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()
"""
Create the new vocabulary tables
"""
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table('Data_Dictionary_Name', 'Dictionary names'))
utils.create_table_if_not_exist(
model, 'Vocab',
utils.define_Vocab_table('Data_Dictionary_Category',
'Dictionary categories'))
"""
Load data into the new vocabulary tables
"""
utils.add_rows_to_vocab_table(catalog, 'Data_Dictionary_Name',
Data_Dictionary_Name_rows)
utils.add_rows_to_vocab_table(catalog, 'Data_Dictionary_Category',
Data_Dictionary_Category_rows)
"""
Create the acls bindings
"""
utils.set_table_acl_bindings(catalog, 'Vocab', 'Data_Dictionary_Name',
acl_bindings)
utils.set_table_acl_bindings(catalog, 'Vocab', 'Data_Dictionary_Category',
acl_bindings)
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()
"""
Create table
"""
utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_cross_link_pseudo_site()) #Requires ihm_cross_link_restraint, ihm_model_list, ihm_pseudo_site, cross_link_partner
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()
"""
Create table
"""
utils.create_table_if_not_exist(model, 'PDB',
define_tdoc_Supported_Dictionary())
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()
"""
Create table
"""
utils.create_table_if_not_exist(model, 'PDB',
define_tdoc_ihm_data_transformation())
"""
Update existing model
"""
update_PDB_ihm_related_datasets(model) #Requires ihm_data_transformation
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()
"""
Create table
"""
utils.create_table_if_not_exist(
model, 'PDB', define_tdoc_ihm_hdx_restraint(
)) #Requires ihm_feature_list, ihm_dataset_list
"""
Update existing model
"""
update_PDB_ihm_derived_distance_restraint(model)
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()
"""
Update existing model
"""
update_PDB_ihm_ensemble_info(
model) #Requires sub_sample_flag and sub_sampling_type
"""
Create table
"""
utils.create_table_if_not_exist(
model, 'PDB', define_tdoc_ihm_ensemble_sub_sample(
)) #Requires ihm_ensemble_info, ihm_model_group, ihm_external_files
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()
#-- clean up
if False:
drop_table(catalog, 'PDB', 'ihm_derived_angle_restraint')
# new changes
if True:
model = catalog.getCatalogModel()
#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'))
#add_rows_to_Vocab_ihm_derived_angle_restraint_group_conditionality(catalog)
#add_rows_to_Vocab_ihm_derived_angle_restraint_restraint_type(catalog)
utils.create_table_if_not_exist(
model, "PDB", define_tdoc_ihm_derived_angle_restraint())
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()
"""
Create table
"""
utils.create_table_if_not_exist(model, 'PDB',
define_tdoc_ihm_pseudo_site())
"""
Create combo1/combo2 keys in existing tables
"""
utils.create_key_if_not_exists(model, 'PDB', 'ihm_model_list',
['RID', 'model_id'],
'ihm_model_list_combo2_key')
utils.create_key_if_not_exists(model, 'PDB', 'ihm_feature_list',
['RID', 'structure_id', 'feature_id'],
'ihm_feature_list_combo1_key')
utils.create_key_if_not_exists(model, 'PDB', 'ihm_dataset_list',
['RID', 'structure_id', 'id'],
'ihm_dataset_list_combo1_key')
"""
Update existing model
"""
update_PDB_ihm_cross_link_restraint(model) #Requires pseudo_site_flag
update_PDB_ihm_pseudo_site_feature(
model) #Requires ihm_pseudo_site and ihm_feature_list_combo1_key
"""
Rename primary keys
"""
utils.rename_key_if_exist(model, 'PDB', 'ihm_model_group',
'ihm_model_group_RID_id_key',
'ihm_model_group_combo2_key')
utils.rename_key_if_exist(model, 'PDB', 'ihm_external_files',
'ihm_external_files_id_RID_key',
'ihm_external_files_combo2_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()
#-- clean up
if False:
drop_table(catalog, 'PDB', 'struct_ref')
drop_table(catalog, 'PDB', 'struct_ref_seq')
drop_table(catalog, 'PDB', 'struct_ref_seq_dif')
# new changes
if True:
model = catalog.getCatalogModel()
#utils.create_table_if_not_exist(model, "Vocab", utils.define_Vocab_table('struct_ref_db_name', 'The name of the database containing reference information'))
#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'))
#add_rows_to_Vocab_struct_ref_db_name(catalog)
#add_rows_to_Vocab_struct_ref_seq_dif_details(catalog)
utils.create_key_if_not_exists(model, 'PDB', 'entity', ['RID', 'structure_id', 'id'], 'entity_combo1_key')
utils.create_table_if_not_exist(model, "PDB", define_tdoc_struct_ref())
utils.create_table_if_not_exist(model, "PDB", define_tdoc_struct_ref_seq())
utils.create_table_if_not_exist(model, "PDB", define_tdoc_struct_ref_seq_dif())
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)