from galaxy import eggs
eggs.require('SQLAlchemy')
from sqlalchemy import and_, desc, false

import galaxy.model
from base.twilltestcase import TwillTestCase
from functional import database_contexts


class TestMetadataEdit( TwillTestCase ):

    def test_00_metadata_edit( self ):
        """test_metadata_edit: Testing metadata editing"""
        sa_session = database_contexts.galaxy_context
        self.logout()
        self.login( email='test@bx.psu.edu', username='admin-user' )
        admin_user = sa_session.query( galaxy.model.User ) \
            .filter( galaxy.model.User.table.c.email == 'test@bx.psu.edu' ) \
            .one()
        self.new_history( name='Test Metadata Edit' )
        history1 = sa_session.query( galaxy.model.History ) \
            .filter( and_( galaxy.model.History.table.c.deleted == false(),
                           galaxy.model.History.table.c.user_id == admin_user.id ) ) \
            .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
            .first()
        self.upload_file( '1.bed' )
        latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
            .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
            .first()
        # Due to twill not being able to handle the permissions forms, we'll eliminate
        # DefaultHistoryPermissions prior to uploading a dataset so that the permission
        # form will not be displayed on ted edit attributes page.
        for dp in latest_hda.dataset.actions:
            sa_session.delete( dp )
            sa_session.flush()
        sa_session.refresh( latest_hda.dataset )
        self.check_history_for_string( '1.bed' )
        self.check_metadata_for_string( '1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=str( latest_hda.hid ) )
        """test editing attributes"""
        self.edit_hda_attribute_info( hda_id=str( latest_hda.id ),
                                      new_name='Testdata',
                                      new_info="Uploaded my file",
                                      new_dbkey='hg16',
                                      new_startcol='6' )
        self.check_metadata_for_string( 'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=str( latest_hda.hid ) )
        """test Auto-detecting attributes"""
        self.auto_detect_metadata( hda_id=str( latest_hda.id ) )
        self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=str( latest_hda.hid ) )
        """test converting formats"""
        self.convert_format( hda_id=str( latest_hda.id ), target_type='gff' )
        self.check_metadata_for_string( '"gff" selected="yes"', hid=str( latest_hda.hid ) )
        """test changing data type"""
        self.change_datatype( hda_id=str( latest_hda.id ), datatype='gff3' )
        self.check_metadata_for_string( 'gff3', hid=str( latest_hda.hid ) )
        self.delete_history( id=self.security.encode_id( history1.id ) )
        self.logout()

5000c54c3edf6544d18924bc4468db8c7f102e11
<mask token>


class TestMetadataEdit(TwillTestCase):
    <mask token>

<mask token>


class TestMetadataEdit(TwillTestCase):

    def test_00_metadata_edit(self):
        """test_metadata_edit: Testing metadata editing"""
        sa_session = database_contexts.galaxy_context
        self.logout()
        self.login(email='test@bx.psu.edu', username='admin-user')
        admin_user = sa_session.query(galaxy.model.User).filter(galaxy.
            model.User.table.c.email == 'test@bx.psu.edu').one()
        self.new_history(name='Test Metadata Edit')
        history1 = sa_session.query(galaxy.model.History).filter(and_(
            galaxy.model.History.table.c.deleted == false(), galaxy.model.
            History.table.c.user_id == admin_user.id)).order_by(desc(galaxy
            .model.History.table.c.create_time)).first()
        self.upload_file('1.bed')
        latest_hda = sa_session.query(galaxy.model.HistoryDatasetAssociation
            ).order_by(desc(galaxy.model.HistoryDatasetAssociation.table.c.
            create_time)).first()
        for dp in latest_hda.dataset.actions:
            sa_session.delete(dp)
            sa_session.flush()
        sa_session.refresh(latest_hda.dataset)
        self.check_history_for_string('1.bed')
        self.check_metadata_for_string(
            '1.bed uploaded file unspecified (\\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked'
            , hid=str(latest_hda.hid))
        """test editing attributes"""
        self.edit_hda_attribute_info(hda_id=str(latest_hda.id), new_name=
            'Testdata', new_info='Uploaded my file', new_dbkey='hg16',
            new_startcol='6')
        self.check_metadata_for_string(
            'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected'
            , hid=str(latest_hda.hid))
        """test Auto-detecting attributes"""
        self.auto_detect_metadata(hda_id=str(latest_hda.id))
        self.check_metadata_for_string(
            'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected'
            , hid=str(latest_hda.hid))
        """test converting formats"""
        self.convert_format(hda_id=str(latest_hda.id), target_type='gff')
        self.check_metadata_for_string('"gff" selected="yes"', hid=str(
            latest_hda.hid))
        """test changing data type"""
        self.change_datatype(hda_id=str(latest_hda.id), datatype='gff3')
        self.check_metadata_for_string('gff3', hid=str(latest_hda.hid))
        self.delete_history(id=self.security.encode_id(history1.id))
        self.logout()

<mask token>
eggs.require('SQLAlchemy')
<mask token>


class TestMetadataEdit(TwillTestCase):

    def test_00_metadata_edit(self):
        """test_metadata_edit: Testing metadata editing"""
        sa_session = database_contexts.galaxy_context
        self.logout()
        self.login(email='test@bx.psu.edu', username='admin-user')
        admin_user = sa_session.query(galaxy.model.User).filter(galaxy.
            model.User.table.c.email == 'test@bx.psu.edu').one()
        self.new_history(name='Test Metadata Edit')
        history1 = sa_session.query(galaxy.model.History).filter(and_(
            galaxy.model.History.table.c.deleted == false(), galaxy.model.
            History.table.c.user_id == admin_user.id)).order_by(desc(galaxy
            .model.History.table.c.create_time)).first()
        self.upload_file('1.bed')
        latest_hda = sa_session.query(galaxy.model.HistoryDatasetAssociation
            ).order_by(desc(galaxy.model.HistoryDatasetAssociation.table.c.
            create_time)).first()
        for dp in latest_hda.dataset.actions:
            sa_session.delete(dp)
            sa_session.flush()
        sa_session.refresh(latest_hda.dataset)
        self.check_history_for_string('1.bed')
        self.check_metadata_for_string(
            '1.bed uploaded file unspecified (\\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked'
            , hid=str(latest_hda.hid))
        """test editing attributes"""
        self.edit_hda_attribute_info(hda_id=str(latest_hda.id), new_name=
            'Testdata', new_info='Uploaded my file', new_dbkey='hg16',
            new_startcol='6')
        self.check_metadata_for_string(
            'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected'
            , hid=str(latest_hda.hid))
        """test Auto-detecting attributes"""
        self.auto_detect_metadata(hda_id=str(latest_hda.id))
        self.check_metadata_for_string(
            'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected'
            , hid=str(latest_hda.hid))
        """test converting formats"""
        self.convert_format(hda_id=str(latest_hda.id), target_type='gff')
        self.check_metadata_for_string('"gff" selected="yes"', hid=str(
            latest_hda.hid))
        """test changing data type"""
        self.change_datatype(hda_id=str(latest_hda.id), datatype='gff3')
        self.check_metadata_for_string('gff3', hid=str(latest_hda.hid))
        self.delete_history(id=self.security.encode_id(history1.id))
        self.logout()

from galaxy import eggs
eggs.require('SQLAlchemy')
from sqlalchemy import and_, desc, false
import galaxy.model
from base.twilltestcase import TwillTestCase
from functional import database_contexts


class TestMetadataEdit(TwillTestCase):

    def test_00_metadata_edit(self):
        """test_metadata_edit: Testing metadata editing"""
        sa_session = database_contexts.galaxy_context
        self.logout()
        self.login(email='test@bx.psu.edu', username='admin-user')
        admin_user = sa_session.query(galaxy.model.User).filter(galaxy.
            model.User.table.c.email == 'test@bx.psu.edu').one()
        self.new_history(name='Test Metadata Edit')
        history1 = sa_session.query(galaxy.model.History).filter(and_(
            galaxy.model.History.table.c.deleted == false(), galaxy.model.
            History.table.c.user_id == admin_user.id)).order_by(desc(galaxy
            .model.History.table.c.create_time)).first()
        self.upload_file('1.bed')
        latest_hda = sa_session.query(galaxy.model.HistoryDatasetAssociation
            ).order_by(desc(galaxy.model.HistoryDatasetAssociation.table.c.
            create_time)).first()
        for dp in latest_hda.dataset.actions:
            sa_session.delete(dp)
            sa_session.flush()
        sa_session.refresh(latest_hda.dataset)
        self.check_history_for_string('1.bed')
        self.check_metadata_for_string(
            '1.bed uploaded file unspecified (\\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked'
            , hid=str(latest_hda.hid))
        """test editing attributes"""
        self.edit_hda_attribute_info(hda_id=str(latest_hda.id), new_name=
            'Testdata', new_info='Uploaded my file', new_dbkey='hg16',
            new_startcol='6')
        self.check_metadata_for_string(
            'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected'
            , hid=str(latest_hda.hid))
        """test Auto-detecting attributes"""
        self.auto_detect_metadata(hda_id=str(latest_hda.id))
        self.check_metadata_for_string(
            'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected'
            , hid=str(latest_hda.hid))
        """test converting formats"""
        self.convert_format(hda_id=str(latest_hda.id), target_type='gff')
        self.check_metadata_for_string('"gff" selected="yes"', hid=str(
            latest_hda.hid))
        """test changing data type"""
        self.change_datatype(hda_id=str(latest_hda.id), datatype='gff3')
        self.check_metadata_for_string('gff3', hid=str(latest_hda.hid))
        self.delete_history(id=self.security.encode_id(history1.id))
        self.logout()

from galaxy import eggs
eggs.require('SQLAlchemy')
from sqlalchemy import and_, desc, false

import galaxy.model
from base.twilltestcase import TwillTestCase
from functional import database_contexts


class TestMetadataEdit( TwillTestCase ):

    def test_00_metadata_edit( self ):
        """test_metadata_edit: Testing metadata editing"""
        sa_session = database_contexts.galaxy_context
        self.logout()
        self.login( email='test@bx.psu.edu', username='admin-user' )
        admin_user = sa_session.query( galaxy.model.User ) \
            .filter( galaxy.model.User.table.c.email == 'test@bx.psu.edu' ) \
            .one()
        self.new_history( name='Test Metadata Edit' )
        history1 = sa_session.query( galaxy.model.History ) \
            .filter( and_( galaxy.model.History.table.c.deleted == false(),
                           galaxy.model.History.table.c.user_id == admin_user.id ) ) \
            .order_by( desc( galaxy.model.History.table.c.create_time ) ) \
            .first()
        self.upload_file( '1.bed' )
        latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
            .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
            .first()
        # Due to twill not being able to handle the permissions forms, we'll eliminate
        # DefaultHistoryPermissions prior to uploading a dataset so that the permission
        # form will not be displayed on ted edit attributes page.
        for dp in latest_hda.dataset.actions:
            sa_session.delete( dp )
            sa_session.flush()
        sa_session.refresh( latest_hda.dataset )
        self.check_history_for_string( '1.bed' )
        self.check_metadata_for_string( '1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=str( latest_hda.hid ) )
        """test editing attributes"""
        self.edit_hda_attribute_info( hda_id=str( latest_hda.id ),
                                      new_name='Testdata',
                                      new_info="Uploaded my file",
                                      new_dbkey='hg16',
                                      new_startcol='6' )
        self.check_metadata_for_string( 'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=str( latest_hda.hid ) )
        """test Auto-detecting attributes"""
        self.auto_detect_metadata( hda_id=str( latest_hda.id ) )
        self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=str( latest_hda.hid ) )
        """test converting formats"""
        self.convert_format( hda_id=str( latest_hda.id ), target_type='gff' )
        self.check_metadata_for_string( '"gff" selected="yes"', hid=str( latest_hda.hid ) )
        """test changing data type"""
        self.change_datatype( hda_id=str( latest_hda.id ), datatype='gff3' )
        self.check_metadata_for_string( 'gff3', hid=str( latest_hda.hid ) )
        self.delete_history( id=self.security.encode_id( history1.id ) )
        self.logout()
