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 create_study_collection_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define(
"Study_Collection",
column_defs=[
Column.define("Study", builtin_types.text, nullok=False),
Column.define("Collection", builtin_types.text, nullok=False)
],
key_defs=[Key.define(["Study", "Collection"])],
fkey_defs=[
ForeignKey.define(["Study"],
self.DATA,
"Study", ["RID"],
constraint_names=[[
self.DATA, "Study_Collection_Study_fkey"
]]),
ForeignKey.define(["Collection"],
self.DATA,
"Collection", ["RID"],
constraint_names=[[
self.DATA,
"Study_Collection_Collection_fkey"
]])
],
comment="Many-to-many associations between studies and collection")
self.try_create_table(schema, table_def)
def unit_setup(self):
# get public schema
model = self._ermrest_catalog.getCatalogModel()
public = model.schemas['public']
assert isinstance(public, Schema)
# create schema
for sname in self._unit_schema_names:
model.create_schema(Schema.define(sname))
# create table
public.create_table(
Table.define(
self.samples,
column_defs=[
Column.define(self.FIELDS[0], builtin_types.int8, False)
] + [
Column.define(field_name, builtin_types.text)
for field_name in self.FIELDS[1:]
],
key_defs=[Key.define(['id'])]))
# insert test data
pb = self._ermrest_catalog.getPathBuilder()
samples = pb.schemas['public'].tables[self.samples]
samples.insert(self.test_data)
def define_tdoc_Data_Dictionary():
table_name = 'Data_Dictionary'
comment = 'Dictionary containing all available versions.'
column_defs = [
Column.define('Name',
builtin_types.text,
comment='The name of the dictionary',
nullok=False),
Column.define('Category',
builtin_types.text,
comment='The category of the dictionary',
nullok=False),
Column.define('Version',
builtin_types.text,
comment='The version of the dictionary',
nullok=False),
Column.define('Location',
builtin_types.text,
comment='The location of the dictionary',
nullok=False)
]
key_defs = [
Key.define(['Name', 'Version'],
constraint_names=[['PDB', 'Data_Dictionary_primary_key']]),
Key.define(
['RID', 'Category'],
constraint_names=[['PDB', 'Data_Dictionary_RID_Category_key']]),
Key.define(['RID'],
constraint_names=[['PDB', 'Data_Dictionary_RID_key']]),
]
fkey_defs = [
ForeignKey.define(
['Name'],
'Vocab',
'Data_Dictionary_Name', ['Name'],
constraint_names=[['PDB', 'Data_Dictionary_Name_fkey']],
on_update='CASCADE',
on_delete='CASCADE'),
ForeignKey.define(
['Category'],
'Vocab',
'Data_Dictionary_Category', ['Name'],
constraint_names=[['PDB', 'Data_Dictionary_Category_fkey']],
on_update='CASCADE',
on_delete='CASCADE')
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def
def define_tdoc_Conform_Dictionary():
table_name = 'Conform_Dictionary'
comment = 'Dictionary associated to the export mmCIF file.'
column_defs = [
Column.define(
'Exported_mmCIF_RID',
builtin_types.text,
comment='The reference to the RID of the exported mmCIF file.',
nullok=False),
Column.define(
'Data_Dictionary_RID',
builtin_types.text,
comment=
'The reference to the RID of the Data_Dictionary version for the mmCIF file.',
nullok=False)
]
key_defs = [
Key.define(['Exported_mmCIF_RID', 'Data_Dictionary_RID'],
constraint_names=[['PDB',
'Conform_Dictionary_primary_key']]),
Key.define(['RID'],
constraint_names=[['PDB', 'Conform_Dictionary_RID_key']]),
]
fkey_defs = [
ForeignKey.define(['Exported_mmCIF_RID'],
'PDB',
'Entry_mmCIF_File', ['RID'],
constraint_names=[[
'PDB', 'Conform_Dictionary_Entry_mmCIF_File_fkey'
]],
on_update='CASCADE',
on_delete='CASCADE'),
ForeignKey.define(['Data_Dictionary_RID'],
'PDB',
'Data_Dictionary', ['RID'],
constraint_names=[[
'PDB', 'Conform_Dictionary_Data_Dictionary_fkey'
]],
on_update='CASCADE',
on_delete='CASCADE')
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def
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 create_chromosome_table(self):
schema = self.model.schemas[self.chromosome_schema]
schema.create_table(
Table.define(self.chromosome_table, [
Column.define("Name", builtin_types.text, nullok=False),
Column.define("Species", builtin_types.text, nullok=False)
],
key_defs=[Key.define(["Name", "Species"])],
fkey_defs=[
ForeignKey.define(["Species"],
self.species_schema,
self.species_table,
self.adjust_fkey_columns_case(
self.species_schema,
self.species_table, ["ID"]))
]))
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 define_tdoc_Supported_Dictionary():
table_name = 'Supported_Dictionary'
comment = 'Dictionary containing the latest supported versions.'
column_defs = [
Column.define(
'Data_Dictionary_RID',
builtin_types.text,
comment=
'The reference to the RID of the latest Data_Dictionary version',
nullok=False),
Column.define(
'Data_Dictionary_Category',
builtin_types.text,
comment=
'The reference to the category of the latest Data_Dictionary version',
nullok=False)
]
key_defs = [
Key.define(
['Data_Dictionary_Category'],
constraint_names=[['PDB', 'Supported_Dictionary_primary_key']]),
Key.define(['RID'],
constraint_names=[['PDB', 'Supported_Dictionary_RID_key']]),
]
fkey_defs = [
ForeignKey.define(
['Data_Dictionary_RID', 'Data_Dictionary_Category'],
'PDB',
'Data_Dictionary', ['RID', 'Category'],
constraint_names=[['PDB', 'Supported_Dictionary_fkey']],
on_update='CASCADE',
on_delete='CASCADE')
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def
def create_study_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define(
"Study",
column_defs=[
Column.define(
"Internal_ID",
builtin_types.text,
nullok=False,
comment="data-provider-defined unique identifier"),
Column.define("Title", builtin_types.text, nullok=False),
Column.define("Summary", builtin_types.text, nullok=False),
Column.define("Pubmed_ID", builtin_types.text, nullok=True),
],
key_defs=[Key.define(["Internal_ID"]),
Key.define(["Title"])],
comment="A sequencing or metabolomics study")
self.try_create_table(schema, table_def)
def tdef(tname):
return Table.define(
tname,
[
Column.define(
"descendant",
builtin_types.text,
nullok=False,
comment="Contained dataset in transitive relationship."
),
Column.define(
"ancestor",
builtin_types.text,
nullok=False,
comment="Containing dataset in transitive relationship."
),
],
[
Key.define(
["descendant", "ancestor"],
constraint_names=[["CFDE", tname + "_assoc_key"]]),
],
[
ForeignKey.define(
["descendant"],
"CFDE",
"dataset",
["id"],
constraint_names=[["CFDE", tname + "_descendant_fkey"]
],
),
ForeignKey.define(
["ancestor"],
"CFDE",
"dataset",
["id"],
constraint_names=[["CFDE", tname + "_ancestor_fkey"]],
),
],
comment=
"Flattened, transitive closure of nested DatasetsInDatasets relationship.",
)
def create_collection_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define("Collection",
column_defs=[
Column.define("Title",
builtin_types.text,
nullok=False),
Column.define("Description",
builtin_types.text,
nullok=False),
Column.define("Persistent_ID",
builtin_types.text,
nullok=True),
Column.define("Details",
builtin_types.markdown,
nullok=True)
],
key_defs=[Key.define(["Title"])],
comment="A collection of data")
self.try_create_table(schema, table_def)
def create_experiment_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define(
"Experiment",
column_defs=[
# rbk Notes becomes experiment Internal_ID
Column.define(
"Internal_ID",
builtin_types.text,
nullok=False,
comment="data-provider-defined unique identifier"),
Column.define("Study",
builtin_types.text,
nullok=False,
comment="study that this experiment is part of"),
Column.define("Molecule_Type",
builtin_types.text,
nullok=False),
Column.define("Cell_Count", builtin_types.int4, nullok=True),
Column.define("Notes", builtin_types.markdown, nullok=True),
],
key_defs=[
Key.define(["Internal_ID"]),
],
fkey_defs=[
ForeignKey.define(
["Study"],
self.DATA,
"Study", ["RID"],
constraint_names=[[self.DATA, "Experiment_Study_fkey"]]),
ForeignKey.define(["Molecule_Type"],
self.VOCABULARY,
"Molecule_Type", ["Name"],
constraint_names=[[
self.DATA,
"Experiment_Molecule_Type_fkey"
]])
],
comment="A sequencing or metabolomics experiment")
self.try_create_table(schema, table_def)
def create_source_file_table(self):
schema = self.model.schemas[self.source_file_schema]
schema.create_table(
Table.define(self.source_file_table, [
Column.define("Species",
builtin_types.text,
nullok=False,
comment="Species this file represents"),
Column.define(
"Downloaded_From",
builtin_types.text,
comment=
"URL of remote file (e.g., from NCBI) that this was downladoed from"
),
Column.define("File_Name", builtin_types.text, nullok=False),
Column.define("File_URL", builtin_types.text, nullok=False),
Column.define("File_Bytes", builtin_types.int4, nullok=False),
Column.define("File_MD5", builtin_types.text, nullok=False)
],
key_defs=[Key.define(["Species"])],
fkey_defs=[
ForeignKey.define(["Species"],
self.species_schema,
self.species_table,
self.adjust_fkey_columns_case(
self.species_schema,
self.species_table, ["ID"]))
]))
def create_dbxref_table(self):
schema = self.model.schemas[self.dbxref_schema]
schema.create_table(
Table.define(self.dbxref_table, [
Column.define("Gene",
builtin_types.text,
nullok=False,
comment='Gene that this identifier refers to'),
Column.define("Alternate_ID", builtin_types.text,
nullok=False),
Column.define("Alternate_Ontology",
builtin_types.text,
nullok=False,
comment='Ontology this identifier is from'),
Column.define(
"Reference_URL",
builtin_types.text,
nullok=True,
comment=
'URL to a description, in this alternate ontology, of this gene'
)
],
key_defs=[Key.define(["Gene", "Alternate_ID"])],
fkey_defs=[
ForeignKey.define(["Gene"], self.gene_schema,
self.gene_table,
self.adjust_fkey_columns_case(
self.gene_schema,
self.gene_table, ["ID"])),
ForeignKey.define(["Alternate_Ontology"],
self.ontology_schema,
self.ontology_table,
self.adjust_fkey_columns_case(
self.ontology_schema,
self.ontology_table,
["ID"]))
],
comment=
'Alternate gene identifiers from different ontologies'
))
def create_file_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define(
"File",
column_defs=[
Column.define("Replicate",
builtin_types.text,
nullok=False,
comment="Replicate that generated this file"),
Column.define("File_URI",
builtin_types.text,
nullok=False,
comment="URI for this file"),
Column.define("File_Name",
builtin_types.text,
nullok=False,
comment="Name of file when uploaded"),
Column.define("File_Size",
builtin_types.int8,
nullok=False,
comment="Size of file in bytes"),
Column.define("File_MD5",
builtin_types.text,
nullok=False,
comment="MD5 checksum of this file"),
Column.define("File_SHA256",
builtin_types.text,
nullok=False,
comment="SHA256 checksum of this file"),
Column.define("File_Type", builtin_types.text, nullok=False),
Column.define("Caption", builtin_types.text, nullok=True)
],
key_defs=[Key.define(["File_MD5"]),
Key.define(["File_URI"])],
fkey_defs=[
ForeignKey.define(
["Replicate"],
self.DATA,
"Replicate", ["RID"],
constraint_names=[[self.DATA, "File_Replicate_fkey"]]),
ForeignKey.define(
["File_Type"],
self.VOCABULARY,
"File_Type", ["Name"],
constraint_names=[[self.DATA, "File_File_Type_fkey"]])
],
comment="Data files")
self.try_create_table(schema, table_def)
def dataset_property(srctable, srccolumn):
tname = 'dataset_denorm_%s' % srccolumn.name
return (
tname,
Table.define(
tname,
[
Column.define(
"dataset", builtin_types.text, nullok=False),
Column.define(srccolumn.name, builtin_types.text,
srccolumn.nullok),
],
[
Key.define(["dataset", srccolumn.name]),
],
[
ForeignKey.define(
["dataset"],
"CFDE",
"dataset",
["id"],
constraint_names=[["CFDE",
"%s_ds_fkey" % tname]],
)
] + [
ForeignKey.define(
[srccolumn.name],
'CFDE',
fkey.referenced_columns[0].table.name,
[c.name for c in fkey.referenced_columns],
constraint_names=[['CFDE',
'%s_prop_fkey' % tname]])
for fkey in srctable.foreign_keys if {srccolumn.name}
== set([c.name for c in fkey.foreign_key_columns])
],
))
def create_ontology_table(self):
schema = self.model.schemas[self.ontology_schema]
table = schema.create_table(
Table.define_vocabulary(
self.ontology_table,
'{prefix}:{{RID}}'.format(prefix=self.curie_prefix),
key_defs=[Key.define(['Name'])],
uri_template='https://{host}/id/{{RID}}'.format(
host=self.host),
comment="Ontologies"))
table.create_column(
Column.define("Ontology_Home",
builtin_types.text,
nullok=True,
comment="Home page for this ontology"))
def make_column(cdef):
cdef = dict(cdef)
constraints = cdef.get("constraints", {})
cdef_name = cdef.pop("name")
nullok = not constraints.pop("required", False)
description = cdef.pop("description", None)
return Column.define(cdef_name,
make_type(
cdef.get("type", "string"),
cdef.get("format", "default"),
),
nullok=nullok,
comment=description,
annotations={
schema_tag: cdef,
})
def create_specimen_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define(
"Specimen",
column_defs=[
Column.define("Species", builtin_types.text, nullok=False),
Column.define("Sex", builtin_types.text, nullok=True),
Column.define("Stage",
builtin_types.text,
nullok=True,
comment="developmental stage of this specimen"),
Column.define("Anatomy", builtin_types.text, nullok=True),
Column.define(
"Assay_Type",
builtin_types.text,
nullok=False,
comment="type of assay performed on this specimen"),
Column.define(
"Internal_ID",
builtin_types.text,
nullok=True,
comment="data-provider-defined unique identifier")
],
key_defs=[Key.define(["Internal_ID"])],
fkey_defs=[
ForeignKey.define(
["Species"],
self.VOCABULARY,
"Species", ["Name"],
constraint_names=[[self.DATA, "Specimen_Species_fkey"]]),
ForeignKey.define(
["Sex"],
self.VOCABULARY,
"Sex", ["Name"],
constraint_names=[[self.DATA, "Specimen_Sex_fkey"]]),
ForeignKey.define(
["Stage"],
self.VOCABULARY,
"Stage", ["Name"],
constraint_names=[[self.DATA, "Specimen_Stage_fkey"]]),
ForeignKey.define(
["Assay_Type"],
self.VOCABULARY,
"Assay_Type", ["Name"],
constraint_names=[[self.DATA,
"Specimen_Assay_Type_fkey"]]),
ForeignKey.define(
["Anatomy"],
self.VOCABULARY,
"Anatomy", ["ID"],
constraint_names=[[self.DATA, "Specimen_Anatomy_fkey"]])
],
comment="A biospeciment")
self.try_create_table(schema, table_def)
def create_replicate_table(self):
schema = self.model.schemas[self.DATA]
table_def = Table.define(
"Replicate",
column_defs=[
Column.define(
"Experiment",
builtin_types.text,
nullok=False,
comment="Experiment that produced this replicate"),
Column.define("Biological_Replicate_Number",
builtin_types.int4,
nullok=False),
Column.define("Technical_Replicate_Number",
builtin_types.int4,
nullok=False),
Column.define("Mapped_Reads",
builtin_types.float8,
nullok=True),
Column.define("RNA_Reads", builtin_types.float8, nullok=True),
Column.define("Specimen", builtin_types.text, nullok=False),
Column.define("Description", builtin_types.text, nullok=True)
],
key_defs=[
Key.define([
"Experiment", "Biological_Replicate_Number",
"Technical_Replicate_Number"
])
],
fkey_defs=[
ForeignKey.define(
["Experiment"],
self.DATA,
"Experiment", ["RID"],
constraint_names=[[self.DATA,
"Replicate_Experiment_fkey"]]),
ForeignKey.define(
["Specimen"],
self.DATA,
"Specimen", ["RID"],
constraint_names=[[self.DATA, "Replicate_Specimen_fkey"]])
],
comment=
"A biological or technical replicate in a sequencing experiment")
self.try_create_table(schema, table_def)
def make_column(tname, cdef, configurator):
cdef = dict(cdef)
constraints = cdef.get("constraints", {})
cdef_name = cdef.pop("name")
title = cdef.get("title", None)
nullok = not constraints.pop("required", False)
default = cdef.pop("default", None)
description = cdef.pop("description", None)
annotations = {
schema_tag: cdef,
}
if title is not None:
annotations[tag.display] = {"name": title}
pre_annotations = cdef.get("deriva", {})
for k, t in tag.items():
if k in pre_annotations:
annotations[t] = pre_annotations.pop(k)
acls = acls_union(
configurator.schema_table_column_acls.get(
(schema_name, tname, cdef_name), {}),
pre_annotations.pop('acls', {}))
acl_bindings = aclbindings_merge(
configurator.schema_table_column_aclbindings.get(
(schema_name, tname, cdef_name), {}),
pre_annotations.pop('acl_bindings', {}))
return Column.define(
cdef_name,
make_type(
cdef.get("type", "string"),
cdef.get("format", "default"),
),
nullok=nullok,
default=default,
comment=description,
annotations=annotations,
acls=acls,
acl_bindings=acl_bindings,
)
def create_gene_table(self, extra_boolean_cols=[]):
schema = self.model.schemas[self.gene_schema]
common_cols = [
Column.define("Gene_Type", builtin_types.text, nullok=False),
Column.define("Species", builtin_types.text, nullok=False),
Column.define("Chromosome", builtin_types.text),
Column.define("Location",
builtin_types.text,
comment="Location on chromosome"),
Column.define(
"Source_Date",
builtin_types.date,
comment="Last-updated date reported by the gene data source")
]
for colname in extra_boolean_cols:
common_cols.append(Column.define(colname, builtin_types.boolean))
fkey_defs = [
ForeignKey.define(["Gene_Type"], self.gene_type_schema,
self.gene_type_table,
self.adjust_fkey_columns_case(["ID"])),
ForeignKey.define(["Species"], self.species_schema,
self.species_table,
self.adjust_fkey_columns_case(
self.species_schema, self.species_table,
["ID"])),
ForeignKey.define(["Chromosome"], self.chromosome_schema,
self.chromosome_table, ["RID"])
]
key_defs = [["NCBI_GeneID"]]
table = schema.create_table(
Table.define_vocabulary(
self.gene_table,
'{prefix}:{{RID}}'.format(prefix=self.curie_prefix),
column_defs=column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment="Genes"))
def define_Vocab_table(table_name, table_comment):
column_defs = [
Column.define(
"ID",
builtin_types.ermrest_curie,
comment='The preferred Compact URI (CURIE) for this term.',
nullok=False,
default="PDB:{RID}"),
Column.define("URI",
builtin_types.ermrest_uri,
nullok=False,
default="/id/{RID}",
comment="The preferred URI for this term."),
Column.define("Name", builtin_types.text, nullok=False),
Column.define("Description", builtin_types.markdown, nullok=False),
Column.define("Synonyms",
builtin_types["text[]"],
nullok=True,
comment="Alternate human-readable names for this term."),
Column.define("Owner",
builtin_types.text,
comment='Group that can update the record.',
nullok=True)
]
key_defs = [
Key.define(
["URI"],
constraint_names=[["Vocab", '{}_URI_key'.format(table_name)]]),
Key.define(
["Name"],
constraint_names=[["Vocab", '{}_Name_key'.format(table_name)]]),
Key.define(["ID"],
constraint_names=[["Vocab",
'{}_ID_key'.format(table_name)]]),
Key.define(
["RID"],
constraint_names=[["Vocab", '{}_RID_key'.format(table_name)]])
]
fkey_defs = [
ForeignKey.define(
["RCB"],
"public",
"ERMrest_Client", ["ID"],
constraint_names=[["Vocab", '{}_RCB_fkey'.format(table_name)]],
on_update="NO ACTION",
on_delete="NO ACTION"),
ForeignKey.define(
["RMB"],
"public",
"ERMrest_Client", ["ID"],
constraint_names=[["Vocab", '{}_RMB_fkey'.format(table_name)]],
on_update="NO ACTION",
on_delete="NO ACTION"),
ForeignKey.define(
["Owner"],
"public",
"Catalog_Group", ["ID"],
constraint_names=[["Vocab", '{}_Owner_fkey'.format(table_name)]],
on_update="NO ACTION",
on_delete="NO ACTION")
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=table_comment,
provide_system=True)
return table_def
def define_tdoc_ihm_hdx_restraint():
table_name = 'ihm_hdx_restraint'
comment = 'Details of restraint derived from hydrogen-deuterium (H/D) exchange experiments; can be uploaded as CSV/TSV file above; mmCIF category: ihm_hdx_restraint'
column_defs = [
Column.define('id',
builtin_types.int8,
comment='A unique id for the H/D exchange restraint',
nullok=False),
Column.define(
'feature_id',
builtin_types.int8,
comment='An identifier for the peptide / residue feature',
nullok=False),
Column.define('Feature_RID',
builtin_types.text,
comment='Identifier to the feature RID',
nullok=False),
Column.define(
'protection_factor',
builtin_types.float8,
comment=
'The value of the protection factor determined from H/D exchange experiments',
nullok=True),
Column.define(
'dataset_list_id',
builtin_types.int8,
comment=
'Identifier to the H/D exchange input data from which the restraints are derived',
nullok=False),
Column.define('Dataset_List_RID',
builtin_types.text,
comment='Identifier to the dataset list RID',
nullok=False),
Column.define(
'details',
builtin_types.text,
comment='Additional details regarding the H/D exchange restraint',
nullok=True),
Column.define('structure_id',
builtin_types.text,
comment='Structure identifier',
nullok=False),
Column.define(
'Entry_Related_File',
builtin_types.text,
comment=
'A reference to the uploaded restraint file in the table Entry_Related_File.id',
nullok=True)
]
key_defs = [
Key.define(['structure_id', 'id'],
constraint_names=[['PDB',
'ihm_hdx_restraint_primary_key']]),
Key.define(['RID'],
constraint_names=[['PDB', 'ihm_hdx_restraint_RID_key']]),
]
fkey_defs = [
ForeignKey.define(
['structure_id'],
'PDB',
'entry', ['id'],
constraint_names=[['PDB', 'ihm_hdx_restraint_structure_id_fkey']],
on_update='CASCADE',
on_delete='NO ACTION'),
ForeignKey.define(['Feature_RID', 'structure_id', 'feature_id'],
'PDB',
'ihm_feature_list',
['RID', 'structure_id', 'feature_id'],
constraint_names=[[
'PDB',
'ihm_hdx_restraint_ihm_feature_list_combo1_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'),
ForeignKey.define(
['Dataset_List_RID', 'structure_id', 'dataset_list_id'],
'PDB',
'ihm_dataset_list', ['RID', 'structure_id', 'id'],
constraint_names=[[
'PDB', 'ihm_hdx_restraint_ihm_dataset_list_combo1_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION'),
ForeignKey.define(['Entry_Related_File'],
'PDB',
'Entry_Related_File', ['RID'],
constraint_names=[[
'PDB',
'ihm_hdx_restraint_Entry_Related_File_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION')
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def
hostname = args.hostname
schema_name = args.schema_name
catalog = args.catalog_number
credential = get_credential(hostname)
server = DerivaServer('https', hostname, credential)
catalog = server.connect_ermrest(catalog)
model = catalog.getCatalogModel()
schema = model.schemas[schema_name]
config = catalog.getCatalogConfig()
column_defs = [
Column.define("Step_RID", typ.text),
Column.define("File_RID", typ.text),
]
key_defs = [
Key.define(
["Step_RID","File_RID"], # this is a list to allow for compound keys
constraint_names=[ [schema_name, "Step_OutputFile_Mapping_RID_key"] ],
comment="Step plus file must be distinct.",
annotations={},
)
]
fkey_defs = [
ForeignKey.define(
["Step_RID"], # this is a list to allow for compound foreign keys
"Core",
def define_tdoc_ihm_cross_link_pseudo_site():
table_name='ihm_cross_link_pseudo_site'
comment='Details of pseudo sites involved in crosslinks; can be uploaded as CSV/TSV file above; mmCIF category: ihm_cross_link_pseudo_site'
column_defs = [
Column.define(
'id',
builtin_types.int8,
comment='An identifier for a pseudo site involved in a crosslink',
nullok=False
),
Column.define(
'restraint_id',
builtin_types.int8,
comment='An identifier for the crosslink restraint between a pair of residues',
nullok=False
),
Column.define(
'cross_link_partner',
builtin_types.text,
comment='The identity of the crosslink partner corresponding to the pseudo site',
nullok=False
),
Column.define(
'pseudo_site_id',
builtin_types.int8,
comment='The pseudo site identifier corresponding to the crosslink partner',
nullok=False
),
Column.define(
'model_id',
builtin_types.int8,
comment='Identifier to the model that the pseudo site corresponds to',
nullok=True
),
Column.define(
'Entry_Related_File',
builtin_types.text,
comment='A reference to the uploaded restraint file in the table Entry_Related_File.id.',
nullok=True
),
Column.define(
'structure_id',
builtin_types.text,
comment='Structure identifier',
nullok=False
),
# HT: to use for Chaise
Column.define(
'Model_RID',
builtin_types.text,
comment='Identifier to the model RID',
nullok=True
),
Column.define(
'Pseudo_Site_RID',
builtin_types.text,
comment='Identifier to the pseudo site RID',
nullok=False
),
Column.define(
'Restraint_RID',
builtin_types.text,
comment='Identifier to the restraint RID',
nullok=False
)
]
#BV: This is a leaf table; so no combo1/combo2 keys required
key_defs = [
Key.define(['structure_id', 'id'], constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_primary_key']] ),
Key.define(['RID'], constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_RID_key']] ),
]
# @brinda: add fk pseudo-definition
fkey_defs = [
# HT: it own fk to Entry table
ForeignKey.define(['structure_id'], 'PDB', 'entry', ['id'],
constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_structure_id_fkey']],
on_update='CASCADE',
on_delete='NO ACTION'
),
# -- begin ihm_cross_link_restraint
# HT: In annotation, apply domain_filter to filter the RID list by constraining structure_id
ForeignKey.define(['Restraint_RID', 'structure_id', 'restraint_id'], 'PDB', 'ihm_cross_link_restraint', ['RID', 'structure_id', 'id'],
constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_ihm_cross_link_restraint_combo1_fkey']],
on_update='CASCADE',
on_delete='NO ACTION'
),
# -- end ihm_cross_link_restraint
# -- begin ihm_model_list table
# HT: This is for chaise optional foreign key --> check naming convention
# HT: In annotation, apply domain_filter to filter the RID list by constraining structure_id
# BV: Not required anymore based on the google doc with fkey conventions
#ForeignKey.define(['Model_RID'], 'PDB', 'ihm_model_list', ['RID'],
# constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_Model_RID_fkey']],
# on_update='CASCADE',
# on_delete='NO ACTION'
#),
# HT: equivalent fk so that Chaise will automatically fill in automatically --> check constraint naming convention
ForeignKey.define(['Model_RID', 'model_id'], 'PDB', 'ihm_model_list', ['RID', 'model_id'],
constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_ihm_model_list_combo2_fkey']],
on_update='CASCADE',
on_delete='NO ACTION'
),
# -- end ihm_model_list table
ForeignKey.define(['Pseudo_Site_RID', 'structure_id', 'pseudo_site_id'], 'PDB', 'ihm_pseudo_site', ['RID', 'structure_id', 'id'],
constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_ihm_pseudo_site_combo1_fkey']],
on_update='CASCADE',
on_delete='NO ACTION'
),
ForeignKey.define(['cross_link_partner'], 'Vocab', 'cross_link_partner', ['Name'],
constraint_names=[ ['Vocab', 'ihm_cross_link_pseudo_site_cross_link_partner_fkey'] ],
on_update='CASCADE',
on_delete='NO ACTION'
),
ForeignKey.define(['Entry_Related_File'], 'PDB', 'Entry_Related_File', ['RID'],
constraint_names=[['PDB', 'ihm_cross_link_pseudo_site_Entry_Related_File_fkey']],
on_update='CASCADE',
on_delete='NO ACTION'
)
]
table_def = Table.define(
table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True
)
return table_def
def define_tdoc_ihm_data_transformation():
table_name = 'ihm_data_transformation'
comment = 'Details of rotation matrix and translation vector that can be applied to transform data; mmCIF category: ihm_data_transformation'
column_defs = [
Column.define('id',
builtin_types.int8,
comment='An identifier to the transformation matrix',
nullok=False),
Column.define(
'rot_matrix[1][1]',
builtin_types.float8,
comment=
'Data item [1][1] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[2][1]',
builtin_types.float8,
comment=
'Data item [2][1] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[3][1]',
builtin_types.float8,
comment=
'Data item [3][1] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[1][2]',
builtin_types.float8,
comment=
'Data item [1][2] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[2][2]',
builtin_types.float8,
comment=
'Data item [2][2] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[3][2]',
builtin_types.float8,
comment=
'Data item [3][2] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[1][3]',
builtin_types.float8,
comment=
'Data item [1][3] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[2][3]',
builtin_types.float8,
comment=
'Data item [2][3] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'rot_matrix[3][3]',
builtin_types.float8,
comment=
'Data item [3][3] of the rotation matrix used in the transformation',
nullok=True),
Column.define(
'tr_vector[1]',
builtin_types.float8,
comment=
'Data item [1] of the translation vector used in the transformation',
nullok=True),
Column.define(
'tr_vector[2]',
builtin_types.float8,
comment=
'Data item [2] of the translation vector used in the transformation',
nullok=True),
Column.define(
'tr_vector[3]',
builtin_types.float8,
comment=
'Data item [3] of the translation vector used in the transformation',
nullok=True),
Column.define('structure_id',
builtin_types.text,
comment='Structure identifier',
nullok=False)
]
#BV: This is a parent table with optional columns in the child table; so combo2 key is defined
key_defs = [
Key.define(
['structure_id', 'id'],
constraint_names=[['PDB', 'ihm_data_transformation_primary_key']]),
Key.define(
['RID'],
constraint_names=[['PDB', 'ihm_data_transformation_RID_key']]),
Key.define(
['RID', 'id'],
constraint_names=[['PDB', 'ihm_data_transformation_combo2_key']])
]
# @brinda: add fk pseudo-definition
#BV: No outgoing fkeys other than structure_id
fkey_defs = [
ForeignKey.define(['structure_id'],
'PDB',
'entry', ['id'],
constraint_names=[[
'PDB',
'ihm_data_transformation_structure_id_fkey'
]],
on_update='CASCADE',
on_delete='NO ACTION')
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def
def define_tdoc_ihm_derived_angle_restraint():
table_name = 'ihm_derived_angle_restraint'
comment = 'Details of angle restraints used in integrative modeling; can be uploaded as CSV/TSV file above; mmCIF category: ihm_derived_angle_restraint'
column_defs = [
Column.define("id",
builtin_types.int8,
comment='An identifier for the angle restraint',
nullok=False),
Column.define("group_id",
builtin_types.int8,
comment='An identifier to group the angle restraints',
nullok=True),
Column.define(
"feature_id_1",
builtin_types.int8,
comment=
'The feature identifier for the first partner in the angle restraint',
nullok=False),
Column.define(
"feature_id_2",
builtin_types.int8,
comment=
'The feature identifier for the second partner in the angle restraint',
nullok=False),
Column.define(
"feature_id_3",
builtin_types.int8,
comment=
'The feature identifier for the third partner in the angle restraint',
nullok=False),
Column.define(
"group_conditionality",
builtin_types.text,
comment=
'If a group of angles are restrained together, this data item defines the conditionality based on which the restraint is applied in the modeling',
nullok=True),
Column.define(
"angle_lower_limit",
builtin_types.float8,
comment=
'The lower limit to the threshold applied to this angle restraint',
nullok=True),
Column.define(
"angle_upper_limit",
builtin_types.float8,
comment=
'The upper limit to the threshold applied to this angle restraint',
nullok=True),
Column.define(
"angle_lower_limit_esd",
builtin_types.float8,
comment=
'The estimated standard deviation of the lower limit angle threshold applied',
nullok=True),
Column.define(
"angle_upper_limit_esd",
builtin_types.float8,
comment=
'The estimated standard deviation of the upper limit angle threshold applied',
nullok=True),
Column.define(
"probability",
builtin_types.float8,
comment='The probability that the angle restraint is correct',
nullok=True),
Column.define("restraint_type",
builtin_types.text,
comment='The type of angle restraint applied',
nullok=False),
Column.define(
"angle_threshold_mean",
builtin_types.float8,
comment='The angle threshold mean applied to the restraint',
nullok=True),
Column.define(
"angle_threshold_mean_esd",
builtin_types.float8,
comment=
'The estimated standard deviation of the angle threshold mean applied to the restraint',
nullok=True),
Column.define(
"dataset_list_id",
builtin_types.int8,
comment=
'Identifier to the input data from which the angle restraint is derived',
nullok=False),
Column.define(
"Entry_Related_File",
builtin_types.text,
comment=
'A reference to the uploaded restraint file in the table Entry_Related_File.id.',
nullok=True),
Column.define("structure_id",
builtin_types.text,
comment='Structure identifier',
nullok=False),
# HT: to use for Chaise
Column.define("Feature_Id_1_RID",
builtin_types.text,
comment='Identifier to the feature 1 RID',
nullok=False),
Column.define("Feature_Id_2_RID",
builtin_types.text,
comment='Identifier to the feature 2 RID',
nullok=False),
Column.define("Feature_Id_3_RID",
builtin_types.text,
comment='Identifier to the feature 3 RID',
nullok=False),
Column.define("Dataset_List_RID",
builtin_types.text,
comment='Identifier to the dataset list RID',
nullok=False)
]
#BV: This is a leaf table; so no combo1/combo2 keys required
key_defs = [
Key.define(["structure_id", "id"],
constraint_names=[[
"PDB", "ihm_derived_angle_restraint_primary_key"
]]),
Key.define(
["RID"],
constraint_names=[["PDB", "ihm_derived_angle_restraint_RID_key"]]),
]
# @brinda: add fk pseudo-definition
fkey_defs = [
# HT: it own fk to Entry table
ForeignKey.define(["structure_id"],
"PDB",
"entry", ["id"],
constraint_names=[[
"PDB",
"ihm_derived_angle_restraint_structure_id_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
# HT: In annotation, apply domain_filter to filter the RID list by constraining structure_id
ForeignKey.define(
["Feature_Id_1_RID", "structure_id", "feature_id_1"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Feature_Id_2_RID", "structure_id", "feature_id_2"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Feature_Id_3_RID", "structure_id", "feature_id_3"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Dataset_List_RID", "structure_id", "dataset_list_id"],
"PDB",
"ihm_dataset_list", ["RID", "structure_id", "id"],
constraint_names=[[
"PDB",
"ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["group_conditionality"],
"Vocab",
"ihm_derived_angle_restraint_group_conditionality", ["Name"],
constraint_names=[[
"Vocab",
"ihm_derived_angle_restraint_group_conditionality_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(["restraint_type"],
"Vocab",
"ihm_derived_angle_restraint_restraint_type",
["Name"],
constraint_names=[[
"Vocab",
"ihm_derived_angle_restraint_restraint_type_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Entry_Related_File"],
"PDB",
"Entry_Related_File", ["RID"],
constraint_names=[[
"PDB", "ihm_derived_angle_restraint_Entry_Related_File_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION")
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def