def test_unused_input():
this_path = current_path / "cwl" / "misc" / "wf-unused-input.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 1
namespace_problem = next(p for p in doc.problems
if p.range.start.line == 4)
assert namespace_problem.message.startswith("Unused input")
def test_implicit_inputs():
this_path = current_path / "cwl" / "misc" / "wf-when-input.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 0
cmpl = doc.completion(Position(12, 8))
assert "new_input" in [c.label for c in cmpl]
def test_docs_on_hover():
this_path = current_path / "cwl" / "misc" / "wf-when-input.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
hov = doc.hover(Position(10, 6))
assert "Sibling" in hov.contents.value
assert hov.contents.kind == "markdown"
def test_definition():
doc = load(doc_path=path, type_dicts=type_dicts)
linked_uri = pathlib.Path(current_path / "cwl" / "ebi" / "utils" /
"concatenate.cwl")
doc_def_loc = doc.definition(loc=Position(50, 20))
assert isinstance(doc_def_loc, Location)
assert doc_def_loc.uri == linked_uri.as_uri()
def test_missing_name_space():
this_path = current_path / "cwl" / "misc" / "cl-missing-namespace.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 1
namespace_problem = next(p for p in doc.problems
if p.range.start.line == 15)
assert namespace_problem.message.startswith("Expecting one of")
def test_mass_wf_load():
type_dicts = load_type_dicts()
for wf_dir in [
"ebi/workflows", "mgi/subworkflows", "mgi/pipelines", "cwl-v1.2"
]:
path = current_path / "cwl" / wf_dir
for fname in path.glob("*.cwl"):
_ = load(doc_path=fname, type_dicts=type_dicts)
def test_plain_text_include():
this_path = current_path / "cwl" / "misc" / "cl-include-text.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 0
hov = doc.hover(Position(9, 21))
assert "We hold" in hov.contents.value
def test_requirements_completion():
this_path = current_path / "cwl" / "misc" / "cl-hints-dict.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(12, 8))
assert "dockerLoad" in [c.label for c in cmpl]
this_path = current_path / "cwl" / "misc" / "cl-hints-list.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(12, 8))
assert "dockerImport" in [c.label for c in cmpl]
this_path = current_path / "cwl" / "misc" / "cl-hints-dict-start.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(12, 5))
assert "dockerLoad" in [c.label for c in cmpl]
def test_hints_imports():
this_path = current_path / "cwl" / "misc" / "cl-hints-import.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 1
missing_error = next(p for p in doc.problems if p.range.start.line == 4)
assert missing_error.message.startswith("Missing document:")
cmpl = doc.completion(Position(4, 20))
assert "cl-schemadef-import.cwl" in [c.label for c in cmpl]
def test_remote_files():
this_path = current_path / "cwl" / "misc" / "wf-remote-steps.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
# Refers to an earlier commit
hov = doc.hover(Position(13, 32))
assert "class:" in hov.contents.value
# Non existent commit
hov = doc.hover(Position(19, 32))
assert hov.contents.value == "```\n\n```"
def test_basic_JS():
path = current_path / "cwl" / "misc" / "clt1.cwl"
doc = load(doc_path=path, type_dicts=type_dicts)
hov = doc.hover(loc=Position(7, 25))
assert isinstance(hov.contents.value, str)
assert hov.contents.value.startswith("```\nA_")
hov = doc.hover(loc=Position(10, 19))
assert isinstance(hov.contents.value, str)
assert "outdirSize" in hov.contents.value
def test_schemadef_include():
this_path = current_path / "cwl" / "misc" / "cl-schemadef-include.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 2
syntax_error = next(p for p in doc.problems if p.range.start.line == 12)
assert syntax_error.message == "Expecting an $import"
type_error = next(p for p in doc.problems if p.range.start.line == 4)
assert type_error.message.startswith("Expecting one of")
def test_ebi_wf_cmsearch_multimodel():
path = current_path / "cwl" / "ebi" / "workflows" / "cmsearch-multimodel-wf.cwl"
doc = load(doc_path=path, type_dicts=load_type_dicts())
step_symbols = next((symb for symb in doc.symbols if symb.name == "steps"),
None)
assert isinstance(step_symbols.children, list)
cmsearch_symbol = next(
(symb for symb in step_symbols.children if symb.name == "cmsearch"),
None)
assert cmsearch_symbol.range.start.line == 33
def test_port_completer():
this_path = current_path / "cwl" / "misc" / "wf-port-completer.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(10, 14)) # Not a list
assert "in1" in [c.label for c in cmpl]
cmpl = doc.completion(Position(23, 11)) # Is a list
assert "out1" in [c.label for c in cmpl]
cmpl = doc.completion(Position(24, 9)) # Is a list
assert "in1" in [c.label for c in cmpl]
def test_v1_1_runtime():
# No exitcode in runtime in v1.0 ever
path = current_path / "cwl" / "misc" / "clt1.cwl"
doc = load(doc_path=path, type_dicts=type_dicts)
hov = doc.hover(loc=Position(10, 19))
assert "exitCode" not in hov.contents.value
hov = doc.hover(loc=Position(17, 33))
assert "exitCode" not in hov.contents.value
# Exitcode in runtime in v1.1 when in output
path = current_path / "cwl" / "misc" / "clt2.cwl"
doc = load(doc_path=path, type_dicts=type_dicts)
hov = doc.hover(loc=Position(24, 20))
assert "exitCode" not in hov.contents.value
hov = doc.hover(loc=Position(31, 34))
assert "exitCode" in hov.contents.value
def __init__(self):
routes = load('handler')
settings = {
'static_path': os.path.join(os.path.dirname(__file__), "static"),
'template_path': os.path.join(os.path.dirname(__file__), "tpl"),
'xsrf_cookies': True,
'cookie_secret': 'tokyo',
'site_title': 'zkdash',
'ui_modules': uimodule,
'ui_methods': uimethods,
'debug': OPTIONS.debug,
}
tornado.web.Application.__init__(self, routes, **settings)
def __init__(self):
routes = load('handler')
settings = {
'static_path': os.path.join(os.path.dirname(__file__), "static"),
'template_path': os.path.join(os.path.dirname(__file__), "tpl"),
'xsrf_cookies': True,
'cookie_secret': 'tokyo',
'site_title': 'zkdash',
'ui_modules': uimodule,
'ui_methods': uimethods,
'debug': OPTIONS.debug,
}
tornado.web.Application.__init__(self, routes, **settings)
def test_schemadef_import():
this_path = current_path / "cwl" / "misc" / "cl-schemadef-import.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 0
cmpl = doc.completion(Position(12, 21))
assert "cl-schemadef-import.cwl" in [c.label for c in cmpl]
# The completer should look for all files in the current directory
cmpl = doc.completion(Position(4, 11))
assert "./paired_end_record.yml#paired_end_options" in [
c.label for c in cmpl
]
def __enter__(self):
if self.dummy:
return self
self.lib = lib.load(os.getcwd() + "/librpicnc/build/cnc.so")
c_axesinfo = (lib.AxisInfo*len(self.config["axes"]))()
for i, (axis, ac) in enumerate(zip(self.config["axes"], self.cache["axes"])):
c_axesinfo[i] = lib.AxisInfo(pins=axis["pins"], pos=ac["pos"], len_=ac["len"])
r = self.lib.cnc_init(len(c_axesinfo), c_axesinfo)
if r != 0:
raise CNCException("cnc_init error")
return self
def test_connections():
path = current_path / "cwl" / "misc" / "wf-port-completer.cwl"
doc = load(doc_path=path, type_dicts=load_type_dicts())
assert len(doc.problems) == 0
def test_requirement_completion():
doc = load(doc_path=path, type_dicts=type_dicts)
cmpl = doc.completion(Position(8, 16))
assert "InlineJavascriptRequirement" in [c.label for c in cmpl]
def test_troublesome_tool_load():
type_dicts = load_type_dicts()
path = current_path / "cwl" / "misc"
for fname in path.glob("*.cwl"):
_ = load(doc_path=fname, type_dicts=type_dicts)
#!-*-coding:utf-8-*-
import lib
import sys
import numpy as np
"""
3 Multiple Regression
"""
lib.title("#############3 Multiple Regression#############")
#####データを読み取る#####
CEOSAL2_dataset = lib.load(filename="CEOSAL2.csv")
explanatories = ["const", "lsales", "lmktval"]
explained = ["lsalary"]
"""
3-1の解答
"""
lib.chaper("大問3.1の回答")
X = lib.df2mat(df=CEOSAL2_dataset, columns=explanatories)
Y = lib.df2mat(df=CEOSAL2_dataset, columns=explained)
b = lib.reg(X=X, Y=Y)
lib.add_suffix(coefs=b, labels=explanatories)
print("\n")
"""
3-2の解答
"""
lib.chaper("大問3.2の回答")
CEOSAL2_dataset = lib.load(filename="CEOSAL2.csv")
explanatories = ["const", "lsales", "lmktval", "profits"]
explained = ["lsalary"]
X = lib.df2mat(df=CEOSAL2_dataset, columns=explanatories)
Y = lib.df2mat(df=CEOSAL2_dataset, columns=explained)
#!-*-coding:utf-8-*-
import lib
import sys
import numpy as np
"""
8 Instrumental Variable And 2SLS
"""
lib.title("#############8 Instrumental Variable And 2SLS#############")
FERTIL2_dataset = lib.load( filename="FERTIL2.csv" )
FERTIL2_dataset = lib.cross_var( df=FERTIL2_dataset , var1="age" , var2="age" )
"""
8-1の解答
"""
lib.chaper("<8.1の解答>")
#####説明変数を定義#####
explanatories = ["const","educ","age","age*age"]
explained = ["children"]
X = lib.df2mat( df=FERTIL2_dataset , columns=explanatories )
Y = lib.df2mat( df=FERTIL2_dataset , columns=explained )
b = lib.reg( X=X , Y=Y )
lib.add_suffix( coefs=b , labels=explanatories )
const , educ , age , age_aqure = b[0] , b[1] , b[2] , b[3]
y = educ * 100
print( y )
print( "9人減る" )
print("\n")
def test_mass_tool_load():
type_dicts = load_type_dicts()
for wf_dir in ["ebi/tools", "mgi/tools"]:
path = current_path / "cwl" / wf_dir
for fname in path.glob("*.cwl"):
_ = load(doc_path=fname, type_dicts=type_dicts)
import lib
import ROOT
lib.load()
crootprob3pp = ROOT.crootprob3pp
Probability = crootprob3pp.Probability
class Flavour:
NU_E = 1
NU_MU = 2
NU_TAU = 3
class CP:
MATTER = 1
ANTI_MATTER = -1
def test_step_input_completion():
doc = load(doc_path=path, type_dicts=type_dicts)
cmpl = doc.completion(Position(37, 38))
assert "covariance_models" in [c.label for c in cmpl]
#!-*-coding:utf-8-*-
import lib
import sys
import numpy as np
"""
1 Matrix Calculus
"""
lib.title("#############1 Matrix Calculus#############")
#####データを読み取る#####
artifical_dataset = lib.load(filename="artificial.csv")
explanatories = ["x1", "x2"]
explained = ["y"]
#####各変数を定義#####
X = lib.df2mat(df=artifical_dataset, columns=explanatories)
Y = lib.df2mat(df=artifical_dataset, columns=explained)
b = lib.reg(X=X, Y=Y)
"""
1-1の解答
"""
lib.chaper("<大問1.1の回答>")
#####解答#####
lib.add_suffix(b)
print("\n")
"""
1-2の解答
"""
lib.chaper("<大問1.2の回答>")
#####各変数を定義#####
def test_invalid_input():
this_path = current_path / "cwl" / "misc" / "wf-invalid-input.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
assert len(doc.problems) == 1
def main(argv):
# pylint: disable=W0612
try:
argv = FLAGS(argv) # parse flags
except gflags.FlagsError, e:
print '%s\\nUsage: %s ARGS\\n%s' % (e, sys.argv[0], FLAGS)
sys.exit(1)
gl.set_runtime_config('GRAPHLAB_DEFAULT_NUM_GRAPH_LAMBDA_WORKERS', 16)
for flag_name in sorted(FLAGS.RegisteredFlags()):
if flag_name not in ["?", "help", "helpshort", "helpxml"]:
fl = FLAGS.FlagDict()[flag_name]
with open('output/main.out', 'a') as f:
f.write(
"# " + fl.help + " (" + flag_name + "): " + str(fl.value) + '\n')
X_train, X_test = load(FLAGS.dataset)
g = get_graph(X_train, FLAGS.rank)
rmse_train, rmse_test, L, R, wu, wm, bu, bm = \
sgd_gl_edge(g, X_train, X_test,
FLAGS.lamb, FLAGS.rank, FLAGS.eta, Niter=FLAGS.maxit,
unified=FLAGS.unified, lambduh_w=FLAGS.lamb_w, output="main")
print 'rmse_train', rmse_train
print 'rmse_test', rmse_test
if __name__ == '__main__':
main(sys.argv)
# overnightRun()
#!-*-coding:utf-8-*-
import lib
import sys
import numpy as np
"""
6 Inference2
"""
lib.title("#############6 Inference2#############")
#####データを読み取る#####
HPRICE_dataset = lib.load(filename="HPRICE1.csv")
explanatories = ["const", "sqrft", "bdrms"]
explained = ["lprice"]
#####各変数を定義#####
X = lib.df2mat(df=HPRICE_dataset, columns=explanatories)
Y = lib.df2mat(df=HPRICE_dataset, columns=explained)
b = lib.reg(X=X, Y=Y)
"""
6-1の解答
"""
lib.chaper("<6.1の解答>")
#####解答#####
lib.add_suffix(b, labels=explanatories)
print("\n")
"""
6-2の解答
"""
lib.chaper("<6.2の解答>")
#####回帰係数の取得#####
const, sqrft, bdrms = b[0], b[1], b[2]
y_bdrms = bdrms
def test_requirement_sub_completion():
this_path = current_path / "cwl" / "ebi" / "workflows" / "InterProScan-v5-chunked-wf.cwl"
doc = load(doc_path=this_path, type_dicts=type_dicts)
cmpl = doc.completion(Position(8, 10))
assert "InlineJavascriptRequirement" in [c.label for c in cmpl]
