'user_id':
user_id,
'provenance': [{
'service': 'GenericsAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.shockURL = cls.cfg['shock-url']
cls.serviceImpl = GenericsAPI(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
cls.pca_util = PCAUtil(cls.cfg)
cls.hs = HandleService(url=cls.cfg['handle-service-url'],
token=cls.token)
suffix = int(time.time() * 1000)
cls.wsName = "test_pca_util_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.wsId = ret[0]
small_file = os.path.join(cls.scratch, 'test.txt')
with open(small_file, "w") as f:
f.write("empty content")
cls.test_shock = cls.dfu.file_to_shock({
'file_path': small_file,
'make_handle': True
})
cls.handles_to_delete = []
cls.nodes_to_delete = []
cls.handles_to_delete.append(cls.test_shock['handle']['hid'])
cls.nodes_to_delete.append(cls.test_shock['shock_id'])
class GenericsAPI:
'''
Module Name:
GenericsAPI
Module Description:
'''
######## 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 = "1.0.8"
GIT_URL = "[email protected]:Tianhao-Gu/GenericsAPI.git"
GIT_COMMIT_HASH = "e5a7c9fc2952bf44ebf8ec76d92322f00b606b3e"
#BEGIN_CLASS_HEADER
#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.attr_util = AttributesUtil(self.config)
self.matrix_util = MatrixUtil(self.config)
self.corr_util = CorrelationUtil(self.config)
self.data_util = DataUtil(self.config)
self.network_util = NetworkUtil(self.config)
self.biom_util = BiomUtil(self.config)
self.pca_util = PCAUtil(self.config)
self.data_table_util = DataTableUtil(self.config)
self.template_util = TemplateUtil(self.config)
logging.basicConfig(format='%(created)s %(levelname)s: %(message)s',
level=logging.INFO)
#END_CONSTRUCTOR
pass
def fetch_data(self, ctx, params):
"""
fetch_data: fetch generics data as pandas dataframe for a generics data object
:param params: instance of type "FetchDataParams" (Input of the
fetch_data function obj_ref: generics object reference Optional
arguments: generics_module: the generics data module to be
retrieved from e.g. for an given data type like below: typedef
structure { FloatMatrix2D data; condition_set_ref
condition_set_ref; } SomeGenericsMatrix; generics_module should be
{'data': 'FloatMatrix2D', 'condition_set_ref':
'condition_set_ref'}) -> structure: parameter "obj_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "generics_module"
of mapping from String to String
:returns: instance of type "FetchDataReturn" (Ouput of the fetch_data
function data_matrix: a pandas dataframe in json format) ->
structure: parameter "data_matrix" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN fetch_data
returnVal = self.data_util.fetch_data(params)
#END fetch_data
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method fetch_data return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def export_matrix(self, ctx, params):
"""
:param params: instance of type "ExportParams" (Input of the
export_matrix function obj_ref: generics object reference Optional
arguments: generics_module: select the generics data to be
retrieved from e.g. for an given data type like below: typedef
structure { FloatMatrix2D data; condition_set_ref
condition_set_ref; } SomeGenericsMatrix; and only 'FloatMatrix2D'
is needed generics_module should be {'data': FloatMatrix2D'}) ->
structure: parameter "obj_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "generics_module" of mapping from String to
String
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN export_matrix
returnVal = self.matrix_util.export_matrix(params)
#END export_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method export_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def validate_data(self, ctx, params):
"""
validate_data: validate data
:param params: instance of type "ValidateParams" (Input of the
validate_data function obj_type: obj type e.g.:
'KBaseMatrices.ExpressionMatrix-1.1' data: data to be validated)
-> structure: parameter "obj_type" of String, parameter "data" of
mapping from String to String
:returns: instance of type "ValidateOutput" -> structure: parameter
"validated" of type "boolean" (A boolean - 0 for false, 1 for
true.), parameter "failed_constraint" of mapping from String to
String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN validate_data
returnVal = self.data_util.validate_data(params)
#END validate_data
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method validate_data return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def import_matrix_from_excel(self, ctx, params):
"""
import_matrix_from_excel: import matrix object from excel
:param params: instance of type "ImportMatrixParams" (Input of the
import_matrix_from_excel function obj_type: a type in
KBaseMatrices input_shock_id: file shock id input_file_path:
absolute file path input_staging_file_path: staging area file path
matrix_name: matrix object name description: optional, a
description of the matrix workspace_name: workspace name matrix
object to be saved to optional: col_attributemapping_ref: column
AttributeMapping reference row_attributemapping_ref: row
AttributeMapping reference genome_ref: genome reference
diff_expr_matrix_ref: DifferentialExpressionMatrix reference
biochemistry_ref: (for ChemicalAbundanceMatrix) reads_set_ref:
(raw data for AmpliconMatrix) sample_set_ref: SampleSet object
reference) -> structure: parameter "obj_type" of String, parameter
"input_shock_id" of String, parameter "input_file_path" of String,
parameter "input_staging_file_path" of String, parameter
"matrix_name" of String, parameter "amplicon_set_name" of String,
parameter "scale" of String, parameter "description" of String,
parameter "workspace_name" of type "workspace_name" (workspace
name of the object), parameter "genome_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "col_attributemapping_ref" of
type "obj_ref" (An X/Y/Z style reference), parameter
"row_attributemapping_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "diff_expr_matrix_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "biochemistry_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "reads_set_ref" of
type "obj_ref" (An X/Y/Z style reference), parameter
"sample_set_ref" of type "obj_ref" (An X/Y/Z style reference),
parameter "unit" of String, parameter "type" of String
:returns: instance of type "ImportMatrixOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN import_matrix_from_excel
returnVal = self.matrix_util.import_matrix_from_excel(params)
#END import_matrix_from_excel
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method import_matrix_from_excel return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def import_matrix_from_biom(self, ctx, params):
"""
import_matrix_from_biom: import matrix object from BIOM file format
:param params: instance of type "ImportOTUParams" -> structure:
parameter "obj_type" of String, parameter
"taxonomic_abundance_tsv" of String, parameter "taxonomic_fasta"
of String, parameter "input_local_file" of String, parameter
"matrix_name" of String, parameter "amplicon_set_name" of String,
parameter "scale" of String, parameter "description" of String,
parameter "workspace_name" of type "workspace_name" (workspace
name of the object), parameter "genome_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "col_attributemapping_ref" of
type "obj_ref" (An X/Y/Z style reference), parameter
"row_attributemapping_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "diff_expr_matrix_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "biochemistry_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "reads_set_ref" of
type "obj_ref" (An X/Y/Z style reference), parameter
"sample_set_ref" of type "obj_ref" (An X/Y/Z style reference),
parameter "metadata_keys" of list of String, parameter
"extraction_kit" of String, parameter "amplicon_type" of String,
parameter "target_gene_region" of String, parameter
"forward_primer_sequence" of String, parameter
"reverse_primer_sequence" of String, parameter
"sequencing_platform" of String, parameter "sequencing_run" of
String, parameter "sequencing_kit" of String, parameter
"sequencing_quality_filter_cutoff" of String, parameter
"clustering_cutoff" of Double, parameter "clustering_method" of
String
:returns: instance of type "ImportMatrixOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN import_matrix_from_biom
returnVal = self.biom_util.import_matrix_from_biom(params)
#END import_matrix_from_biom
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method import_matrix_from_biom return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def save_object(self, ctx, params):
"""
save_object: validate data constraints and save matrix object
:param params: instance of type "SaveObjectParams" (Input of the
import_matrix_from_excel function obj_type: saving object data
type obj_name: saving object name data: data to be saved
workspace_name: workspace name matrix object to be saved to) ->
structure: parameter "obj_type" of String, parameter "obj_name" of
String, parameter "data" of mapping from String to String,
parameter "workspace_name" of type "workspace_name" (workspace
name of the object)
:returns: instance of type "SaveObjectOutput" -> structure: parameter
"obj_ref" of type "obj_ref" (An X/Y/Z style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN save_object
returnVal = self.data_util.save_object(params)
#END save_object
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method save_object return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def search_matrix(self, ctx, params):
"""
search_matrix: generate a HTML report that allows users to select feature ids
:param params: instance of type "MatrixSelectorParams" (Input of the
search_matrix function matrix_obj_ref: object reference of a
matrix workspace_name: workspace name objects to be saved to) ->
structure: parameter "matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference), parameter "workspace_name" of type
"workspace_name" (workspace name of the object)
:returns: instance of type "MatrixSelectorOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN search_matrix
returnVal = self.matrix_util.search_matrix(params)
#END search_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method search_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def filter_matrix(self, ctx, params):
"""
filter_matrix: create sub-matrix based on input filter_ids
:param params: instance of type "MatrixFilterParams" (Input of the
filter_matrix function matrix_obj_ref: object reference of a
matrix workspace_name: workspace name objects to be saved to
filter_ids: string of column or row ids that result matrix
contains filtered_matrix_name: name of newly created filtered
matrix object) -> structure: parameter "matrix_obj_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "workspace_name"
of type "workspace_name" (workspace name of the object), parameter
"filtered_matrix_name" of String, parameter "remove_ids" of
String, parameter "dimension" of String
:returns: instance of type "MatrixFilterOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "matrix_obj_refs" of list of type "obj_ref" (An
X/Y/Z style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN filter_matrix
returnVal = self.matrix_util.filter_matrix(params)
#END filter_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method filter_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def standardize_matrix(self, ctx, params):
"""
standardize_matrix: standardize a matrix
:param params: instance of type "StandardizeMatrixParams" (Input of
the standardize_matrix function input_matrix_ref: object reference
of a matrix workspace_name: workspace name objects to be saved to
with_mean: center data before scaling with_std: scale data to unit
variance new_matrix_name: name of newly created matrix object) ->
structure: parameter "input_matrix_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "workspace_name" of type
"workspace_name" (workspace name of the object), parameter
"with_mean" of type "boolean" (A boolean - 0 for false, 1 for
true.), parameter "with_std" of type "boolean" (A boolean - 0 for
false, 1 for true.), parameter "dimension" of String, parameter
"new_matrix_name" of String
:returns: instance of type "StandardizeMatrixOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "new_matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN standardize_matrix
returnVal = self.matrix_util.standardize_matrix(params)
#END standardize_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method standardize_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def transform_matrix(self, ctx, params):
"""
:param params: instance of type "TransformMatrixParams" -> structure:
parameter "input_matrix_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "workspace_name" of type "workspace_name"
(workspace name of the object), parameter "workspace_id" of Long,
parameter "new_matrix_name" of String, parameter
"abundance_filtering_params" of mapping from String to String,
parameter "standardization_params" of mapping from String to
String, parameter "ratio_transformation_params" of mapping from
String to String, parameter "perform_relative_abundance" of type
"boolean" (A boolean - 0 for false, 1 for true.)
:returns: instance of type "TransformMatrixOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "new_matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN transform_matrix
returnVal = self.matrix_util.transform_matrix(params)
#END transform_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method transform_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def perform_rarefy(self, ctx, params):
"""
:param params: instance of type "RarefyMatrixParams" -> structure:
parameter "input_matrix_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "workspace_id" of Long, parameter
"new_matrix_name" of String, parameter "seed_number" of Long,
parameter "dimension" of String
:returns: instance of type "RarefyMatrixOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "new_matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN perform_rarefy
returnVal = self.matrix_util.perform_rarefy(params)
#END perform_rarefy
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method perform_rarefy return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def perform_variable_stats_matrix(self, ctx, params):
"""
:param params: instance of type "VariableStatsParams" -> structure:
parameter "input_matrix_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "attribute_mapping_obj_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "workspace_id" of
Long, parameter "dist_metric" of String, parameter "dimension" of
String, parameter "grouping" of String, parameter "permutations"
of Long, parameter "perform_anosim" of type "boolean" (A boolean -
0 for false, 1 for true.), parameter "perform_permanova" of type
"boolean" (A boolean - 0 for false, 1 for true.), parameter
"perform_permdisp" of type "boolean" (A boolean - 0 for false, 1
for true.)
:returns: instance of type "VariableStatsOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN perform_variable_stats_matrix
returnVal = self.matrix_util.perform_variable_stats_matrix(params)
#END perform_variable_stats_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method perform_variable_stats_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def perform_mantel_test(self, ctx, params):
"""
:param params: instance of type "MantelTestParams" -> structure:
parameter "input_matrix_refs" of list of type "obj_ref" (An X/Y/Z
style reference), parameter "workspace_id" of Long, parameter
"dist_metric" of String, parameter "dimension" of String,
parameter "correlation_method" of String, parameter "permutations"
of Long, parameter "alternative_hypothesis" of String
:returns: instance of type "MantelTestOutput" -> structure: parameter
"report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN perform_mantel_test
returnVal = self.matrix_util.perform_mantel_test(params)
#END perform_mantel_test
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method perform_mantel_test return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def file_to_attribute_mapping(self, ctx, params):
"""
:param params: instance of type "FileToAttributeMappingParams"
(input_shock_id and input_file_path - alternative input params,)
-> structure: parameter "input_shock_id" of String, parameter
"input_file_path" of String, parameter "output_ws_id" of String,
parameter "output_obj_name" of String
:returns: instance of type "FileToAttributeMappingOutput" ->
structure: parameter "attribute_mapping_ref" of type "obj_ref" (An
X/Y/Z style reference)
"""
# ctx is the context object
# return variables are: result
#BEGIN file_to_attribute_mapping
logging.info(
"Starting 'file_to_attribute_mapping' with params:{}".format(
params))
self.attr_util.validate_params(params,
("output_ws_id", "output_obj_name"),
('input_shock_id', 'input_file_path'))
result = self.attr_util.file_to_attribute_mapping(params)
#END file_to_attribute_mapping
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method file_to_attribute_mapping return value ' +
'result is not type dict as required.')
# return the results
return [result]
def file_to_fbamodel_attribute_mapping(self, ctx, params):
"""
:param params: instance of type "FileToAttributeMappingParams"
(input_shock_id and input_file_path - alternative input params,)
-> structure: parameter "input_shock_id" of String, parameter
"input_file_path" of String, parameter "output_ws_id" of String,
parameter "output_obj_name" of String
:returns: instance of type "FileToAttributeMappingOutput" ->
structure: parameter "attribute_mapping_ref" of type "obj_ref" (An
X/Y/Z style reference)
"""
# ctx is the context object
# return variables are: result
#BEGIN file_to_fbamodel_attribute_mapping
logging.info(
"Starting 'file_to_fbamodel_attribute_mapping' with params:{}".
format(params))
self.attr_util.validate_params(params,
("output_ws_id", "output_obj_name"),
('input_shock_id', 'input_file_path'))
params['import_fbamodel_attri_mapping'] = True
result = self.attr_util.file_to_attribute_mapping(params)
#END file_to_fbamodel_attribute_mapping
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method file_to_fbamodel_attribute_mapping return value ' +
'result is not type dict as required.')
# return the results
return [result]
def update_matrix_attribute_mapping(self, ctx, params):
"""
:param params: instance of type "UpdateMatrixAMParams" -> structure:
parameter "staging_file_subdir_path" of String, parameter
"dimension" of String, parameter "input_matrix_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "workspace_name"
of String, parameter "output_am_obj_name" of String, parameter
"output_matrix_obj_name" of String
:returns: instance of type "UpdateMatrixAMOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "new_matrix_obj_ref" of type "obj_ref" (An X/Y/Z
style reference), parameter "new_attribute_mapping_ref" of type
"obj_ref" (An X/Y/Z style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN update_matrix_attribute_mapping
logging.info(
"Starting 'update_matrix_attribute_mapping' with params:{}".format(
params))
self.attr_util.validate_params(
params, ("staging_file_subdir_path", "dimension", "workspace_name",
"output_am_obj_name", "input_matrix_ref",
"output_matrix_obj_name"))
returnVal = self.attr_util.update_matrix_attribute_mapping(params)
#END update_matrix_attribute_mapping
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method update_matrix_attribute_mapping return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def attribute_mapping_to_tsv_file(self, ctx, params):
"""
:param params: instance of type "AttributeMappingToTsvFileParams" ->
structure: parameter "input_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "destination_dir" of String
:returns: instance of type "AttributeMappingToTsvFileOutput" ->
structure: parameter "file_path" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN attribute_mapping_to_tsv_file
logging.info(
"Starting 'attribute_mapping_to_tsv_file' with params:{}".format(
params))
self.attr_util.validate_params(params,
("destination_dir", "input_ref"))
am_id, result = self.attr_util.to_tsv(params)
#END attribute_mapping_to_tsv_file
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method attribute_mapping_to_tsv_file return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_attribute_mapping_tsv(self, ctx, params):
"""
:param params: instance of type "ExportObjectParams" -> structure:
parameter "input_ref" of type "obj_ref" (An X/Y/Z style reference)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_attribute_mapping_tsv
logging.info(
"Starting 'export_attribute_mapping_tsv' with params:{}".format(
params))
self.attr_util.validate_params(params, ("input_ref", ))
params['destination_dir'] = self.scratch
am_id, files = self.attr_util.to_tsv(params)
result = self.attr_util.export(files['file_path'], am_id,
params['input_ref'])
#END export_attribute_mapping_tsv
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method export_attribute_mapping_tsv return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_attribute_mapping_excel(self, ctx, params):
"""
:param params: instance of type "ExportObjectParams" -> structure:
parameter "input_ref" of type "obj_ref" (An X/Y/Z style reference)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_attribute_mapping_excel
logging.info(
"Starting 'export_attribute_mapping_excel' with params:{}".format(
params))
self.attr_util.validate_params(params, ("input_ref", ))
params['destination_dir'] = self.scratch
am_id, files = self.attr_util.to_excel(params)
result = self.attr_util.export(files['file_path'], am_id,
params['input_ref'])
#END export_attribute_mapping_excel
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method export_attribute_mapping_excel return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_cluster_set_excel(self, ctx, params):
"""
:param params: instance of type "ExportObjectParams" -> structure:
parameter "input_ref" of type "obj_ref" (An X/Y/Z style reference)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_cluster_set_excel
logging.info(
"Starting 'export_cluster_set_excel' with params:{}".format(
params))
self.attr_util.validate_params(params, ("input_ref", ))
params['destination_dir'] = self.scratch
cs_id, files = self.attr_util.to_excel(params)
result = self.attr_util.export(files['file_path'], cs_id,
params['input_ref'])
#END export_cluster_set_excel
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_cluster_set_excel return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_corr_matrix_excel(self, ctx, params):
"""
:param params: instance of type "ExportObjectParams" -> structure:
parameter "input_ref" of type "obj_ref" (An X/Y/Z style reference)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_corr_matrix_excel
logging.info(
"Starting 'export_corr_matrix_excel' with params:{}".format(
params))
result = self.corr_util.export_corr_matrix_excel(params)
#END export_corr_matrix_excel
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_corr_matrix_excel return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_pca_matrix_excel(self, ctx, params):
"""
:param params: instance of type "ExportObjectParams" -> structure:
parameter "input_ref" of type "obj_ref" (An X/Y/Z style reference)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_pca_matrix_excel
result = self.pca_util.export_pca_matrix_excel(params)
#END export_pca_matrix_excel
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_pca_matrix_excel return value ' +
'result is not type dict as required.')
# return the results
return [result]
def export_amplicon_set_tsv(self, ctx, params):
"""
:param params: instance of type "ExportObjectParams" -> structure:
parameter "input_ref" of type "obj_ref" (An X/Y/Z style reference)
:returns: instance of type "ExportOutput" -> structure: parameter
"shock_id" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN export_amplicon_set_tsv
result = self.biom_util.export_amplicon_set_tsv(params)
#END export_amplicon_set_tsv
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method export_amplicon_set_tsv return value ' +
'result is not type dict as required.')
# return the results
return [result]
def compute_correlation_matrix(self, ctx, params):
"""
compute_correlation_matrix: create sub-matrix based on input filter_ids
:param params: instance of type "CompCorrParams" (Input of the
compute_correlation_matrix function input_obj_ref: object
reference of a matrix workspace_name: workspace name objects to be
saved to corr_matrix_name: correlation matrix object name
dimension: compute correlation on column or row, one of ['col',
'row'] method: correlation method, one of ['pearson', 'kendall',
'spearman'] plot_corr_matrix: plot correlation matrix in report,
default False plot_scatter_matrix: plot scatter matrix in report,
default False compute_significance: also compute Significance in
addition to correlation matrix) -> structure: parameter
"input_obj_ref" of type "obj_ref" (An X/Y/Z style reference),
parameter "workspace_name" of type "workspace_name" (workspace
name of the object), parameter "corr_matrix_name" of String,
parameter "dimension" of String, parameter "method" of String,
parameter "plot_corr_matrix" of type "boolean" (A boolean - 0 for
false, 1 for true.), parameter "plot_scatter_matrix" of type
"boolean" (A boolean - 0 for false, 1 for true.), parameter
"compute_significance" of type "boolean" (A boolean - 0 for false,
1 for true.)
:returns: instance of type "CompCorrOutput" -> structure: parameter
"report_name" of String, parameter "report_ref" of String,
parameter "corr_matrix_obj_ref" of type "obj_ref" (An X/Y/Z style
reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN compute_correlation_matrix
returnVal = self.corr_util.compute_correlation_matrix(params)
#END compute_correlation_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method compute_correlation_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def compute_correlation_across_matrices(self, ctx, params):
"""
compute_correlation_across_matrices: compute correlation matrix across matrices
:param params: instance of type "CompCorrMetriceParams" (Input of the
compute_correlation_across_matrices function matrix_ref_1: object
reference of a matrix matrix_ref_2: object reference of a matrix
workspace_name: workspace name objects to be saved to
corr_matrix_name: correlation matrix object name dimension:
compute correlation on column or row, one of ['col', 'row']
method: correlation method, one of ['pearson', 'kendall',
'spearman'] plot_corr_matrix: plot correlation matrix in report,
default False compute_significance: also compute Significance in
addition to correlation matrix) -> structure: parameter
"matrix_ref_1" of type "obj_ref" (An X/Y/Z style reference),
parameter "matrix_ref_2" of type "obj_ref" (An X/Y/Z style
reference), parameter "workspace_name" of type "workspace_name"
(workspace name of the object), parameter "corr_matrix_name" of
String, parameter "dimension" of String, parameter "method" of
String, parameter "plot_corr_matrix" of type "boolean" (A boolean
- 0 for false, 1 for true.), parameter "compute_significance" of
type "boolean" (A boolean - 0 for false, 1 for true.), parameter
"corr_threshold" of Double
:returns: instance of type "CompCorrOutput" -> structure: parameter
"report_name" of String, parameter "report_ref" of String,
parameter "corr_matrix_obj_ref" of type "obj_ref" (An X/Y/Z style
reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN compute_correlation_across_matrices
returnVal = self.corr_util.compute_correlation_across_matrices(params)
#END compute_correlation_across_matrices
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method compute_correlation_across_matrices return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def build_network(self, ctx, params):
"""
build_network: filter correlation matrix and build network
:param params: instance of type "BuildNetworkParams" (Input of the
build_network function corr_matrix_ref: CorrelationMatrix object
workspace_name: workspace name objects to be saved to
network_obj_name: Network object name filter_on_threshold: Dictory
holder that holds filter on thredshold params params in
filter_on_threshold: coefficient_threshold: correlation
coefficient threshold (select pairs with greater correlation
coefficient)) -> structure: parameter "corr_matrix_ref" of type
"obj_ref" (An X/Y/Z style reference), parameter "workspace_name"
of type "workspace_name" (workspace name of the object), parameter
"network_obj_name" of String, parameter "filter_on_threshold" of
mapping from String to String
:returns: instance of type "BuildNetworkOutput" -> structure:
parameter "report_name" of String, parameter "report_ref" of
String, parameter "network_obj_ref" of type "obj_ref" (An X/Y/Z
style reference)
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN build_network
returnVal = self.network_util.build_network(params)
#END build_network
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method build_network return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def run_pca(self, ctx, params):
"""
run_pca: PCA analysis on matrix
:param params: instance of type "PCAParams" (Input of the run_pca
function input_obj_ref: object reference of a matrix
workspace_name: the name of the workspace pca_matrix_name: name of
PCA (KBaseExperiments.PCAMatrix) object dimension: compute PCA on
column or row, one of ['col', 'row'] n_components - number of
components (default 2) attribute_mapping_obj_ref - associated
attribute_mapping_obj_ref scale_size_by - used for PCA plot to
scale data size color_marker_by - used for PCA plot to group data)
-> structure: parameter "input_obj_ref" of type "obj_ref" (An
X/Y/Z style reference), parameter "workspace_name" of String,
parameter "pca_matrix_name" of String, parameter "dimension" of
String, parameter "n_components" of Long, parameter
"attribute_mapping_obj_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "scale_size_by" of mapping from String to
String, parameter "color_marker_by" of mapping from String to
String
:returns: instance of type "PCAOutput" (Ouput of the run_pca function
pca_ref: PCA object reference (as KBaseExperiments.PCAMatrix data
type) report_name: report name generated by KBaseReport
report_ref: report reference generated by KBaseReport) ->
structure: parameter "pca_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 run_pca
returnVal = self.pca_util.run_pca(params)
#END run_pca
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method run_pca return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def view_matrix(self, ctx, params):
"""
view_matrix: generate a report for matrix viewer
:param params: instance of type "ViewMatrixParams" -> structure:
parameter "input_matrix_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "workspace_name" of String, parameter
"with_attribute_info" of type "boolean" (A boolean - 0 for false,
1 for true.)
:returns: instance of type "ViewMatrixOutput" -> structure: parameter
"report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN view_matrix
returnVal = self.data_table_util.view_matrix_as_table(params)
#END view_matrix
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError('Method view_matrix return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
def build_chemical_abundance_template(self, ctx, params):
"""
:param params: instance of type "ChemAbunTempParams" -> structure:
parameter "workspace_name" of String, parameter "workspace_id" of
Long, parameter "sample_set_ref" of type "obj_ref" (An X/Y/Z style
reference), parameter "chemical_data_included" of mapping from
String to Long, parameter "chemical_ids_included" of mapping from
String to Long
:returns: instance of type "ViewMatrixOutput" -> structure: parameter
"report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN build_chemical_abundance_template
returnVal = self.template_util.build_chemical_abundance_template(
params)
#END build_chemical_abundance_template
# At some point might do deeper type checking...
if not isinstance(returnVal, dict):
raise ValueError(
'Method build_chemical_abundance_template return value ' +
'returnVal is not type dict as required.')
# return the results
return [returnVal]
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]