def update_PDB_ihm_cross_link_restraint(model):
# Add the PDB.ihm_cross_link_restraint.pseudo_site_flag column
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_cross_link_restraint',
Column.define(
'pseudo_site_flag',
builtin_types.text,
comment=
'A flag indicating if the cross link involves a pseudo site that is not part of the model representation',
nullok=True))
# Create the foreign key PDB.ihm_cross_link_restraint.pseudo_site_flag references Vocab.pseudo_site_flag.Name
utils.create_foreign_key_if_not_exists(
model, 'PDB', 'ihm_cross_link_restraint',
'ihm_cross_link_restraint_pseudo_site_flag_fkey',
ForeignKey.define(['pseudo_site_flag'],
'Vocab',
'pseudo_site_flag', ['Name'],
constraint_names=[[
'Vocab',
'ihm_cross_link_restraint_pseudo_site_flag_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'))
# Create combo1 key
utils.create_key_if_not_exists(model, 'PDB', 'ihm_cross_link_restraint',
['RID', 'structure_id', 'id'],
'ihm_cross_link_restraint_combo1_key')
def update_PDB_ihm_related_datasets(model):
# -- add columns
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_related_datasets',
Column.define(
'transformation_id',
builtin_types.int8,
comment=
'Identifier corresponding to the transformation matrix to be applied to the derived dataset in order to transform it to the primary dataset',
nullok=True))
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_related_datasets',
Column.define('Transformation_RID',
builtin_types.text,
comment='Identifier to the transformation RID',
nullok=True))
# -- add fk
utils.create_foreign_key_if_not_exists(
model, 'PDB', 'ihm_related_datasets',
'ihm_related_datasets_ihm_data_transformation_combo2_fkey',
ForeignKey.define(
['Transformation_RID', 'transformation_id'],
'PDB',
'ihm_data_transformation', ['RID', 'id'],
constraint_names=[[
'PDB',
'ihm_related_datasets_ihm_data_transformation_combo2_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'))
def update_Data_Dictionary_Name(catalog, model):
try:
utils.create_column_if_not_exist(model, 'Vocab',
'Data_Dictionary_Name', column)
url = '/attribute/Vocab:{}/RID,Name'.format('Data_Dictionary_Name')
resp = catalog.get(url)
resp.raise_for_status()
rows = resp.json()
#print(json.dumps(rows, indent=4))
values = []
for row in rows:
values.append({
'RID': row['RID'],
'Location': location[row['Name']]
})
columns = ['RID', 'Location']
url = '/attributegroup/Vocab:{}/RID;Location'.format(
'Data_Dictionary_Name')
resp = catalog.put(url, json=values)
resp.raise_for_status()
print('Updated {}'.format('Data_Dictionary_Name'))
except:
et, ev, tb = sys.exc_info()
print('got exception "%s"' % str(ev))
print('%s' % ''.join(traceback.format_exception(et, ev, tb)))
def update_PDB_ihm_derived_distance_restraint(model):
# -- add columns
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_derived_distance_restraint',
Column.define(
'distance_threshold_mean',
builtin_types.float8,
comment='The distance threshold mean applied to the restraint',
nullok=True))
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_derived_distance_restraint',
Column.define(
'distance_threshold_esd',
builtin_types.float8,
comment=
'The estimated standard deviation of the distance threshold applied to the restraint',
nullok=True))
def update_PDB_ihm_ensemble_info(model):
# Add the PDB.ihm_ensemble_info.sub_sample_flag and PDB.ihm_ensemble_info.sub_sampling_type columns
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_ensemble_info',
Column.define(
'sub_sample_flag',
builtin_types.text,
comment=
'A flag that indicates whether the ensemble consists of sub samples',
nullok=True))
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_ensemble_info',
Column.define('sub_sampling_type',
builtin_types.text,
comment='Type of sub sampling',
nullok=True))
# Create the foreign keys
utils.create_foreign_key_if_not_exists(
model, 'PDB', 'ihm_ensemble_info',
'ihm_ensemble_info_sub_sample_flag_fkey',
ForeignKey.define(['sub_sample_flag'],
'Vocab',
'sub_sample_flag', ['Name'],
constraint_names=[[
'Vocab', 'ihm_ensemble_info_sub_sample_flag_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'))
utils.create_foreign_key_if_not_exists(
model, 'PDB', 'ihm_ensemble_info',
'ihm_ensemble_info_sub_sampling_type_fkey',
ForeignKey.define(['sub_sampling_type'],
'Vocab',
'sub_sampling_type', ['Name'],
constraint_names=[[
'Vocab',
'ihm_ensemble_info_sub_sampling_type_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'))
utils.create_key_if_not_exists(model, 'PDB', 'ihm_ensemble_info',
['RID', 'structure_id', 'ensemble_id'],
'ihm_ensemble_info_combo1_key')
def main(server_name, catalog_id, credentials):
server = DerivaServer('https', server_name, credentials)
catalog = server.connect_ermrest(catalog_id)
catalog.dcctx['cid'] = 'oneoff/model'
model = catalog.getCatalogModel()
utils.alter_on_update_fkey_if_exist(model, 'PDB', 'Entry_Related_File', 'Entry_Related_File_File_Type_fkey', 'CASCADE')
utils.create_column_if_not_exist(model, 'PDB', 'ihm_starting_computational_models',
Column.define(
'External_Files_RID',
builtin_types.text,
comment='Identifier to the external files RID',
nullok=True
))
utils.create_column_if_not_exist(model, 'PDB', 'ihm_starting_computational_models',
Column.define(
'Software_RID',
builtin_types.text,
comment='Identifier to the software RID',
nullok=True
))
utils.create_column_if_not_exist(model, 'PDB', 'ihm_interface_residue_feature',
Column.define(
'Dataset_List_RID',
builtin_types.text,
comment='Identifier to the dataset list RID',
nullok=True
))
utils.create_column_if_not_exist(model, 'PDB', 'ihm_derived_distance_restraint',
Column.define(
'Dataset_List_RID',
builtin_types.text,
comment='Identifier to the dataset list RID',
nullok=True
))
utils.create_column_if_not_exist(model, 'PDB', 'ihm_geometric_object_distance_restraint',
Column.define(
'Dataset_List_RID',
builtin_types.text,
comment='Identifier to the dataset list RID',
nullok=True
))
utils.rename_fkey_if_exist(model, 'PDB', 'ihm_starting_computational_models', 'ihm_starting_computational_models_script_file_id_fkey', 'ihm_starting_computational_models_script_file_id_fk')
utils.rename_fkey_if_exist(model, 'PDB', 'ihm_starting_computational_models', 'ihm_starting_computational_models_software_id_fkey', 'ihm_starting_computational_models_software_id_fk')
utils.rename_fkey_if_exist(model, 'PDB', 'ihm_interface_residue_feature', 'ihm_interface_residue_feature_dataset_list_id_fkey', 'ihm_interface_residue_feature_dataset_list_id_fk')
utils.rename_fkey_if_exist(model, 'PDB', 'ihm_derived_distance_restraint', 'ihm_derived_distance_restraint_dataset_list_id_fkey', 'ihm_derived_distance_restraint_dataset_list_id_fk')
utils.rename_fkey_if_exist(model, 'PDB', 'ihm_geometric_object_distance_restraint', 'ihm_geometric_object_distance_restraint_dataset_list_id_fkey', 'ihm_geometric_object_distance_restraint_dataset_list_id_fk')
utils.create_key_if_not_exists(model, 'PDB', 'ihm_dataset_list', ['RID', 'id'], 'ihm_dataset_list_combo2_key')
model = catalog.getCatalogModel()
utils.create_foreign_key_if_not_exists(model, 'PDB', 'ihm_starting_computational_models', 'ihm_starting_computational_models_script_file_id_fkey',
ForeignKey.define(['External_Files_RID', 'script_file_id'], 'PDB', 'ihm_external_files', ['RID', 'id'],
constraint_names=[ ['PDB', 'ihm_starting_computational_models_script_file_id_fkey'] ],
on_update='CASCADE',
on_delete='NO ACTION')
)
model = catalog.getCatalogModel()
utils.create_foreign_key_if_not_exists(model, 'PDB', 'ihm_starting_computational_models', 'ihm_starting_computational_models_software_id_fkey',
ForeignKey.define(['Software_RID', 'software_id'], 'PDB', 'software', ['RID', 'pdbx_ordinal'],
constraint_names=[ ['PDB', 'ihm_starting_computational_models_software_id_fkey'] ],
on_update='CASCADE',
on_delete='NO ACTION')
)
model = catalog.getCatalogModel()
utils.create_foreign_key_if_not_exists(model, 'PDB', 'ihm_interface_residue_feature', 'ihm_interface_residue_feature_dataset_list_id_fkey',
ForeignKey.define(['Dataset_List_RID', 'dataset_list_id'], 'PDB', 'ihm_dataset_list', ['RID', 'id'],
constraint_names=[ ['PDB', 'ihm_interface_residue_feature_dataset_list_id_fkey'] ],
on_update='CASCADE',
on_delete='NO ACTION')
)
model = catalog.getCatalogModel()
utils.create_foreign_key_if_not_exists(model, 'PDB', 'ihm_derived_distance_restraint', 'ihm_derived_distance_restraint_dataset_list_id_fkey',
ForeignKey.define(['Dataset_List_RID', 'dataset_list_id'], 'PDB', 'ihm_dataset_list', ['RID', 'id'],
constraint_names=[ ['PDB', 'ihm_derived_distance_restraint_dataset_list_id_fkey'] ],
on_update='CASCADE',
on_delete='NO ACTION')
)
model = catalog.getCatalogModel()
utils.create_foreign_key_if_not_exists(model, 'PDB', 'ihm_geometric_object_distance_restraint', 'ihm_geometric_object_distance_restraint_dataset_list_id_fkey',
ForeignKey.define(['Dataset_List_RID', 'dataset_list_id'], 'PDB', 'ihm_dataset_list', ['RID', 'id'],
constraint_names=[ ['PDB', 'ihm_geometric_object_distance_restraint_dataset_list_id_fkey'] ],
on_update='CASCADE',
on_delete='NO ACTION')
)
def update_PDB_ihm_pseudo_site_feature(model):
# Drop fkeys from ihm_pseudo_site_feature
utils.drop_fkey_if_exist(model, 'PDB', 'ihm_pseudo_site_feature',
'ihm_pseudo_site_feature_feature_id_fkey')
# -- Remove columns from the PDB.ihm_pseudo_site_feature table
utils.drop_column_if_exist(model, 'PDB', 'ihm_pseudo_site_feature',
'Cartn_x')
utils.drop_column_if_exist(model, 'PDB', 'ihm_pseudo_site_feature',
'Cartn_y')
utils.drop_column_if_exist(model, 'PDB', 'ihm_pseudo_site_feature',
'Cartn_z')
utils.drop_column_if_exist(model, 'PDB', 'ihm_pseudo_site_feature',
'radius')
utils.drop_column_if_exist(model, 'PDB', 'ihm_pseudo_site_feature',
'description')
# -- add columns
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_pseudo_site_feature',
Column.define(
'pseudo_site_id',
builtin_types.int8,
comment='Pseudo site identifier corresponding to this feature',
nullok=False))
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_pseudo_site_feature',
Column.define('Pseudo_Site_RID',
builtin_types.text,
comment='Identifier to the pseudo site RID',
nullok=False))
utils.create_column_if_not_exist(
model, 'PDB', 'ihm_pseudo_site_feature',
Column.define('Feature_RID',
builtin_types.text,
comment='Identifier to the feature RID',
nullok=False))
# -- add fk
utils.create_foreign_key_if_not_exists(
model, 'PDB', 'ihm_pseudo_site_feature',
'ihm_pseudo_site_feature_ihm_pseudo_site_combo1_fkey',
ForeignKey.define(
['Pseudo_Site_RID', 'structure_id', 'pseudo_site_id'],
'PDB',
'ihm_pseudo_site', ['RID', 'structure_id', 'id'],
constraint_names=[[
'PDB', 'ihm_pseudo_site_feature_ihm_pseudo_site_combo1_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'))
utils.create_foreign_key_if_not_exists(
model,
'PDB',
'ihm_pseudo_site_feature',
'ihm_pseudo_site_feature_ihm_feature_list_combo1_fkey',
ForeignKey.define(
['Feature_RID', 'structure_id', 'feature_id'],
'PDB',
'ihm_feature_list', ['RID', 'structure_id', 'feature_id'],
constraint_names=[[
'PDB', 'ihm_pseudo_site_feature_ihm_feature_list_combo1_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'
) # won't allow delete until there is no reference
)
def main(server_name, catalog_id, credentials):
server = DerivaServer('https', server_name, credentials)
catalog = server.connect_ermrest(catalog_id)
catalog.dcctx['cid'] = "oneoff/model"
model = catalog.getCatalogModel()
"""
Add the Table_Name column to the Vocab.File_Type table
"""
utils.create_column_if_not_exist(
model, 'Vocab', 'File_Type',
Column.define('Table_Name', builtin_types.text, nullok=True))
"""
Create the new vocabulary tables
"""
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table('cross_link_partner',
'Identity of the crosslink partner'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table(
'sub_sample_flag', 'Flag for ensembles consisting of sub samples'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table('sub_sampling_type',
'Types of sub samples in ensembles'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table('pseudo_site_flag',
'Flag for crosslinks involving pseudo sites'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table(
'ihm_derived_angle_restraint_group_conditionality',
'Conditionality of a group of angles restrained together'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table('ihm_derived_angle_restraint_restraint_type',
'The type of angle restraint'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table(
'ihm_derived_dihedral_restraint_group_conditionality',
'Conditionality of a group of dihedrals restrained together'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table(
'ihm_derived_dihedral_restraint_restraint_type',
'The type of dihedral restraint'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table(
'struct_ref_seq_dif_details',
'Details about the special aspects of point differences in the alignment of the macromolecular sequence in the integrative model and the sequence in the reference database'
))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table(
'struct_ref_db_name',
'The name of the database containing reference information'))
"""
Load data into the new vocabulary tables
"""
utils.add_rows_to_vocab_table(catalog, 'cross_link_partner',
cross_link_partner_rows)
utils.add_rows_to_vocab_table(catalog, 'sub_sample_flag',
sub_sample_flag_rows)
utils.add_rows_to_vocab_table(catalog, 'sub_sampling_type',
sub_sampling_type_rows)
utils.add_rows_to_vocab_table(catalog, 'pseudo_site_flag',
pseudo_site_flag_rows)
utils.add_rows_to_vocab_table(
catalog, 'ihm_derived_angle_restraint_group_conditionality',
ihm_derived_angle_restraint_group_conditionality_rows)
utils.add_rows_to_vocab_table(
catalog, 'ihm_derived_angle_restraint_restraint_type',
ihm_derived_angle_restraint_restraint_type_rows)
utils.add_rows_to_vocab_table(
catalog, 'ihm_derived_dihedral_restraint_group_conditionality',
ihm_derived_dihedral_restraint_group_conditionality_rows)
utils.add_rows_to_vocab_table(
catalog, 'ihm_derived_dihedral_restraint_restraint_type',
ihm_derived_dihedral_restraint_restraint_type_rows)
utils.add_rows_to_vocab_table(catalog, 'struct_ref_seq_dif_details',
struct_ref_seq_dif_details_rows)
utils.add_rows_to_vocab_table(catalog, 'struct_ref_db_name',
struct_ref_db_name_rows)
"""
Load data into existing vocabulary tables
"""
utils.add_rows_to_vocab_table(catalog, 'ihm_cross_link_list_linker_type',
ihm_cross_link_list_linker_type_rows)
utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_list_data_type',
ihm_dataset_list_data_type_rows)
utils.add_rows_to_vocab_table(
catalog, 'ihm_dataset_related_db_reference_db_name',
ihm_dataset_related_db_reference_db_name_rows)
utils.add_rows_to_vocab_table(
catalog, 'ihm_derived_distance_restraint_restraint_type',
ihm_derived_distance_restraint_restraint_type_rows)
utils.add_rows_to_vocab_table(catalog, 'File_Type', File_Type_rows)
"""
Create the acls bindings
"""
utils.set_table_acl_bindings(catalog, 'Vocab', 'cross_link_partner',
acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab', 'sub_sample_flag',
acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab', 'sub_sampling_type',
acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab', 'pseudo_site_flag',
acl_bindings)
utils.set_table_acl_bindings(
catalog, 'Vocab', 'ihm_derived_angle_restraint_group_conditionality',
acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab',
'ihm_derived_angle_restraint_restraint_type',
acl_bindings)
utils.set_table_acl_bindings(
catalog, 'Vocab',
'ihm_derived_dihedral_restraint_group_conditionality', acl_bindings)
utils.set_table_acl_bindings(
catalog, 'Vocab', 'ihm_derived_dihedral_restraint_restraint_type',
acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab',
'struct_ref_seq_dif_details', acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab', 'struct_ref_db_name',
acl_bindings)