import biokbase.narrative.common.service as service
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.workspace.client import Workspace as workspaceService
from biokbase.InvocationService.Client import InvocationService
from biokbase.fbaModelServices.Client import fbaModelServices
from biokbase.GenomeComparison.Client import GenomeComparison
from biokbase.assembly.client import Client as ArastClient
from biokbase.KBaseTrees.Client import KBaseTrees
## Globals
VERSION = (0, 0, 1)
NAME = "Microbes Comparative Genomics"
# Initialize
init_service(name=NAME, desc="Demo workflow microbes service", version=VERSION)
@method(name="Compute Pangenome")
def _compute_pan_genome(meth, genome_set,pangenome_id):
""" Rapidly compute gene families for a set of phylogenetically close genomes
:param genome_set: a Genome Set to compute pangenome for
:type genome_set: kbtypes.KBaseSearch.GenomeSet
:ui_name genome_set: Genome Set ID
:param pangenome_id: ID for output pangenome
:type pangenome_id: kbtypes.KBaseGenomes.Pangenome
:ui_name pangenome_id: Pangenome ID
:return: Generated Pangenome Object
:rtype: kbtypes.KBaseGenomes.Pangenome
from biokbase.InvocationService.Client import InvocationService
from biokbase.shock import Client as shockService
## Globals
VERSION = (0, 0, 1)
NAME = "KBase Commands"
class URLS:
shock = "http://shock.metagenomics.anl.gov"
workspace = "https://kbase.us/services/ws"
invocation = "https://kbase.us/services/invocation"
# Initialize
init_service(name=NAME, desc="Functions for executing KBase commands and manipulating the results", version=VERSION)
def _list_cmds():
token = os.environ["KB_AUTH_TOKEN"]
invo = InvocationService(url=URLS.invocation, token=token)
return invo.valid_commands()
def _run_invo(cmd):
token = os.environ["KB_AUTH_TOKEN"]
invo = InvocationService(url=URLS.invocation, token=token)
stdout, stderr = invo.run_pipeline("", cmd, [], 0, "/")
return "".join(stdout), "".join(stderr)
from biokbase.shock import Client as shockService
## Globals
VERSION = (0, 0, 1)
NAME = "KBase Commands"
class URLS:
shock = "http://shock.metagenomics.anl.gov"
workspace = "https://kbase.us/services/ws"
invocation = "https://kbase.us/services/invocation"
# Initialize
init_service(
name=NAME,
desc="Functions for executing KBase commands and manipulating the results",
version=VERSION)
def _list_cmds():
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
return invo.valid_commands()
def _run_invo(cmd):
token = os.environ['KB_AUTH_TOKEN']
invo = InvocationService(url=URLS.invocation, token=token)
stdout, stderr = invo.run_pipeline("", cmd, [], 0, '/')
return "".join(stdout), "".join(stderr)
import random
import numbers
import uuid
import hashlib
# Local
import biokbase.narrative.common.service as service
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.userandjobstate.client import UserAndJobState
## Globals
VERSION = (0, 0, 1)
NAME = "Test Service"
# Initialize
init_service(name=NAME, desc="Testing Service!", version=VERSION)
@method(name="Register Fake Job")
def _reg_fake_job(meth):
"""Tries to register a fake job id. Will fail like SO HARD.
:return: Test. And a job id.
:rtype: kbtypes.Unicode
"""
meth.stages = 2
meth.advance("Testing.")
job_id = "12345"
meth.register_job(job_id)
meth.advance("Done testing!")
## Imports
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.narrative.common import kbtypes
## Globals
VERSION = (0, 0, 1) # We use Semantic Versioning
NAME = 'MyExampleService' # Each service needs a name
DESC = 'This is an example service'
# Initialization
# This initializes a service to have the given attributes described above.
# Added service methods fall below.
init_service(name=NAME, desc=DESC, version=VERSION)
# Define one function
# Note that the user will see the text in this decorator, so consider that
# when writing the name.
@method(name='My Example Function')
def _my_service_function(meth, param1, param2):
"""This is an example function.
:param param1: Input Genome
:type param1: kbtypes.Genome
:ui_name param1: Genome ID (what the user sees)
:param param2: Some text
:type param2: kbtypes.Unicode
import json
# Local
import biokbase.narrative.common.service as service
from biokbase.narrative.common.service import init_service
from biokbase.narrative.common.service import finalize_service
from biokbase.narrative.common.service import method
from biokbase.Transform.Client import Transform
# Global vars
VERSION = (0, 0, 1)
NAME = "Transform Service"
# Initialize
init_service(name=NAME, desc="KBase Transform Service Calls", version=VERSION)
@method(name="Assy to ContigSet")
def _assy_to_cs(meth, input_assyfile, output_contigset):
"""Makes a call to the app service
:param input_assyfile: the KBaseFile.AssemblyFile to convert
:type input_assyfile: kbtypes.Unicode
:ui_name input_assyfile: assembly file
:param output_contigset: the name for the output ContigSet
:type output_contigset: kbtypes.Unicode
:ui_name output_contigset: output ContigSet name
:rtype: kbtypes.Unicode
:return: running job info
"""
import json
# Local
import biokbase.narrative.common.service as service
from biokbase.narrative.common.service import init_service
from biokbase.narrative.common.service import finalize_service
from biokbase.narrative.common.service import method
from biokbase.Transform.Client import Transform
# Global vars
VERSION = (0, 0, 1)
NAME = "Transform Service"
# Initialize
init_service(name=NAME, desc="KBase Transform Service Calls", version=VERSION)
@method(name="Assy to ContigSet")
def _assy_to_cs(meth, input_assyfile, output_contigset):
"""Makes a call to the app service
:param input_assyfile: the KBaseFile.AssemblyFile to convert
:type input_assyfile: kbtypes.Unicode
:ui_name input_assyfile: assembly file
:param output_contigset: the name for the output ContigSet
:type output_contigset: kbtypes.Unicode
:ui_name output_contigset: output ContigSet name
:rtype: kbtypes.Unicode
:return: running job info
"""
__date__ = 'MM/DD/YYYY'
## Imports
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.narrative.common import kbtypes
import json
## Globals
VERSION = (0, 0, 1)
NAME = "MyExampleService"
# Initialization
init_service(name=NAME, desc="This is an example", version=VERSION)
# Define one service
@method(name="MyExampleFunction")
def _my_service_function(meth, param1, param2):
"""This is an example function.
:param param1: Input Genome
:type param1: kbtypes.Genome
:ui_name param1: Genome ID (what the user sees)
:param param2: Some text
:type param2: kbtypes.Unicode
:ui_name param2: Text
:return: Workspace object ID
## Imports
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.narrative.common import kbtypes
## Globals
VERSION = (0, 0, 1) # We use Semantic Versioning
NAME = 'MyExampleService' # Each service needs a name
DESC = 'This is an example service'
# Initialization
# This initializes a service to have the given attributes described above.
# Added service methods fall below.
init_service(name=NAME, desc=DESC, version=VERSION)
# Define one function
# Note that the user will see the text in this decorator, so consider that
# when writing the name.
@method(name='My Example Function')
def _my_service_function(meth, param1, param2):
"""This is an example function.
:param param1: Input Genome
:type param1: kbtypes.Genome
:ui_name param1: Genome ID (what the user sees)
:param param2: Some text
:type param2: kbtypes.Unicode
:ui_name param2: Text
cdmi = "http://kbase.us/services/cdmi_api"
#cdmi = "http://140.221.85.181:7032"
ontology = "http://kbase.us/services/ontology_service"
#gwas = "http://140.221.85.182:7086"
gwas = "https://kbase.us/services/GWAS"
ujs = "https://kbase.us/services/userandjobstate"
networks = "http://kbase.us/services/networks"
#networks = "http://140.221.85.172:7064/KBaseNetworksRPC/networks"
idmap = "http://kbase.us/services/id_map"
#idmap = "http://140.221.85.181:7111"
AweJob.URL = URLS.awe
# Initialize
init_service(name=NAME, desc="Plants GWAS service", version=VERSION)
def _output_object(name):
"""Format an object ID as JSON output, for returning from a narr. function.
"""
return json.dumps({'output': name})
def _workspace_output(wsid):
return json.dumps({'values': [["Workspace object", wsid]]})
class Node:
nodes = []
edges = []
"taskid": "1",
"skip": 0,
"totalwork": 1
}
]
}
"""
def gnid(s):
return s if s.startswith('kb|g.') else 'kb|g.' + s
def nbconsole(x):
sys.stderr.write('@ ' + x + '\n')
sys.stderr.flush()
# Initialize
init_service(name=NAME, desc="Plants Coexpression service", version=VERSION)
def join_stripped(iterable):
return ''.join((s.strip() for s in iterable))
def upload_file(uri, filename, att_content):
file_contents = open(filename).read()
data = {'upload': (filename, file_contents),
'attributes': ('', att_content)}
r = requests.post("%s/node" % uri, files=data)
response = json.loads(r.text)
if response['data'] is None:
raise UploadException("Response from upload has no data: {}".format(response))
datatabletype = 'MAK.FloatDataTable'
class IDServerids:
### variation
var_vcf = 'kb|variant'
###RNASeq
rnaseq_expsample = 'kb|sample'
rnaseq_series = 'kb|series'
rnaseq_alignment = 'kb|alignment'
rnaseq_difexp = 'kb|differentialExpression'
dt_type = 'kb|dataTable'
# Init logging.
g_log = logging.getLogger(__name__)
init_service(name = NAME, desc="Variation and Expression service", version = VERSION)
clients = {}
##
##Decorators for control logic
##
def _get_wsname(meth, ws):
'''gets the workspace name
'''
if ws:
return ws
elif meth.workspace_id and (meth.workspace_id != 'null'):
return meth.workspace_id
ids = "http://kbase.us/services/idserver"
cdmi = "http://kbase.us/services/cdmi_api"
#cdmi = "http://140.221.85.181:7032"
ontology = "http://kbase.us/services/ontology_service"
#gwas = "http://140.221.85.182:7086"
gwas = "https://kbase.us/services/GWAS"
ujs = "https://kbase.us/services/userandjobstate"
networks = "http://kbase.us/services/networks"
#networks = "http://140.221.85.172:7064/KBaseNetworksRPC/networks"
idmap = "http://kbase.us/services/id_map"
#idmap = "http://140.221.85.181:7111"
AweJob.URL = URLS.awe
# Initialize
init_service(name=NAME, desc="Plants GWAS service", version=VERSION)
def _output_object(name):
"""Format an object ID as JSON output, for returning from a narr. function.
"""
return json.dumps({'output': name})
def _workspace_output(wsid):
return json.dumps({'values': [["Workspace object", wsid]]})
class Node:
nodes = []
edges = []
ugids = {}
__author__ = 'Bill Riehl <*****@*****.**>'
__date__ = '9/30/14'
## Imports
# Stdlib
import json
# Local
import biokbase.narrative.common.service as service
from biokbase.narrative.common.service import init_service, method, finalize_service
## Globals
VERSION = (0, 0, 1)
NAME = "Bill Test"
# Initialize
init_service(name=NAME, desc="Bill Demo!", version=VERSION)
@method(name="Try some Perl")
def _try_perl(meth):
"""Run a Perl command. Maybe.
:return: A string
:rtype: kbtypes.Unicode
"""
meth.stages = 2 # for reporting progress
meth.advance("Starting...")
from IPython import get_ipython
ipy = get_ipython()
]
}
"""
def gnid(s):
return s if s.startswith('kb|g.') else 'kb|g.' + s
def nbconsole(x):
sys.stderr.write('@ ' + x + '\n')
sys.stderr.flush()
# Initialize
init_service(name=NAME, desc="Plants Coexpression service", version=VERSION)
def join_stripped(iterable):
return ''.join((s.strip() for s in iterable))
def upload_file(uri, filename, att_content):
file_contents = open(filename).read()
data = {
'upload': (filename, file_contents),
'attributes': ('', att_content)
}
r = requests.post("%s/node" % uri, files=data)
response = json.loads(r.text)
if response['data'] is None:
import random
import numbers
import uuid
import hashlib
# Local
import biokbase.narrative.common.service as service
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.userandjobstate.client import UserAndJobState
## Globals
VERSION = (0, 0, 1)
NAME = "Test Service"
# Initialize
init_service(name=NAME, desc="Testing Service!", version=VERSION)
@method(name="Register Fake Job")
def _reg_fake_job(meth):
"""Tries to register a fake job id. Will fail like SO HARD.
:return: Test. And a job id.
:rtype: kbtypes.Unicode
"""
meth.stages = 2
meth.advance("Testing.")
job_id = "12345"
meth.register_job(job_id)
__date__ = 'MM/DD/YYYY'
## Imports
from biokbase.narrative.common.service import init_service, method, finalize_service
from biokbase.narrative.common import kbtypes
import json
## Globals
VERSION = (0, 0, 1)
NAME = "MyExampleService"
# Initialization
init_service(name=NAME, desc="This is an example", version=VERSION)
# Define one service
@method(name="MyExampleFunction")
def _my_service_function(meth, param1, param2):
"""This is an example function.
:param param1: Input Genome
:type param1: kbtypes.Genome
:ui_name param1: Genome ID (what the user sees)
:param param2: Some text
:type param2: kbtypes.Unicode
:ui_name param2: Text
:return: Workspace object ID
:rtype: kbtypes.Unicode
