Merge remote-tracking branch 'origin/release_16.07' into backport-har…

…dening-16.10

cron/build_chrom_db.py

@@ -17,8 +17,8 @@
 import os
 import sys
 
+import requests
 from six.moves.urllib.parse import urlencode
-from six.moves.urllib.request import urlopen
 
 import parse_builds
 
@@ -36,8 +36,8 @@ def getchrominfo(url, db):
         "hgta_regionType": "",
         "position": "",
         "hgta_doTopSubmit": "get info"})
-    page = urlopen(URL)
-    for line in page:
+    page = requests.get(URL).text
+    for line in page.split('\n'):
         line = line.rstrip( "\r\n" )
         if line.startswith("#"):
             continue

cron/parse_builds.py

@@ -9,18 +9,17 @@
 import sys
 import xml.etree.ElementTree as ElementTree
 
-from six.moves.urllib.request import urlopen
+import requests
 
 
 def getbuilds(url):
     try:
-        page = urlopen(url)
+        text = requests.get(url).text
     except:
         print("#Unable to open " + url)
         print("?\tunspecified (?)")
         sys.exit(1)
 
-    text = page.read()
     try:
         tree = ElementTree.fromstring(text)
     except:

cron/parse_builds_3_sites.py

@@ -6,7 +6,7 @@
 
 import xml.etree.ElementTree as ElementTree
 
-from six.moves.urllib.request import urlopen
+import requests
 
 sites = ['http://genome.ucsc.edu/cgi-bin/',
          'http://archaea.ucsc.edu/cgi-bin/',
@@ -20,11 +20,11 @@ def main():
         trackurl = sites[i] + "hgTracks?"
         builds = []
         try:
-            page = urlopen(site)
+            text = requests.get(site).text
         except:
             print("#Unable to connect to " + site)
             continue
-        text = page.read()
+
         try:
             tree = ElementTree.fromstring(text)
         except:

lib/galaxy/datatypes/binary.py

@@ -285,10 +285,8 @@ def merge(split_files, output_file):
 
     def _is_coordinate_sorted( self, file_name ):
         """See if the input BAM file is sorted from the header information."""
-        params = [ "samtools", "view", "-H", file_name ]
-        output = subprocess.Popen( params, stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[0]
-        # find returns -1 if string is not found
-        return output.find( "SO:coordinate" ) != -1 or output.find( "SO:sorted" ) != -1
+        output = subprocess.check_output(["samtools", "view", "-H", file_name])
+        return 'SO:coordinate' in output or 'SO:sorted' in output
 
     def dataset_content_needs_grooming( self, file_name ):
         """See if file_name is a sorted BAM file"""
@@ -313,8 +311,7 @@ def dataset_content_needs_grooming( self, file_name ):
                 return False
             index_name = tempfile.NamedTemporaryFile( prefix="bam_index" ).name
             stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name
-            command = 'samtools index %s %s' % ( file_name, index_name )
-            proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
+            proc = subprocess.Popen(['samtools', 'index', file_name, index_name], stderr=open(stderr_name, 'wb'))
             proc.wait()
             stderr = open( stderr_name ).read().strip()
             if stderr:
@@ -357,8 +354,8 @@ def groom_dataset_content( self, file_name ):
         tmp_sorted_dataset_file_name_prefix = os.path.join( tmp_dir, 'sorted' )
         stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="bam_sort_stderr" ).name
         samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix  # samtools accepts a prefix, not a filename, it always adds .bam to the prefix
-        command = "samtools sort %s %s" % ( file_name, tmp_sorted_dataset_file_name_prefix )
-        proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
+        proc = subprocess.Popen(['samtools', 'sort', file_name, tmp_sorted_dataset_file_name_prefix],
+                                cwd=tmp_dir, stderr=open(stderr_name, 'wb'))
         exit_code = proc.wait()
         # Did sort succeed?
         stderr = open( stderr_name ).read().strip()

lib/galaxy/datatypes/converters/interval_to_coverage.py

@@ -133,8 +133,9 @@ def close(self):
     # Sort through a tempfile first
     temp_file = tempfile.NamedTemporaryFile(mode="r")
     environ['LC_ALL'] = 'POSIX'
-    commandline = "sort -f -n -k %d -k %d -k %d -o %s %s" % (chr_col_1 + 1, start_col_1 + 1, end_col_1 + 1, temp_file.name, in_fname)
-    subprocess.check_call(commandline, shell=True)
+    subprocess.check_call([
+        'sort', '-f', '-n', '-k', chr_col_1 + 1, '-k', start_col_1 + 1, '-k', end_col_1 + 1, '-o', temp_file.name, in_fname
+    ])
 
     coverage = CoverageWriter( out_stream=open(out_fname, "a"),
                                chromCol=chr_col_2, positionCol=position_col_2,

lib/galaxy/datatypes/converters/lped_to_pbed_converter.py

@@ -72,9 +72,9 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
     if not missval:
         print('### lped_to_pbed_converter.py cannot identify missing value in %s' % pedf)
         missval = '0'
-    cl = '%s --noweb --file %s --make-bed --out %s --missing-genotype %s' % (plink, inpedfilepath, outroot, missval)
-    p = subprocess.Popen(cl, shell=True, cwd=outfilepath)
-    p.wait()  # run plink
+    subprocess.check_call([plink, '--noweb', '--file', inpedfilepath,
+                           '--make-bed', '--out', outroot,
+                           '--missing-genotype', missval], cwd=outfilepath)
 
 
 def main():

lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py

@@ -41,8 +41,7 @@ def pruneLD(plinktasks=[], cd='./', vclbase=[]):
     for task in plinktasks:  # each is a list
         vcl = vclbase + task
         with open(plog, 'w') as sto:
-            x = subprocess.Popen(' '.join(vcl), shell=True, stdout=sto, stderr=sto, cwd=cd)
-            x.wait()
+            subprocess.check_call(vcl, stdout=sto, stderr=sto, cwd=cd)
         try:
             lplog = open(plog, 'r').readlines()
             lplog = [elem for elem in lplog if elem.find('Pruning SNP') == -1]

lib/galaxy/datatypes/converters/pbed_to_lped_converter.py

@@ -40,9 +40,7 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath, plink):
     """
     basename = os.path.split(inpedfilepath)[-1]  # get basename
     outroot = os.path.join(outfilepath, basename)
-    cl = '%s --noweb --bfile %s --recode --out %s ' % (plink, inpedfilepath, outroot)
-    p = subprocess.Popen(cl, shell=True, cwd=outfilepath)
-    p.wait()  # run plink
+    subprocess.check_call([plink, '--noweb', '--bfile', inpedfilepath, '--recode', '--out', outroot], cwd=outfilepath)
 
 
 def main():

lib/galaxy/datatypes/converters/sam_to_bam.py

@@ -68,8 +68,10 @@ def __main__():
     # convert to SAM
     unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' )
     unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' )
-    cmd = "samtools view -bS '%s' > '%s'" % ( input_filename, unsorted_bam_filename )
-    proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
+    proc = subprocess.Popen(['samtools', 'view', '-bS', input_filename],
+                            stdout=open(unsorted_bam_filename, 'wb'),
+                            stderr=open(unsorted_stderr_filename, 'wb'),
+                            cwd=tmp_dir)
     return_code = proc.wait()
     if return_code:
         stderr_target = sys.stderr
@@ -90,10 +92,13 @@ def __main__():
     # samtools changed sort command arguments (starting from version 1.3)
     samtools_version = LooseVersion(_get_samtools_version())
     if samtools_version < LooseVersion('1.0'):
-        cmd = "samtools sort -o '%s' '%s' > '%s'" % ( unsorted_bam_filename, sorting_prefix, output_filename )
+        sort_args = ['-o', unsorted_bam_filename, sorting_prefix]
     else:
-        cmd = "samtools sort -T '%s' '%s' > '%s'" % ( sorting_prefix, unsorted_bam_filename, output_filename )
-    proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
+        sort_args = ['-T', sorting_prefix, unsorted_bam_filename]
+    proc = subprocess.Popen(['samtools', 'sort'] + sort_args,
+                            stdout=open(output_filename, 'wb'),
+                            stderr=open(sorted_stderr_filename, 'wb'),
+                            cwd=tmp_dir)
     return_code = proc.wait()
 
     if return_code:

lib/galaxy/datatypes/sequence.py

@@ -8,6 +8,7 @@
 import os
 import re
 import string
+import subprocess
 import sys
 from cgi import escape
 
@@ -662,8 +663,7 @@ def process_split_file(data):
         else:
             commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count)
         for cmd in commands:
-            if 0 != os.system(cmd):
-                raise Exception("Executing '%s' failed" % cmd)
+            subprocess.check_call(cmd, shell=True)
         return True
     process_split_file = staticmethod(process_split_file)
 

lib/galaxy/datatypes/tabular.py

@@ -9,6 +9,7 @@
 import logging
 import os
 import re
+import shutil
 import subprocess
 import sys
 import tempfile
@@ -519,15 +520,12 @@ def merge( split_files, output_file):
         Multiple SAM files may each have headers. Since the headers should all be the same, remove
         the headers from files 1-n, keeping them in the first file only
         """
-        cmd = 'mv %s %s' % ( split_files[0], output_file )
-        result = os.system(cmd)
-        if result != 0:
-            raise Exception('Result %s from %s' % (result, cmd))
+        shutil.move(split_files[0], output_file)
+
         if len(split_files) > 1:
-            cmd = 'egrep -v -h "^@" %s >> %s' % ( ' '.join(split_files[1:]), output_file )
-        result = os.system(cmd)
-        if result != 0:
-            raise Exception('Result %s from %s' % (result, cmd))
+            cmd = ['egrep', '-v', '-h', '^@'] + split_files[1:] + ['>>', output_file]
+            subprocess.check_call(cmd, shell=True)
+
     merge = staticmethod(merge)
 
     # Dataproviders

lib/galaxy/datatypes/text.py

@@ -10,6 +10,8 @@
 import subprocess
 import tempfile
 
+from six.moves import shlex_quote
+
 from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
 from galaxy.datatypes.sniff import get_headers
@@ -144,13 +146,12 @@ def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to
             ofilename = ofile_handle.name
             ofile_handle.close()
             try:
-                cmd = 'ipython nbconvert --to html --template full %s --output %s' % (dataset.file_name, ofilename)
-                log.info("Calling command %s" % cmd)
-                subprocess.call(cmd, shell=True)
+                cmd = ['ipython', 'nbconvert', '--to', 'html', '--template', 'full', dataset.file_name, '--output', ofilename]
+                subprocess.check_call(cmd)
                 ofilename = '%s.html' % ofilename
-            except:
+            except subprocess.CalledProcessError:
                 ofilename = dataset.file_name
-                log.exception( 'Command "%s" failed. Could not convert the IPython Notebook to HTML, defaulting to plain text.' % cmd )
+                log.exception('Command "%s" failed. Could not convert the IPython Notebook to HTML, defaulting to plain text.', ' '.join(map(shlex_quote, cmd)))
             return open( ofilename )
 
     def set_meta( self, dataset, **kwd ):

lib/galaxy/external_services/actions.py

@@ -1,6 +1,6 @@
 # Contains actions that are used in External Services
 import logging
-from urllib import urlopen
+import requests
 from galaxy.web import url_for
 from galaxy.util.template import fill_template
 from result_handlers.basic import ExternalServiceActionResultHandler
@@ -104,7 +104,7 @@ def __init__( self, name, param_dict, url, method, target ):  # display_handler
     @property
     def content( self ):
         if self._content is None:
-            self._content = urlopen( self.url ).read()
+            self._content = requests.get(self.url).text
         return self._content
 
 

lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py

@@ -2,14 +2,14 @@
 Module for managing jobs in Pacific Bioscience's SMRT Portal and automatically transferring files
 produced by SMRT Portal.
 """
-import json
 import logging
 from string import Template
 
-from six.moves.urllib.request import urlopen
+import requests
 
 from .data_transfer import DataTransfer
 
+
 log = logging.getLogger( __name__ )
 
 __all__ = ( 'SMRTPortalPlugin', )
@@ -87,9 +87,9 @@ def check_job( self, job ):
         if job.params[ 'type' ] == 'init_transfer':
             if self._missing_params( job.params, [ 'smrt_host', 'smrt_job_id' ] ):
                 return self.job_states.INVALID
-            url = 'http://' + job.params[ 'smrt_host' ] + self.api_path + '/Jobs/' + job.params[ 'smrt_job_id' ] + '/Status'
-            r = urlopen( url )
-            status = json.loads( r.read() )
+            url = 'http://' + job.params['smrt_host'] + self.api_path + '/Jobs/' + job.params['smrt_job_id'] + '/Status'
+            r = requests.get(url)
+            status = r.json()
             # TODO: error handling: unexpected json or bad response, bad url, etc.
             if status[ 'Code' ] == 'Completed':
                 log.debug( "SMRT Portal job '%s' is Completed.  Initiating transfer." % job.params[ 'smrt_job_id' ] )

lib/galaxy/jobs/runners/pulsar.py

@@ -7,6 +7,7 @@
 import errno
 import logging
 import os
+import subprocess
 from distutils.version import LooseVersion
 from time import sleep
 
@@ -217,7 +218,7 @@ def __init_pulsar_app( self, pulsar_conf_path ):
         else:
             log.info("Loading Pulsar app configuration from %s" % pulsar_conf_path)
             with open(pulsar_conf_path, "r") as f:
-                conf.update(yaml.load(f) or {})
+                conf.update(yaml.safe_load(f) or {})
         if "job_metrics_config_file" not in conf:
             conf["job_metrics"] = self.app.job_metrics
         if "staging_directory" not in conf:
@@ -382,8 +383,7 @@ def __prepare_input_files_locally(self, job_wrapper):
         prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None)
         if prepare_input_files_cmds is not None:
             for cmd in prepare_input_files_cmds:  # run the commands to stage the input files
-                if 0 != os.system(cmd):
-                    raise Exception('Error running file staging command: %s' % cmd)
+                subprocess.check_call(cmd, shell=True)
             job_wrapper.prepare_input_files_cmds = None  # prevent them from being used in-line
 
     def _populate_parameter_defaults( self, job_destination ):

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -1,3 +1,4 @@
+import logging
 import os
 import subprocess
 import time
@@ -8,6 +9,7 @@
 
 from galaxy.util import unicodify
 
+log = logging.getLogger(__name__)
 DEFAULT_SHELL = '/bin/bash'
 
 DEFAULT_JOB_FILE_TEMPLATE = Template(
@@ -118,24 +120,27 @@ def _handle_script_integrity(path, config):
     sleep_amt = getattr(config, "check_job_script_integrity_sleep", DEFAULT_INTEGRITY_SLEEP)
     for i in range(count):
         try:
-            proc = subprocess.Popen([path], shell=True, env={"ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ": "1"})
-            proc.wait()
-            if proc.returncode == 42:
+            returncode = subprocess.call([path], env={"ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ": "1"})
+            if returncode == 42:
                 script_integrity_verified = True
                 break
 
+            log.debug("Script integrity error: returncode was %d", returncode)
+
             # Else we will sync and wait to see if the script becomes
             # executable.
             try:
                 # sync file system to avoid "Text file busy" problems.
                 # These have occurred both in Docker containers and on EC2 clusters
                 # under high load.
                 subprocess.check_call(INTEGRITY_SYNC_COMMAND)
-            except Exception:
-                pass
-            time.sleep(sleep_amt)
-        except Exception:
-            pass
+            except Exception as e:
+                log.debug("Error syncing the filesystem: %s", unicodify(e))
+
+        except Exception as exc:
+            log.debug("Script not available yet: %s", unicodify(exc))
+
+        time.sleep(sleep_amt)
 
     if not script_integrity_verified:
         raise Exception("Failed to write job script, could not verify job script integrity.")

lib/galaxy/jobs/runners/util/kill.py

@@ -1,7 +1,7 @@
 import os
+import subprocess
 from platform import system
 from time import sleep
-from subprocess import Popen
 
 try:
     from psutil import Process, NoSuchProcess
@@ -41,8 +41,8 @@ def _stock_kill_pid(pid):
 
 def __kill_windows(pid):
     try:
-        Popen("taskkill /F /T /PID %i" % pid, shell=True)
-    except Exception:
+        subprocess.check_call(['taskkill', '/F', '/T', '/PID', pid])
+    except subprocess.CalledProcessError:
         pass