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Commiting changes from central to security:

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This commit is contained in:
Guruprasad Anada
2008-12-17 11:03:27 -05:00
parent b84c1cb2ab d7bb37c95c
commit 8bd7ce669b
126 changed files with 9561 additions and 1030 deletions
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scripts/cleanup_datasets/cleanup_datasets.py
+24
View File
@@ -207,6 +207,12 @@ def purge_histories( h, d, m, cutoff_time, remove_from_disk ):
metadata_file.purged = True
metadata_file.flush()
print "%s" % metadata_file.file_name()
for lda in dataset.library_associations:
for metadata_file in m.filter( m.table.c.lda_id==lda.id ).all():
metadata_file.deleted = True
metadata_file.purged = True
metadata_file.flush()
print "%s" % metadata_file.file_name()
dataset_count += 1
try:
disk_space += file_size
@@ -275,6 +281,12 @@ def purge_datasets( d, m, cutoff_time, remove_from_disk ):
metadata_file.purged = True
metadata_file.flush()
print "%s" % metadata_file.file_name()
for lda in dataset.library_associations:
for metadata_file in m.filter( m.table.c.lda_id==lda.id ).all():
metadata_file.deleted = True
metadata_file.purged = True
metadata_file.flush()
print "%s" % metadata_file.file_name()
dataset_count += 1
try:
disk_space += file_size
@@ -310,6 +322,12 @@ def purge_dataset( dataset, d, m ):
if not shared_data.deleted:
purgable = False
break
if purgable:
# This check handles the library_folder_dataset_association approach to sharing.
for shared_data in dataset.library_associations:
if not shared_data.deleted:
purgable = False
break
if purgable:
dataset.purged = True
dataset.file_size = 0
@@ -326,6 +344,12 @@ def purge_dataset( dataset, d, m ):
metadata_file.purged = True
metadata_file.flush()
print "%s" % metadata_file.file_name()
for lda in dataset.library_associations:
for metadata_file in m.filter( m.table.c.lda_id==lda.id ).all():
metadata_file.deleted = True
metadata_file.purged = True
metadata_file.flush()
print "%s" % metadata_file.file_name()
try:
# Remove associated extra files from disk if they exist
os.unlink( dataset.extra_files_path )
scripts/get_platforms.py
+6 -3
View File
@@ -1,9 +1,12 @@
#!/usr/bin/env python
import sys
import sys, os
assert sys.version_info[:2] >= ( 2, 4 )
from eggs import get_full_platform, get_noplatform
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) )
sys.path.append( lib )
from galaxy.eggs import get_platform, get_noplatform
print get_noplatform()
print get_full_platform()
print get_platform( platform=True )
scripts/update_database/update_database_with_security_libraries.py
+179
View File
@@ -0,0 +1,179 @@
#!/usr/bin/env python
#Dan Blankenberg
"""
Backup your database before running.
Updates a pre-security/library database with necessary schema changes
and sets default roles/permissions for users and their histories and datasets.
It will reset permissions on histories and datasets if are already set.
This has been tested with Postgres, SQLite, and MySQL databases.
Due to limitations of SQLite this script is unable to add
foreign keys to existing SQLite tables (fks are ignored anyway).
Remember to backup your database before running.
"""
import sys, os, ConfigParser, tempfile
import galaxy.app, galaxy.model
import sqlalchemy
assert sys.version_info[:2] >= ( 2, 4 )
def main():
def print_warning( warning_text ):
print "\nWarning: %s\n" % ( warning_text )
print
print "The purpose of this script is to update an existing Galaxy database that does not have Library or Security settings to a version that does."
print
print "This script will set default roles for users (If run on an already updated database this will reset all datasets to initial permissions - public)."
print
print "*** It is important to backup your database before you continue. ***"
print
print "If you have backed up your database and would like to run this script, type 'yes'."
print
should_continue = raw_input("enter 'yes' to continue>")
if should_continue.lower() != "yes":
print "Script aborted by user."
sys.exit(0)
#Load Configuration from file
ini_file = sys.argv.pop(1)
conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()})
conf_parser.read(ini_file)
configuration = {}
for key, value in conf_parser.items("app:main"): configuration[key] = value
#if we don't load the tools, the app will startup much faster
empty_xml = tempfile.NamedTemporaryFile()
empty_xml.write( "<root/>" )
empty_xml.flush()
configuration['tool_config_file'] = empty_xml.name
#No need to load job runners
configuration['enable_job_running'] = False
print
print "Loading app, with database_create_tables=False, to add Columns to existing tables"
print
#we set database_create_tables to False, then load the app
configuration['database_create_tables'] = False
app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
#try to guess the database type that we have, in order to execute the proper raw SQL commands
if app.config.database_connection:
dialect = galaxy.model.mapping.guess_dialect_for_url( app.config.database_connection )
else:
dialect = "sqlite" #default dialect is sqlite
#Now we alter exisiting tables
#Unfortunately SQLAlchemy does not support this
#SQLite is very lacking in its implementation of the ALTER command, we'll do what we can...
#we cannot check with SA to see if new columns exist, so we will try and except (trying to access the table with our current SA Metadata which references missing columns will cause exception)
#user table
#this table needs to be altered differently depending on if we are using sqlite or not
if dialect == "sqlite":
try:
app.model.session.execute( "ALTER TABLE 'galaxy_user' ADD COLUMN 'deleted' BOOLEAN default 0" ) #'true' and 'false' doesn't work properly in SQLite --> both are always True (is sqlite actually storing a string here, which is always true when not empty?)
except sqlalchemy.exceptions.OperationalError, e:
print_warning( "adding column 'deleted' failed: %s" % ( e ) )
try:
app.model.session.execute( "ALTER TABLE 'galaxy_user' ADD COLUMN 'purged' BOOLEAN default 0" )
except sqlalchemy.exceptions.OperationalError, e:
print_warning( "adding column 'purged' failed: %s" % ( e ) )
else:
try:
app.model.session.execute( "ALTER TABLE galaxy_user ADD COLUMN deleted BOOLEAN default false" )
except ( sqlalchemy.exceptions.ProgrammingError, sqlalchemy.exceptions.OperationalError ), e: #Postgres and MySQL raise different Exceptions for this same failure.
print_warning( "adding column 'deleted' failed: %s" % ( e ) )
try:
app.model.session.execute( "ALTER TABLE galaxy_user ADD COLUMN purged BOOLEAN default false" )
except ( sqlalchemy.exceptions.ProgrammingError, sqlalchemy.exceptions.OperationalError ), e:
print_warning( "adding column 'purged' failed: %s" % ( e ) )
#these alters are the same, regardless if we are using sqlite
#hda table
try:
app.model.session.execute( "ALTER TABLE history_dataset_association ADD COLUMN copied_from_library_folder_dataset_association_id INTEGER" )
except ( sqlalchemy.exceptions.ProgrammingError, sqlalchemy.exceptions.OperationalError ), e:
print_warning( "adding column 'copied_from_library_folder_dataset_association_id' failed: %s" % ( e ) )
#MetadataFile table
try:
app.model.session.execute( "ALTER TABLE metadata_file ADD COLUMN lda_id INTEGER" )
except ( sqlalchemy.exceptions.ProgrammingError, sqlalchemy.exceptions.OperationalError ), e:
print_warning( "adding column 'lda_id' failed: %s" % ( e ) )
#now create indexes for new columns in user and metadata file tables
try:
i = sqlalchemy.Index( 'ix_galaxy_user_deleted', app.model.User.table.c.deleted )
i.create()
except Exception, e:
print_warning( "Adding index failed: %s" % ( e ) )
try:
i = sqlalchemy.Index( 'ix_galaxy_user_purged', app.model.User.table.c.purged )
i.create()
except Exception, e:
print_warning( "Adding index failed: %s" % ( e ) )
try:
i = sqlalchemy.Index( 'ix_metadata_file_lda_id', app.model.MetadataFile.table.c.lda_id )
i.create()
except Exception, e:
print_warning( "Adding index failed: %s" % ( e ) )
#Now we shutdown the app
app.shutdown()
del app
print
print "Columns added to tables, restarting app, with database_create_tables=True"
#We restart the app, this time with create_tables == True
configuration['database_create_tables'] = True
app = galaxy.app.UniverseApplication( global_conf = ini_file, **configuration )
##Now we add foreign key constraints as necessary for columns added above
print "Adding foreign key constraints"
if dialect != "sqlite":
try:
app.model.session.execute( "ALTER TABLE history_dataset_association ADD FOREIGN KEY (copied_from_library_folder_dataset_association_id) REFERENCES library_folder_dataset_association(id)" )
except Exception, e:
print_warning( "Adding foreign key constraint to table has failed for an unknown reason: %s" % ( e ) )
try:
app.model.session.execute( "ALTER TABLE metadata_file ADD FOREIGN KEY (lda_id) REFERENCES library_folder_dataset_association(id)" )
except Exception, e:
print_warning( "Adding foreign key constraint to table has failed for an unknown reason: %s" % ( e ) )
else:
#Can't do this in SQLite
#SQLite ignores (but parses on initial table creation) foreign key constraints anyway, see: http://www.sqlite.org/omitted.html (there is someway to set up behavior using triggers)
print_warning( "Adding foreign key constraints to table is not supported in SQLite." )
#create default permisions for users, histories, etc
print "creating private roles and setting defaults for existing users and their histories and datasets"
#Setup each user with a private role and then set their default permisions and set permisions on existing histories and datasets
for user in app.model.User.query().all():
print "Setting up user: %s." % user.email
if not app.model.security_agent.get_private_user_role( user ):
app.model.security_agent.create_private_user_role( user )
else:
print_warning( "user (%s) already has a private role, (re)setting defaults anyway" % ( user.email ) )
#set default permissions and permissions on existing items
#we will do this even if a role for the user already exists (slower, but safer)
app.model.security_agent.user_set_default_permissions( user, history=True, dataset=True, bypass_manage_permission=True )
app.model.flush()
app.shutdown()
print
print "Update finished, please review output for warnings and errors."
empty_xml.close() #close tempfile, it will automatically be deleted off system
if __name__ == "__main__":
main()
scripts/update_database/update_database_with_security_libraries.sh
+9
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@@ -0,0 +1,9 @@
#!/bin/sh
# This script must be executed from the $UNIVERSE_HOME directory
# e.g., sh ./scripts/update_database/update_database_with_security_libraries.sh
. ./scripts/get_python.sh
. ./setup_paths.sh
$GALAXY_PYTHON ./scripts/update_database/update_database_with_security_libraries.py ./universe_wsgi.ini $@