def download(self, synid):
"""Download a file into the dreamtools directory
:param synid: a valid synapse id (e.g., syn123456)
You must have a login on synapse website.
"""
# If not connected, nothing will be possible, so just skip the download
# step.
if self.client._connected is False:
print(
red("You do not seem to have a network connection. ") +
red("Downloading required data is not possible"))
sys.exit(1)
assert synid.startswith('syn'), \
"synid must be a valid synapse identifier e.g., syn123456"
try:
self.client.get(synid, downloadLocation=self.directory)
except Exception as err:
print('Original error message from synapseclient:')
print(err)
print(
"DREAMTools warning: this is most probably a file that requires you to accept the conditions of use of the data. We will open the relevant page for you now. Please click 'show; on the RHS of the Conditions of use and Accept the terms of use"
)
sys.exit()
def download(self, synid):
"""Download a file into the dreamtools directory
:param synid: a valid synapse id (e.g., syn123456)
You must have a login on synapse website.
"""
# If not connected, nothing will be possible, so just skip the download
# step.
if self.client._connected is False:
print(red("You do not seem to have a network connection. ") +
red("Downloading required data is not possible"))
sys.exit(1)
assert synid.startswith('syn'), \
"synid must be a valid synapse identifier e.g., syn123456"
try:
self.client.get(synid, downloadLocation=self.directory)
except Exception as err:
print('Original error message from synapseclient:')
print(err)
print("DREAMTools warning: this is most probably a file that requires you to accept the conditions of use of the data. We will open the relevant page for you now. Please click 'show; on the RHS of the Conditions of use and Accept the terms of use")
sys.exit()
def anova_one_drug_one_feature(anova, options):
"""Analyse the entire data set"""
from gdsctools import anova_report
if options.tissue is not None:
anova.set_cancer_type(options.tissue)
odof = anova_report.Association(anova,
drug=options.drug,
feature=options.feature)
#print(odof.settings)
# for the HTML
#odof.add_dependencies = True
#odof.add_settings = True
df = odof.run()
if df.ix[1]['FEATURE_IC50_effect_size'] is None:
msg = "association %s vs %s not valid for testing (not enough" +\
" MSI or positives for that features ? Try with "+\
" --exclude-msi (you must then set a tissue with "+\
" --tissue"
print(red(msg % (options.drug, options.feature)))
else:
print(df.T)
# HTML report
if options.no_html is True:
return
odof.create_report(onweb=options.onweb)
def anova_one_drug_one_feature(anova, options):
"""Analyse the entire data set"""
from gdsctools import anova_report
from gdsctools.report import ReportMain
if options.tissue is not None:
anova.set_cancer_type(options.tissue)
# just to create the directory
ReportMain(directory=options.directory)
odof = anova_report.Association(anova,
drug=int(options.drug),
feature=options.feature)
odof.add_href = False
df = odof.run()
if df.loc[1]['FEATURE_IC50_effect_size'] is None:
msg = "association %s vs %s not valid for testing (not enough" +\
" MSI or positives for that features ? Try with "+\
" --exclude-msi (you must then set a tissue with "+\
" --tissue"
print(red(msg % (options.drug, options.feature)))
else:
print(df.T)
# HTML report
if options.no_html is True:
return
odof.create_report(onweb=options.onweb)
def anova_one_drug_one_feature(anova, options):
"""Analyse the entire data set"""
from gdsctools import anova_report
if options.tissue is not None:
anova.set_cancer_type(options.tissue)
odof = anova_report.Association(anova,
drug=options.drug,
feature=options.feature)
#print(odof.settings)
# for the HTML
#odof.add_dependencies = True
#odof.add_settings = True
df = odof.run()
if df.ix[1]['FEATURE_IC50_effect_size'] is None:
msg = "association %s vs %s not valid for testing (not enough" +\
" MSI or positives for that features ? Try with "+\
" --exclude-msi (you must then set a tissue with "+\
" --tissue"
print(red(msg % (options.drug, options.feature)))
else:
print(df.T)
# HTML report
if options.no_html is True:
return
odof.create_report(onweb=options.onweb)
def standalone(args=None):
"""This function is used by the standalone application called cellnopt_boolean
::
cno_milp --help
"""
if args is None:
args = sys.argv[:]
user_options = OptionsMILP()
if len(args) == 1:
user_options.parse_args(["prog", "--help"])
else:
options = user_options.parse_args(args[1:])
if options.onweb is True or options.report is True:
o = MILPTrain(options.pknmodel, options.data, verbose=options.verbose
)
if options.onweb is True:
o.optimise()
o.onweb()
elif options.report is True:
o.optimise()
o.report()
else:
from easydev.console import red
print(red("No report requested; nothing will be saved or shown"))
print("use --on-web or --report options")
def anova_one_drug(anova, options):
"""Analyse one specific drug"""
from gdsctools import ANOVAReport
anova.set_cancer_type(options.tissue)
if options.feature:
anova.feature_names = options.features
results = anova.anova_one_drug(options.drug)
print("\nFound %s associations" % len(results))
if len(results)==0:
print(red("\nPlease try with another drug or no --drug option"))
return
# ?? is this required ?
N = len(results)
results.df.insert(0, 'ASSOC_ID', range(1, N+1))
if options.no_html is True:
return
r = ANOVAReport(anova, results=results)
print(darkgreen("\nCreating all figure and html documents in %s" %
r.settings.directory))
r.create_html_pages(onweb=options.onweb)
def anova_one_drug(anova, options):
"""Analyse one specific drug"""
from gdsctools import ANOVAReport
anova.set_cancer_type(options.tissue)
if options.feature:
anova.feature_names = options.features
results = anova.anova_one_drug(options.drug)
print("\nFound %s associations" % len(results))
if len(results) == 0:
print(red("\nPlease try with another drug or no --drug option"))
return
# ?? is this required ?
N = len(results)
results.df.insert(0, 'ASSOC_ID', range(1, N + 1))
if options.no_html is True:
return
r = ANOVAReport(anova, results=results)
print(
darkgreen("\nCreating all figure and html documents in %s" %
r.settings.directory))
r.create_html_pages(onweb=options.onweb)
def report(self):
"""Create report and shows report (or not)"""
if self.options.onweb is True:
self.trainer.report(show=True)
elif self.options.report is True:
self.trainer.report(show=False)
else:
from easydev.console import red
print(red("No report requested; nothing will be saved or shown"))
print("use --on-web or --report options")
def create_summary_pages(self):
"""Create summary pages
Once the main analyis is done (:meth:`analyse`), and the company
packages have been created (:meth:`create_data_packages_for_companies`),
you can run this method that will creade a summary HTML page
(index.html) for the tissue, and a similar summary HTML page for the
tissues of each company. Finally, an HTML summary page for the
companies is also created.
The final tree direcorty looks like::
|-- index.html
|-- company_packages
| |-- index.html
| |-- Company1
| | |-- Tissue1
| | |-- Tissue2
| | |-- index.html
| |-- Company2
| | |-- Tissue1
| | |-- Tissue2
| | |-- index.html
|-- tissue_packages
| |-- index.html
| |-- Tissue1
| |-- Tissue2
"""
# First for the main directory (tissue_packages):
print(purple("Creating summary index.html for the tissues"))
self._create_summary_pages(self.main_directory, verbose=False)
# Then for each companies:
print(purple("Creating summary index.html for each company"))
pb = Progress(len(self.companies))
for i, company in enumerate(self.companies):
try:
self._create_summary_pages(self.company_directory + os.sep +
company,
verbose=False,
company=company)
except Exception as err:
print(
red("Issue with %s. Continue with other companies" %
company))
print(err)
pb.animate(i + 1)
# Finally, an index towards each company
self._create_main_index()
def create_summary_pages(self):
"""Create summary pages
Once the main analyis is done (:meth:`analyse`), and the company
packages have been created (:meth:`create_data_packages_for_companies`),
you can run this method that will creade a summary HTML page
(index.html) for the tissue, and a similar summary HTML page for the
tissues of each company. Finally, an HTML summary page for the
companies is also created.
The final tree direcorty looks like::
|-- index.html
|-- company_packages
| |-- index.html
| |-- Company1
| | |-- Tissue1
| | |-- Tissue2
| | |-- index.html
| |-- Company2
| | |-- Tissue1
| | |-- Tissue2
| | |-- index.html
|-- tissue_packages
| |-- index.html
| |-- Tissue1
| |-- Tissue2
"""
# First for the main directory (tissue_packages):
print(purple("Creating summary index.html for the tissues"))
self._create_summary_pages(self.main_directory, verbose=False)
# Then for each companies:
print(purple("Creating summary index.html for each company"))
pb = Progress(len(self.companies))
for i, company in enumerate(self.companies):
try:
self._create_summary_pages(self.company_directory + os.sep +
company, verbose=False, company=company)
except Exception as err:
print(red("Issue with %s. Continue with other companies" % company))
print(err)
pb.animate(i+1)
# Finally, an index towards each company
self._create_main_index()
def sequana_init(options):
import sequana
from sequana.misc import textwrap
from sequana import SequanaConfig, sequana_data
sa = Tools(verbose=options.verbose)
# Check that the pipeline is well defined
module = Module(options.pipeline)
if os.path.exists(options.target_dir):
txt = "Will override the following files if present: %s.rules " +\
"config.yaml, runme.sh, ..."
sa.blue(txt % options.pipeline)
if options.force is True:
choice = "y"
else:
choice = input(
red("Do you want to proceed (to avoid this " +
" message, use --force)? [y]/n:"))
if choice == "n":
sys.exit(0)
# Copying snakefile
logger.info("Copying snakefile")
sa.mkdir(options.target_dir)
shutil.copy(module.snakefile,
options.target_dir + os.sep + options.pipeline + ".rules")
# Creating README to print on the screen and in a file
txt = "User command::\n\n"
txt += " %s \n\n" % " ".join(sys.argv)
txt += "You can now run snakemake yourself or type::"
txt += purple("""
snakemake -s %s.rules --stats stats.txt -p -j 4
""" % options.pipeline)
txt += """
# -j 4 means you will use 4 cores
# -p prints the commands used
# --stats stats.txt must be used since stats.txt is expected to be found.
or just run the bash script::
sh runme.sh
EDIT THE config.yaml if needed
Once finished with success, the report/ directory contains a summary.html
and relevant files (depends on the pipeline).
"""
logger.info("Creating README")
with open(options.target_dir + os.sep + "README", "w") as fh:
fh.write(txt.replace("\x1b[35m", "").replace("\x1b[39;49;00m", ""))
# Creating Config file
logger.info("Creating the config file")
# Create (if needed) and update the config file
config_filename = options.target_dir + os.sep + "config.yaml"
if options.config:
# full existing path
if os.path.exists(options.config):
shutil.copy(options.config, config_filename)
else: # or a sequana config file in the module path ?
raise (IOError("Config file %s not found locally" %
options.config))
else:
copy_config_from_sequana(module, "config.yaml", config_filename)
# Copy multiqc if it is available
multiqc_filename = options.target_dir + os.sep + "multiqc_config.yaml"
copy_config_from_sequana(module, "multiqc_config.yaml", multiqc_filename)
cluster_cfg_filename = options.target_dir + os.sep + "cluster_config.json"
copy_config_from_sequana(module, "cluster_config.json",
cluster_cfg_filename)
# The input
cfg = SequanaConfig(config_filename)
cfg.config.input_directory = options.input_directory
cfg.config.input_pattern = options.pattern
cfg.config.input_extension = options.extension
cfg.config.input_samples.file1 = options.file1
cfg.config.input_samples.file2 = options.file2
cfg.config.input_readtag = options.input_readtag
# Dedicated section for quality control section
if options.pipeline == "quality_control":
if options.design:
shutil.copy(options.design, options.target_dir + os.sep)
cfg.config['cutadapt'].design_file = os.path.basename(
options.design)
if options.kraken:
cfg.config.kraken.database_directory = os.path.abspath(
options.kraken)
cfg.config.kraken.do = True
else:
cfg.config.kraken.do = False
cfg.config['cutadapt'].fwd = options.adapter_fwd
cfg.config['cutadapt'].rev = options.adapter_rev
cfg.config['cutadapt'].adapter_type = options.adapters
# Foir all pipeline using BWA
if options.reference:
cfg.config.bwa_mem.reference = os.path.abspath(options.reference)
if options.pipeline == "variant_calling":
if options.reference:
cfg.config.bwa_mem_ref.reference = os.path.abspath(
options.reference)
if options.pipeline in ["rnaseq", "smallrnaseq"]:
if options.design:
shutil.copy(options.design, options.target_dir + os.sep)
cfg.config['cutadapt'].design_file = os.path.basename(
options.design)
cfg.config['cutadapt'].fwd = options.adapter_fwd
cfg.config['cutadapt'].rev = options.adapter_rev
cfg.config['cutadapt'].adapter_choice = options.adapters
cfg.copy_requirements(target=options.target_dir)
# FIXME If invalid, no error raised
if options.config_params:
params = [this.strip() for this in options.config_params.split(",")]
for param in params:
if param.count(":") not in [1, 2, 3]:
txt = "incorrect format following --config-params"
txt += "Expected at least one : sign or at most 2 of them"
txt += "Config file section such as :\n"
txt += "project: tutorial\n"
txt += "should be encoded project:tutorial"
raise ValueError(txt)
if param.count(":") == 1:
k, v = param.split(':')
cfg.config[k] = v
elif param.count(":") == 2:
k1, k2, v = param.split(":")
cfg.config[k1][k2] = v
elif param.count(":") == 3:
k1, k2, k3, v = param.split(":")
cfg.config[k1][k2][k3] = v
# important to update yaml with content of config
cfg._update_yaml()
cfg.save(config_filename)
# Creating a unique runme.sh file
runme_filename = options.target_dir + os.sep + "runme.sh"
with open(runme_filename, "w") as fout:
cmd = "#!/bin/sh\n"
cmd += "# generated with sequana version %s with this command:\n" % sequana.version
cmd += "# %s\n" % " ".join(sys.argv)
cmd += "snakemake -s %(project)s.rules --stats stats.txt -p -j %(jobs)s --nolock"
if options.forceall:
cmd += " --forceall "
if options.cluster:
# Do we want to include the cluster config option ?
cluster_config = Module(options.pipeline).cluster_config
if options.ignore_cluster_config is True:
cluster_config = None
if cluster_config is None:
cmd += ' --cluster "%s"' % options.cluster
else:
cmd += ' --cluster "%s" --cluster-config %s' %\
(options.cluster, os.path.basename(cluster_config))
if options.redirection:
cmd += " 1>run.out 2>run.err"
fout.write(
cmd % {
'project': options.pipeline,
'jobs': options.jobs,
"version": sequana.version
})
# change permission of runme.sh to 755
st = os.stat(runme_filename)
os.chmod(runme_filename, st.st_mode | 0o755)
sa.green("Initialisation of %s succeeded" % options.target_dir)
sa.green("Please, go to the project directory ")
sa.purple("\n cd %s\n" % options.target_dir)
sa.green("Check out the README and config.yaml files")
sa.green("A basic script to run the analysis is named runme.sh ")
sa.purple("\n sh runme.sh\n")
sa.purple("On a slurm cluster, you may type:")
sa.purple("\n srun --qos normal runme.sh\n")
sa.green(
"In case of trouble, please post an issue on https://github.com/sequana/sequana/issue "
)
sa.green(
"or type sequana --issue and fill a post with the error and the config file (NO DATA PLEASE)"
)
# Change permission
try: #python 3
os.chmod(runme_filename, 0o755)
except:
logger.info(
"Please use Python3. Change the mode of %s manually to 755" %
runme_filename)
def red(self, txt, force=False):
if self.verbose or force is True:
print(red(txt))
def run(self, color=True):
"""Executes 'python setup.py' with the user commands on all packages. """
if color:
try:
from easydev.console import bold, red, green, \
color_terminal, nocolor, underline, purple
except:
try:
sys.path.insert(0, os.path.join('deploy', 'src', 'deploy'))
from console import bold, red, green, \
color_terminal, nocolor, underline, purple
except:
pass
if not color_terminal():
# Windows' poor cmd box doesn't understand ANSI sequences
nocolor()
else:
bold = purple = red = green = underline = str
print(bold("Running multisetup version %s" % __revision__.split()[2]))
#project_dir = self.curdir.basename()
directories = [package for package in self.packages]
print('Will process the following directories: ', )
for directory in directories:
print(bold(directory)),
#print bold(directory.basename()),
print('')
try:
for directory in directories:
try:
os.chdir(directory)
print(
underline('Entering %s package' %
os.path.basename(directory)))
# % directory.basename())
except OSError as err:
print(
underline('Entering %s package' %
os.path.basename(directory)))
print(
red("cannot find this directory (%s)" %
os.path.basename(directory)))
print(err)
print('Python exec : ', sys.executable)
#print underline('Entering %s package' % directory.basename())
for cmd in self.commands:
setup_command = '%s setup.py %s ' % (sys.executable, cmd)
print("\tExecuting " + setup_command + '...processing', )
#Run setup.py with user commands
outputs = None
errors = None
if self.verbose:
process = Popen(setup_command, shell=True)
status = process.wait()
else:
process = Popen(setup_command,
stdout=PIPE,
stderr=PIPE,
shell=True)
#status = process.wait()
outputs, errors = process.communicate()
if process.returncode == 0:
print(green('done'))
else:
if not self.verbose:
print(
red('\tFailed. ( error code %s) ' %
(process.returncode)))
os.chdir(self.curdir)
if not self.force:
raise RuntimeError()
if 'pylint' in cmd:
if outputs is not None:
for x in outputs.split('\n'):
if x.startswith('Your code has been'):
print(purple('\t%s' % x))
if 'nosetests' in cmd:
if errors is not None:
for x in errors.split('\n'):
if x.startswith('TOTAL'):
res = x.replace('TOTAL', 'Total coverage')
res = " ".join(res.split())
print(purple('\t%s' % res))
if x.startswith('Ran'):
print(purple('\t%s' % x))
if x.startswith('FAILED'):
print(purple('\t%s' % x))
else:
print(purple('all right'))
os.chdir(self.curdir)
except RuntimeError:
sys.exit()
os.chdir(self.curdir)
def anova_pipeline(args=None):
"""This function is used by the standalone application called
**gdsctools_anova**
Type::
gdsctools_anova --help
to get some help.
"""
msg = "Welcome to GDSCTools standalone"
print_color(msg, purple, underline=True)
# Keep the argument args as None by default to
# allow testing e.g., in nosetests
if args is None:
args = sys.argv[:]
elif len(args) == 1:
args += ['--help']
user_options = ANOVAOptions(prog="gdsctools_anova")
try:
options = user_options.parse_args(args[1:])
except SystemExit:
return
# -----------------------------------------------------------------
# ---------------------------------------- options without analysis
# -----------------------------------------------------------------
if options.version is True:
print("This is version %s of gdsctools_anova" % gdsctools.version)
return
if options.testing is True:
print('Testing mode:')
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
df = an.anova_one_drug_one_feature('Drug_1047_IC50', 'TP53_mut')
assert df.loc[1,'N_FEATURE_pos'] == 554, \
"N_feature_pos must be equal to 554"
print(df.T)
print(darkgreen("\nGDSCTools seems to be installed properly"))
return
if options.save_settings:
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
an.settings.to_json(options.save_settings)
print('Save a default parameter set in %s' % options.save_settings)
return
if options.license is True:
print(gdsctools.license)
return
if options.summary is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
print(an)
return
if options.print_tissues is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
tissues = an.tissue_factor
try:
tissues = tissues.sort_values('Tissue Factor').unique()
except:
tissues = tissues.sort(inplace=False).unique()
for name in tissues:
print(name)
return
if options.print_drugs is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.drugIds))))
return
if options.print_features is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.feature_names))))
return
# -----------------------------------------------------------------
# --------------------------------------------------- real analysis
# -----------------------------------------------------------------
# dispatcher to the functions according to the user parameters
from gdsctools import ANOVA, ANOVAReport
anova = ANOVA(options.input_ic50,
options.input_features,
options.input_drug,
low_memory=not options.fast)
anova = _set_settings(anova, options)
if options.drug and options.drug not in anova.ic50.df.columns:
print(red("Invalid Drug. Try --print-drug-names"))
sys.exit(1)
if options.drug is not None and options.feature is not None:
print_color("ODOF mode", purple)
anova_one_drug_one_feature(anova, options)
elif options.drug is not None:
print_color("ODAF mode", purple)
anova_one_drug(anova, options)
else: # analyse everything
if options.feature is None:
print_color("ADAF mode", purple)
else:
print_color("ADOF mode", purple)
anova_all(anova, options)
if options.onweb is False and options.no_html is False:
msg = "\nNote that a directory {} was created and files saved into it"
print(purple(msg.format(options.directory)))
return
def anova_pipeline(args=None):
"""This function is used by the standalone application called
**gdsctools_anova**
Type::
gdsctools_anova --help
to get some help.
"""
msg = "Welcome to GDSCTools standalone"
print_color(msg, purple, underline=True)
# Keep the argument args as None by default to
# allow testing e.g., in nosetests
if args is None:
args = sys.argv[:]
elif len(args) == 1:
args += ['--help']
user_options = ANOVAOptions(prog="gdsctools_anova")
try:
options = user_options.parse_args(args[1:])
except SystemExit:
return
# -----------------------------------------------------------------
# ---------------------------------------- options without analysis
# -----------------------------------------------------------------
if options.version is True:
print("This is version %s of gdsctools_anova" % gdsctools.version)
return
if options.testing is True:
print('Testing mode:')
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
df = an.anova_one_drug_one_feature('Drug_1047_IC50', 'TP53_mut')
assert df.loc[1,'N_FEATURE_pos'] == 554, \
"N_feature_pos must be equal to 554"
print(df.T)
print(darkgreen("\nGDSCTools seems to be installed properly"))
return
if options.save_settings:
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
an.settings.to_json(options.save_settings)
print('Save a default parameter set in %s' % options.save_settings)
return
if options.license is True:
print(gdsctools.license)
return
if options.summary is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
print(an)
return
if options.print_tissues is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
tissues = an.tissue_factor
try:
tissues = tissues.sort_values('Tissue Factor').unique()
except:
tissues = tissues.sort(inplace=False).unique()
for name in tissues:
print(name)
return
if options.print_drugs is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.drugIds))))
return
if options.print_features is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.feature_names))))
return
# -----------------------------------------------------------------
# --------------------------------------------------- real analysis
# -----------------------------------------------------------------
# dispatcher to the functions according to the user parameters
from gdsctools import ANOVA, ANOVAReport
anova = ANOVA(options.input_ic50, options.input_features,
options.input_drug,
low_memory=not options.fast)
anova = _set_settings(anova, options)
if options.drug and options.drug not in anova.ic50.df.columns:
print(red("Invalid Drug. Try --print-drug-names"))
sys.exit(1)
if options.drug is not None and options.feature is not None:
print_color("ODOF mode", purple)
anova_one_drug_one_feature(anova, options)
elif options.drug is not None:
print_color("ODAF mode", purple)
anova_one_drug(anova, options)
else: # analyse everything
if options.feature is None:
print_color("ADAF mode", purple)
else:
print_color("ADOF mode", purple)
anova_all(anova, options)
if options.onweb is False and options.no_html is False:
msg = "\nNote that a directory {} was created and files saved into it"
print(purple(msg.format(options.directory)))
return
def run(self, color=True):
"""Executes 'python setup.py' with the user commands on all packages. """
if color:
try:
from easydev.console import bold, red, green, \
color_terminal, nocolor, underline, purple
except:
try:
sys.path.insert(0, os.path.join('deploy', 'src', 'deploy'))
from console import bold, red, green, \
color_terminal, nocolor, underline, purple
except:
pass
if not color_terminal():
# Windows' poor cmd box doesn't understand ANSI sequences
nocolor()
else:
bold = purple = red = green = underline = str
print(bold("Running multisetup version %s" % __revision__.split()[2]))
#project_dir = self.curdir.basename()
directories = [package for package in self.packages]
print('Will process the following directories: ',)
for directory in directories:
print(bold(directory)),
#print bold(directory.basename()),
print('')
try:
for directory in directories:
try:
os.chdir(directory)
print(underline('Entering %s package'
% os.path.basename(directory)))
# % directory.basename())
except OSError as err:
print(underline('Entering %s package'
% os.path.basename(directory)))
print(red("cannot find this directory (%s)"
% os.path.basename(directory)))
print(err)
print('Python exec : ' , sys.executable)
#print underline('Entering %s package' % directory.basename())
for cmd in self.commands:
setup_command = '%s setup.py %s ' % (sys.executable,cmd)
print("\tExecuting " + setup_command + '...processing',)
#Run setup.py with user commands
outputs = None
errors = None
if self.verbose:
process = Popen(setup_command,
shell=True)
status = process.wait()
else:
process = Popen(setup_command, stdout=PIPE, stderr=PIPE,
shell=True)
#status = process.wait()
outputs, errors = process.communicate()
if process.returncode == 0:
print(green('done'))
else:
if not self.verbose:
print(red('\tFailed. ( error code %s) ' %
(process.returncode)))
os.chdir(self.curdir)
if not self.force:
raise RuntimeError()
if 'pylint' in cmd:
if outputs is not None:
for x in outputs.split('\n'):
if x.startswith('Your code has been'):
print(purple('\t%s' % x))
if 'nosetests' in cmd:
if errors is not None:
for x in errors.split('\n'):
if x.startswith('TOTAL'):
res = x.replace('TOTAL', 'Total coverage')
res = " ".join (res.split())
print(purple('\t%s' % res))
if x.startswith('Ran'):
print(purple('\t%s' % x))
if x.startswith('FAILED'):
print(purple('\t%s' % x))
else:
print(purple('all right'))
os.chdir(self.curdir)
except RuntimeError:
sys.exit()
os.chdir(self.curdir)