Remove egg cruft from scripts/

scripts/api/common.py

@@ -7,13 +7,6 @@ import os
 import sys
 import urllib2
 
-new_path = [ os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, 'lib' ) ]
-new_path.extend( sys.path[1:] )
-sys.path = new_path
-
-from galaxy import eggs
-eggs.require( "pycrypto" )
-
 from Crypto.Cipher import Blowfish
 
 log = logging.getLogger( __name__ )

scripts/check_galaxy.py

@@ -97,8 +97,6 @@ If the user does not exist, check_galaxy will create it for you.""" % login_file
 # find/import twill
 lib_dir = os.path.join( scripts_dir, os.pardir, "lib" )
 sys.path.insert( 1, lib_dir )
-from galaxy import eggs
-eggs.require( "twill" )
 import twill
 import twill.commands as tc
 

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -49,11 +49,8 @@ from time import strftime
 
 from cleanup_datasets import CleanupDatasetsApplication
 
-from galaxy import eggs
-eggs.require('SQLAlchemy')
 import sqlalchemy as sa
 from sqlalchemy import and_, false
-eggs.require("Mako")
 from mako.template import Template
 
 import galaxy.config

scripts/cleanup_datasets/cleanup_datasets.py

@@ -10,16 +10,14 @@ from datetime import datetime, timedelta
 from optparse import OptionParser
 from time import strftime
 
-new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-new_path.extend( sys.path[1:] )  # remove scripts/ from the path
-sys.path = new_path
-
-from galaxy import eggs
-eggs.require('SQLAlchemy')
 import sqlalchemy as sa
 from sqlalchemy import and_, false, null, true
 from sqlalchemy.orm import eagerload
 
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] )  # remove scripts/ from the path
+sys.path = new_path
+
 import galaxy.config
 import galaxy.model.mapping
 from galaxy.exceptions import ObjectNotFound

scripts/cleanup_datasets/pgcleanup.py

@@ -17,10 +17,7 @@ from optparse import OptionParser
 galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
 sys.path.insert(0, os.path.join(galaxy_root, 'lib'))
 
-from galaxy import eggs
-eggs.require('psycopg2')
 import psycopg2
-eggs.require('SQLAlchemy')
 from sqlalchemy.engine.url import make_url
 
 import galaxy.config

scripts/data_libraries/build_lucene_index.py

@@ -20,11 +20,8 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
 import galaxy.model.mapping
 from galaxy import config, model
-import pkg_resources
-pkg_resources.require( "SQLAlchemy >= 0.4" )
 
 def main( ini_file ):
     sa_session, gconfig = get_sa_session( ini_file )

scripts/data_libraries/build_whoosh_index.py

@@ -14,12 +14,9 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
 
 # Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether search is enabled.
 try:
-    eggs.require( "Whoosh" )
-
     from whoosh.filedb.filestore import FileStorage
     from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT
     from whoosh.index import Index

scripts/db_shell.py

@@ -22,10 +22,6 @@ sys.path = new_path
 
 from galaxy.model.orm.scripts import get_config
 
-from galaxy import eggs
-eggs.require( "decorator" )
-eggs.require( "Tempita" )
-eggs.require( "SQLAlchemy" )
 
 db_url = get_config( sys.argv )['db_url']
 

scripts/drmaa_external_killer.py

@@ -9,12 +9,6 @@ import os
 import pwd
 import sys
 
-new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-new_path.extend( sys.path[1:] )  # remove scripts/ from the path
-sys.path = new_path
-
-from galaxy import eggs
-eggs.require("drmaa")
 import drmaa
 
 

scripts/drmaa_external_runner.py

@@ -12,12 +12,6 @@ import os
 import pwd
 import sys
 
-new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-new_path.extend( sys.path[1:] )  # remove scripts/ from the path
-sys.path = new_path
-
-from galaxy import eggs
-eggs.require("drmaa")
 import drmaa
 
 DRMAA_jobTemplate_attributes = [ 'args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification',

scripts/egg_packager_template.py

@@ -1,245 +0,0 @@
-#!/usr/bin/env python
-
-# Configure stdout logging
-
-import glob
-import HTMLParser
-import logging
-import os
-import re
-import shutil
-import sys
-import urllib
-import urllib2
-import zipfile
-
-log = logging.getLogger()
-log.setLevel( 10 )
-log.addHandler( logging.StreamHandler( sys.stdout ) )
-
-# Fake pkg_resources
-
-macosVersionString = re.compile(r"macosx-(\d+)\.(\d+)-(.*)")
-darwinVersionString = re.compile(r"darwin-(\d+)\.(\d+)\.(\d+)-(.*)")
-solarisVersionString = re.compile(r"solaris-(\d)\.(\d+)-(.*)")
-
-
-def compatible_platforms(provided, required):
-    """Can code for the `provided` platform run on the `required` platform?
-
-    Returns true if either platform is ``None``, or the platforms are equal.
-
-    XXX Needs compatibility checks for Linux and other unixy OSes.
-    """
-    if provided is None or required is None or provided == required:
-        return True  # easy case
-
-    # Mac OS X special cases
-    reqMac = macosVersionString.match(required)
-    if reqMac:
-        provMac = macosVersionString.match(provided)
-
-        # is this a Mac package?
-        if not provMac:
-            # this is backwards compatibility for packages built before
-            # setuptools 0.6. All packages built after this point will
-            # use the new macosx designation.
-            provDarwin = darwinVersionString.match(provided)
-            if provDarwin:
-                dversion = int(provDarwin.group(1))
-                macosversion = "%s.%s" % (reqMac.group(1), reqMac.group(2))
-                if dversion == 7 and macosversion >= "10.3" or \
-                        dversion == 8 and macosversion >= "10.4":
-
-                    # import warnings
-                    # warnings.warn("Mac eggs should be rebuilt to "
-                    #    "use the macosx designation instead of darwin.",
-                    #    category=DeprecationWarning)
-                    return True
-            return False    # egg isn't macosx or legacy darwin
-
-        # are they the same major version and machine type?
-        if provMac.group(1) != reqMac.group(1) or \
-                provMac.group(3) != reqMac.group(3):
-            return False
-
-        # is the required OS major update >= the provided one?
-        if int(provMac.group(2)) > int(reqMac.group(2)):
-            return False
-
-        return True
-
-    # Solaris' special cases
-    reqSol = solarisVersionString.match(required)
-    if reqSol:
-        provSol = solarisVersionString.match(provided)
-        if not provSol:
-            return False
-        if provSol.group(1) != reqSol.group(1) or \
-                provSol.group(3) != reqSol.group(3):
-            return False
-        if int(provSol.group(2)) > int(reqSol.group(2)):
-            return False
-        return True
-
-    # XXX Linux and other platforms' special cases should go here
-    return False
-
-EGG_NAME = re.compile(
-    r"(?P<name>[^-]+)"
-    r"( -(?P<ver>[^-]+) (-py(?P<pyver>[^-]+) (-(?P<plat>.+))? )? )?",
-    re.VERBOSE | re.IGNORECASE
-).match
-
-
-class Distribution( object ):
-    def __init__( self, egg_name, project_name, version, py_version, platform ):
-        self._egg_name = egg_name
-        self.project_name = project_name
-        if project_name is not None:
-            self.project_name = project_name.replace( '-', '_' )
-        self.version = version
-        if version is not None:
-            self.version = version.replace( '-', '_' )
-        self.py_version = py_version
-        self.platform = platform
-        self.location = os.path.join( tmpd, egg_name ) + '.egg'
-
-    def egg_name( self ):
-        return self._egg_name
-
-    @classmethod
-    def from_filename( cls, basename ):
-        project_name, version, py_version, platform = [None] * 4
-        basename, ext = os.path.splitext(basename)
-        if ext.lower() == '.egg':
-            match = EGG_NAME( basename )
-            if match:
-                project_name, version, py_version, platform = match.group( 'name', 'ver', 'pyver', 'plat' )
-        return cls( basename, project_name, version, py_version, platform )
-
-
-class pkg_resources( object ):
-    pass
-
-pkg_resources.Distribution = Distribution
-
-# Fake galaxy.eggs
-
-env = None
-
-
-def get_env():
-    return None
-
-
-class URLRetriever( urllib.FancyURLopener ):
-    def http_error_default( *args ):
-        urllib.URLopener.http_error_default( *args )
-
-
-class Egg( object ):
-    def __init__( self, distribution ):
-        self.url = url + '/' + distribution.project_name.replace( '-', '_' )
-        self.dir = tmpd
-        self.distribution = distribution
-
-    def set_distribution( self ):
-        pass
-
-    def unpack_if_needed( self ):
-        pass
-
-    def remove_doppelgangers( self ):
-        pass
-
-    def fetch( self, requirement ):
-        """
-        fetch() serves as the install method to pkg_resources.working_set.resolve()
-        """
-        def find_alternative():
-            """
-            Some platforms (e.g. Solaris) support eggs compiled on older platforms
-            """
-            class LinkParser( HTMLParser.HTMLParser ):
-                """
-                Finds links in what should be an Apache-style directory index
-                """
-                def __init__( self ):
-                    HTMLParser.HTMLParser.__init__( self )
-                    self.links = []
-
-                def handle_starttag( self, tag, attrs ):
-                    if tag == 'a' and 'href' in dict( attrs ):
-                        self.links.append( dict( attrs )['href'] )
-            parser = LinkParser()
-            try:
-                parser.feed( urllib2.urlopen( self.url + '/' ).read() )
-            except urllib2.HTTPError, e:
-                if e.code == 404:
-                    return None
-            parser.close()
-            for link in parser.links:
-                file = urllib.unquote( link ).rsplit( '/', 1 )[-1]
-                tmp_dist = pkg_resources.Distribution.from_filename( file )
-                if tmp_dist.platform is not None and \
-                        self.distribution.project_name == tmp_dist.project_name and \
-                        self.distribution.version == tmp_dist.version and \
-                        self.distribution.py_version == tmp_dist.py_version and \
-                        compatible_platforms( tmp_dist.platform, self.distribution.platform ):
-                    return file
-            return None
-        if self.url is None:
-            return None
-        alternative = None
-        try:
-            url = self.url + '/' + self.distribution.egg_name() + '.egg'
-            URLRetriever().retrieve( url, self.distribution.location )
-            log.debug( "Fetched %s" % url )
-        except IOError, e:
-            if e[1] == 404 and self.distribution.platform != py:
-                alternative = find_alternative()
-                if alternative is None:
-                    return None
-            else:
-                return None
-        if alternative is not None:
-            try:
-                url = '/'.join( ( self.url, alternative ) )
-                URLRetriever().retrieve( url, os.path.join( self.dir, alternative ) )
-                log.debug( "Fetched %s" % url )
-            except IOError, e:
-                return None
-            self.platform = alternative.split( '-', 2 )[-1].rsplit( '.egg', 1 )[0]
-            self.set_distribution()
-        self.unpack_if_needed()
-        self.remove_doppelgangers()
-        global env
-        env = get_env()  # reset the global Environment object now that we've obtained a new egg
-        return self.distribution
-
-
-def create_zip():
-    fname = 'galaxy_eggs-%s.zip' % platform
-    z = zipfile.ZipFile( fname, 'w', zipfile.ZIP_STORED )
-    for egg in glob.glob( os.path.join( tmpd, '*.egg' ) ):
-        z.write( egg, 'eggs/' + os.path.basename( egg ) )
-    z.close()
-    print 'Egg package is in %s' % fname
-    print "To install the eggs, please copy this file to your Galaxy installation's root"
-    print "directory and unpack with:"
-    print "  unzip %s" % fname
-
-
-def clean():
-    shutil.rmtree( tmpd )
-
-import tempfile
-tmpd = tempfile.mkdtemp()
-
-failures = []
-platform = None
-py = None
-url = None
-
-# Automatically generated egg definitions follow

scripts/functional_tests.py

@@ -16,20 +16,8 @@ sys.path = new_path
 from base.test_logging import logging_config_file
 from base.tool_shed_util import parse_tool_panel_config
 
-from galaxy import eggs
 from galaxy.util.properties import load_app_properties
 
-eggs.require( "nose" )
-eggs.require( "NoseHTML" )
-eggs.require( "NoseTestDiff" )
-eggs.require( "Paste" )
-eggs.require( "PasteDeploy" )
-eggs.require( "Cheetah" )
-
-# this should not be required, but it is under certain conditions, thanks to this bug:
-# http://code.google.com/p/python-nose/issues/detail?id=284
-eggs.require( "pysqlite" )
-
 import logging
 import os.path
 import time

scripts/manage_db.py

@@ -8,15 +8,6 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] )  # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
-
-eggs.require( "decorator" )
-eggs.require( "Tempita" )
-eggs.require( "SQLAlchemy" )
-eggs.require( "six" )  # Required by sqlalchemy-migrate
-eggs.require( "sqlparse" )  # Required by sqlalchemy-migrate
-eggs.require( "sqlalchemy_migrate" )
-
 from migrate.versioning.shell import main
 
 from galaxy.model.orm.scripts import get_config

scripts/manage_tools.py

@@ -6,19 +6,9 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] )  # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
-
-eggs.require( "SQLAlchemy" )
-eggs.require( "decorator" )
-eggs.require( "Tempita " )
-eggs.require( "six" )  # Required by sqlalchemy-migrate
-eggs.require( "sqlparse" )  # Required by sqlalchemy-migrate
-eggs.require( "sqlalchemy-migrate" )
-
 from migrate.versioning.shell import main
 from ConfigParser import SafeConfigParser
 
-from galaxy.model.orm.scripts import require_dialect_egg
 from galaxy.model.orm.scripts import read_config_file_arg
 from galaxy.util.properties import load_app_properties
 
@@ -46,6 +36,4 @@ elif "database_file" in properties:
 else:
     db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
 
-require_dialect_egg( db_url )
-
 main( repository=repo, url=db_url )

scripts/nosetests.py

@@ -4,14 +4,6 @@
 import os
 import sys
 
-new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-new_path.extend( sys.path[1:] )
-sys.path = new_path
-
-from galaxy import eggs
-eggs.require( 'nose' )
-eggs.require( 'NoseHTML' )
-
 from pkg_resources import load_entry_point
 
 assert sys.version_info[:2] >= ( 2, 4 )

scripts/others/incorrect_gops_jobs.py

@@ -4,13 +4,10 @@ Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gop
 wherein the second dataset doesn't have chr, start and end in standard columns 1, 2 and 3.
 """
 
-from galaxy import eggs
 import sys, os, ConfigParser, tempfile
 import galaxy.app
 import galaxy.model.mapping
-import pkg_resources
-        
-pkg_resources.require( "SQLAlchemy >= 0.4" )
+
 import sqlalchemy as sa
 
 assert sys.version_info[:2] >= ( 2, 4 )

scripts/others/incorrect_gops_join_jobs.py

@@ -3,13 +3,10 @@
 Fetch gops_join wherein the use specified minimum coverage is not 1.
 """
 
-from galaxy import eggs
 import sys, os, ConfigParser, tempfile
 import galaxy.app
 import galaxy.model.mapping
-import pkg_resources
-        
-pkg_resources.require( "SQLAlchemy >= 0.4" )
+
 import sqlalchemy as sa
 
 assert sys.version_info[:2] >= ( 2, 4 )

scripts/paster.py

@@ -19,14 +19,9 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] )  # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
-
 if 'LOG_TEMPFILES' in os.environ:
     from log_tempfile import TempFile
     _log_tempfile = TempFile()
 
-eggs.require( "Paste" )
-eggs.require( "PasteDeploy" )
-
 from galaxy.util.pastescript import serve
 serve.run()

scripts/summarize_timings.py

@@ -3,21 +3,12 @@ from __future__ import print_function
 import os
 import sys
 
-new_path = [ os.path.join( os.path.dirname(__file__), os.pardir, "lib" ) ]
-new_path.extend( sys.path[1:] )  # remove scripts/ from the path
-sys.path = new_path
-
 try:
     from argparse import ArgumentParser
 except ImportError:
     ArgumentParser = None
 import re
 
-try:
-    from galaxy import eggs
-    eggs.require("numpy")
-except ImportError:
-    pass
 import numpy
 
 

scripts/tool_shed/build_ts_whoosh_index.py

@@ -26,9 +26,6 @@ from galaxy.webapps.tool_shed import config
 from galaxy.webapps.tool_shed import model
 from galaxy.tools.loader_directory import load_tool_elements_from_path
 
-from galaxy import eggs
-eggs.require( "SQLAlchemy" )
-eggs.require( "Whoosh" )
 from whoosh.filedb.filestore import FileStorage
 from whoosh.fields import Schema, STORED, TEXT
 

scripts/tool_shed/migrate_tools_to_repositories.py

@@ -27,9 +27,6 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "psycopg2" )
 import psycopg2
 
 import galaxy.webapps.tool_shed.app

scripts/tools/maf/check_loc_file.py

@@ -1,8 +1,6 @@
 #Dan Blankenberg
 #This script checks maf_index.loc file for inconsistencies between what is listed as available and what is really available.
 #Make sure that required dependencies (e.g. galaxy_root/lib and galaxy_root/eggs) are included in your PYTHONPATH
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
 import bx.align.maf
 from galaxy.tools.util import maf_utilities
 import sys

scripts/transfer.py

@@ -9,24 +9,18 @@ import os, sys, optparse, ConfigParser, socket, SocketServer, threading, logging
 galaxy_root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir ) )
 sys.path.insert( 0, os.path.abspath( os.path.join( galaxy_root, 'lib' ) ) )
 
-from galaxy import eggs
-
 try:
     import pexpect
 except ImportError:
     pexpect = None
 
-eggs.require( "SQLAlchemy >= 0.4" )
-
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from galaxy.model.mapping import load_egg_for_url
+from daemon import DaemonContext
 
 import galaxy.model
 from galaxy.util import json, bunch
 
-eggs.require( 'python_daemon' )
-from daemon import DaemonContext
 
 PEXPECT_IMPORT_MESSAGE = ('The Python pexpect package is required to use this '
                           'feature, please install it')
@@ -88,7 +82,6 @@ class GalaxyApp( object ):
             dburl = self.config.get( 'app:main', 'database_connection' )
         except ConfigParser.NoOptionError:
             dburl = default_dburl
-        load_egg_for_url( dburl )
         engine = create_engine( dburl )
         metadata = MetaData( engine )
         self.sa_session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )

scripts/update_shed_config_path.py

@@ -6,8 +6,6 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] )
 sys.path = new_path
 
-from galaxy import eggs
-eggs.require('SQLAlchemy')
 from sqlalchemy import create_engine, MetaData
 from sqlalchemy.orm import scoped_session, sessionmaker
 
@@ -41,25 +39,6 @@ def create_database( config_file ):
         exit(1)
 
     '''Initialize the database file.'''
-    dialect_to_egg = {
-        "sqlite" : "pysqlite>=2",
-        "postgres" : "psycopg2",
-        "postgresql" : "psycopg2",
-        "mysql" : "MySQL_python"
-    }
-    dialect = ( database_connection.split( ':', 1 ) )[0]
-    try:
-        egg = dialect_to_egg[ dialect ]
-        try:
-            eggs.require( egg )
-            print( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
-        except:
-            # If the module is in the path elsewhere (i.e. non-egg), it'll still load.
-            print( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
-    except KeyError:
-        # Let this go, it could possibly work with db's we don't support.
-        print( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
-
     # Initialize the database connection.
     engine = create_engine( database_connection )
     MetaData( bind=engine )