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 """
__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