mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-29 02:26:59 +08:00
Push scripts into subpackages.
This commit is contained in:
John Chilton
@@ -102,6 +102,8 @@ PACKAGES = [
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]
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ENTRY_POINTS = '''
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[console_scripts]
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galaxy-main=galaxy.main:main
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galaxy-config=galaxy.config.script:main
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'''
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PACKAGE_DATA = {
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# Be sure to update MANIFEST.in for source dist.
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@@ -47,7 +47,8 @@ PACKAGES = [
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]
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ENTRY_POINTS = '''
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[console_scripts]
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gx-build-objects=galaxy.model.store.build_objects:main
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galaxy-build-objects=galaxy.model.store.build_objects:main
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galaxy-manage-db=galaxy.model.orm.scripts:manage_db
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'''
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PACKAGE_DATA = {
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# Be sure to update MANIFEST.in for source dist.
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@@ -32,10 +32,6 @@ TEST_DIR = 'tests'
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PACKAGES = []
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ENTRY_POINTS = '''
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[console_scripts]
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galaxy-paster=galaxy.util.pastescript.serve:run
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galaxy-main=galaxy.main:main
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galaxy-config=galaxy.config.script:main
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galaxy-manage-db=galaxy.model.orm.scripts:manage_db
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'''
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PACKAGE_DATA = {
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# Be sure to update MANIFEST.in for source dist.
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@@ -1,35 +0,0 @@
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from os import listdir
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from os.path import join
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from re import match
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from sys import argv
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from six.moves.configparser import ConfigParser
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def merge():
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"""
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Merges all .ini files in a specified directory into a file (defaults to
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./config/galaxy.ini ).
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"""
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if len(argv) < 2:
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message = "%s: Must specify directory to merge configuration files from." % argv[0]
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raise Exception(message)
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conf_directory = argv[1]
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conf_files = [f for f in listdir(conf_directory) if match(r'.*\.ini', f)]
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conf_files.sort()
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parser = ConfigParser()
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for conf_file in conf_files:
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parser.read([join(conf_directory, conf_file)])
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# TODO: Expand enviroment variables here, that would
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# also make Galaxy much easier to configure.
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destination = "config/galaxy.ini"
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if len(argv) > 2:
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destination = argv[2]
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parser.write(open(destination, 'w'))
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if __name__ == '__main__':
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merge()
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@@ -1,416 +0,0 @@
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#!/usr/bin/env python
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"""
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check_galaxy can be run by hand, although it is meant to run from cron
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via the check_galaxy.sh script in Galaxy's cron/ directory.
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"""
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from __future__ import print_function
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import filecmp
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import formatter
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import getopt
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import htmllib
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import os
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import socket
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import sys
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import tempfile
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import time
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import twill
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import twill.commands as tc
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# options
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if "DEBUG" in os.environ:
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debug = os.environ["DEBUG"]
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else:
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debug = False
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scripts_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
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test_data_dir = os.path.join(scripts_dir, os.pardir, "test-data")
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# what tools to run - not so pretty
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tools = {
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"gops_intersect_1":
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[
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{
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"inputs":
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(
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os.path.join(test_data_dir, "1.bed"),
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os.path.join(test_data_dir, "2.bed")
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)
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},
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{"check_file": os.path.join(test_data_dir, "gops_intersect_out.bed")},
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{
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"tool_run_options":
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{
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"input1": "1.bed",
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"input2": "2.bed",
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"min": "1",
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"returntype": ""
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}
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}
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]
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}
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# handle arg(s)
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def usage():
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sys.exit("usage: check_galaxy.py <server>")
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try:
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opts, args = getopt.getopt(sys.argv[1:], 'n')
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except getopt.GetoptError as e:
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print(str(e))
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usage()
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if len(args) < 1:
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usage()
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server = args[0]
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if server.endswith(".g2.bx.psu.edu"):
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if debug:
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print("Checking a PSU Galaxy server, using maint file")
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maint = "/errordocument/502/%s/maint" % args[0].split('.', 1)[0]
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else:
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maint = None
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new_history = False
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for o, a in opts:
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if o == "-n":
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if debug:
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print("Specified -n, will create a new history")
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new_history = True
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else:
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usage()
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# state information
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var_dir = os.path.join(os.path.expanduser('~'), ".check_galaxy", server)
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if not os.access(var_dir, os.F_OK):
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os.makedirs(var_dir, 0o700)
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# get user/pass
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login_file = os.path.join(var_dir, "login")
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try:
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f = open(login_file, 'r')
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except Exception:
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message = """Please create the file:
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%s
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This should contain a username and password to log in to Galaxy with,
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on one line, separated by whitespace, e.g.:
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check_galaxy@example.com password
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If the user does not exist, check_galaxy will create it for you.""" % login_file
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sys.exit(message)
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(username, password) = f.readline().split()
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# default timeout for twill browser is never
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socket.setdefaulttimeout(300)
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# user-agent
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tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.1)")
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tc.config('use_tidy', 0)
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class Browser(object):
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def __init__(self):
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self.server = server
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self.maint = maint
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self.tool = None
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self.tool_opts = None
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self.id = None
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self.status = None
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self.check_file = None
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self.hid = None
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self.cookie_jar = os.path.join(var_dir, "cookie_jar")
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dprint("cookie jar path: %s" % self.cookie_jar)
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if not os.access(self.cookie_jar, os.R_OK):
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dprint("no cookie jar at above path, creating")
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tc.save_cookies(self.cookie_jar)
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tc.load_cookies(self.cookie_jar)
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def get(self, path):
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tc.go("http://%s%s" % (self.server, path))
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tc.code(200)
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def reset(self):
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self.tool = None
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self.tool_opts = None
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self.id = None
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self.status = None
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self.check_file = None
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self.delete_datasets()
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self.get("/root/history")
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p = didParser()
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p.feed(tc.browser.get_html())
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if len(p.dids) > 0:
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print("Remaining datasets ids:", " ".join(p.dids))
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raise Exception("History still contains datasets after attempting to delete them")
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if new_history:
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self.get("/history/delete_current")
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tc.save_cookies(self.cookie_jar)
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def check_redir(self, url):
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try:
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tc.get_browser()._browser.set_handle_redirect(False)
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tc.go(url)
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tc.code(302)
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tc.get_browser()._browser.set_handle_redirect(True)
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dprint("%s is returning redirect (302)" % url)
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return(True)
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except twill.errors.TwillAssertionError as e:
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tc.get_browser()._browser.set_handle_redirect(True)
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dprint("%s is not returning redirect (302): %s" % (url, e))
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code = tc.browser.get_code()
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if code == 502:
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is_maint = self.check_maint()
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if is_maint:
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dprint("Galaxy is down, but a maint file was found, so not sending alert")
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sys.exit(0)
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else:
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sys.exit("Galaxy is down (code 502)")
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return(False)
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# checks for a maint file
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def check_maint(self):
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if self.maint is None:
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# dprint( "Warning: unable to check maint file for %s" % self.server )
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return(False)
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try:
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self.get(self.maint)
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return(True)
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except twill.errors.TwillAssertionError:
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return(False)
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def login(self, user, pw):
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self.get("/user/login")
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tc.fv("1", "email", user)
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tc.fv("1", "password", pw)
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tc.submit("Login")
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tc.code(200)
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if len(tc.get_browser().get_all_forms()) > 0:
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# uh ohs, fail
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p = userParser()
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p.feed(tc.browser.get_html())
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if p.no_user:
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dprint("user does not exist, will try creating")
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self.create_user(user, pw)
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elif p.bad_pw:
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raise Exception("Password is incorrect")
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else:
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raise Exception("Unknown error logging in")
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tc.save_cookies(self.cookie_jar)
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def create_user(self, user, pw):
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self.get("/user/create")
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tc.fv("1", "email", user)
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tc.fv("1", "password", pw)
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tc.fv("1", "confirm", pw)
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tc.submit("Submit")
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tc.code(200)
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if len(tc.get_browser().get_all_forms()) > 0:
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p = userParser()
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p.feed(tc.browser.get_html())
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if p.already_exists:
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raise Exception('The user you were trying to create already exists')
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def upload(self, file):
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self.get("/tool_runner/index?tool_id=upload1")
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tc.fv("1", "file_type", "bed")
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tc.formfile("1", "file_data", file)
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tc.submit("runtool_btn")
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tc.code(200)
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def runtool(self):
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self.get("/tool_runner/index?tool_id=%s" % self.tool)
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for k, v in self.tool_opts.items():
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tc.fv("1", k, v)
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tc.submit("runtool_btn")
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tc.code(200)
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def wait(self):
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sleep_amount = 1
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count = 0
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maxiter = 16
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while count < maxiter:
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count += 1
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self.get("/root/history")
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page = tc.browser.get_html()
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if page.find('<!-- running: do not change this comment, used by TwillTestCase.wait -->') > -1:
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time.sleep(sleep_amount)
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sleep_amount += 1
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else:
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break
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if count == maxiter:
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raise Exception("Tool never finished")
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def check_status(self):
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self.get("/root/history")
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p = historyParser()
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p.feed(tc.browser.get_html())
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if p.status != "ok":
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raise Exception("JOB %s NOT OK: %s" % (p.id, p.status))
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self.id = p.id
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self.status = p.status
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# return((p.id, p.status))
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def diff(self):
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self.get("/datasets/%s/display/display?to_ext=bed" % self.id)
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data = tc.browser.get_html()
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tmp = tempfile.mkstemp()
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dprint("tmp file: %s" % tmp[1])
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tmpfh = os.fdopen(tmp[0], 'w')
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tmpfh.write(data)
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tmpfh.close()
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if filecmp.cmp(tmp[1], self.check_file):
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dprint("Tool output is as expected")
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else:
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if not debug:
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os.remove(tmp[1])
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raise Exception("Tool output differs from expected")
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if not debug:
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os.remove(tmp[1])
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def delete_datasets(self):
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self.get("/root/history")
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p = didParser()
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p.feed(tc.browser.get_html())
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dids = p.dids
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for did in dids:
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self.get("/datasets/%s/delete" % did)
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def check_if_logged_in(self):
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self.get("/user?cntrller=user")
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p = loggedinParser()
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p.feed(tc.browser.get_html())
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return p.logged_in
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class userParser(htmllib.HTMLParser):
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def __init__(self):
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htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
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self.in_span = False
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self.in_div = False
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self.no_user = False
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self.bad_pw = False
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self.already_exists = False
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def start_span(self, attrs):
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self.in_span = True
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def start_div(self, attrs):
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self.in_div = True
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def end_span(self):
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self.in_span = False
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def end_div(self):
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self.in_div = False
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def handle_data(self, data):
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if self.in_span or self.in_div:
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if data == "No such user (please note that login is case sensitive)":
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self.no_user = True
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elif data == "Invalid password":
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self.bad_pw = True
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elif data == "User with that email already exists":
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self.already_exists = True
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class historyParser(htmllib.HTMLParser):
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def __init__(self):
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htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
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self.status = None
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self.id = None
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def start_div(self, attrs):
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# find the top history item
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for i in attrs:
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if i[0] == "class" and i[1].startswith("historyItemWrapper historyItem historyItem-"):
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self.status = i[1].rsplit("historyItemWrapper historyItem historyItem-", 1)[1]
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dprint("status: %s" % self.status)
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if i[0] == "id" and i[1].startswith("historyItem-"):
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self.id = i[1].rsplit("historyItem-", 1)[1]
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dprint("id: %s" % self.id)
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if self.status is not None:
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self.reset()
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class didParser(htmllib.HTMLParser):
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def __init__(self):
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htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
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self.dids = []
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def start_div(self, attrs):
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for i in attrs:
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if i[0] == "id" and i[1].startswith("historyItemContainer-"):
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self.dids.append(i[1].rsplit("historyItemContainer-", 1)[1])
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dprint("got a dataset id: %s" % self.dids[-1])
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class loggedinParser(htmllib.HTMLParser):
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def __init__(self):
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htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
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self.in_p = False
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self.logged_in = False
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def start_p(self, attrs):
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self.in_p = True
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def end_p(self):
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self.in_p = False
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def handle_data(self, data):
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if self.in_p:
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if data == "You are currently not logged in.":
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self.logged_in = False
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elif data.startswith("You are currently logged in as "):
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self.logged_in = True
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def dprint(str):
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if debug:
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print(str)
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if __name__ == "__main__":
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dprint("checking %s" % server)
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b = Browser()
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# login (or not)
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if b.check_if_logged_in():
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dprint("we are already logged in (via cookies), hooray!")
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else:
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dprint("not logged in... logging in")
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b.login(username, password)
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for tool, params in tools.items():
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check_file = ""
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# make sure history and state is clean
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b.reset()
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b.tool = tool
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# get all the tool run conditions
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for dict in params:
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for k, v in dict.items():
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if k == 'inputs':
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for file in v:
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b.upload(file)
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elif k == 'check_file':
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b.check_file = v
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elif k == 'tool_run_options':
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b.tool_opts = v
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else:
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raise Exception("Unknown key in tools dict: %s" % k)
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b.runtool()
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b.wait()
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b.check_status()
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b.diff()
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b.delete_datasets()
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# by this point, everything else has succeeded. there should be no maint.
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is_maint = b.check_maint()
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if is_maint:
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sys.exit("Galaxy is up and fully functional, but a maint file is in place.")
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sys.exit(0)
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Reference in New Issue
Block a user