Deriva Ermrest Catalog Snapshot Examples

This notebook gives examples of connecting to ERMrest versioned catalogs.



In [1]:

    
from deriva.core import DerivaServer, get_credential, ErmrestCatalogMutationError

Fill in your desired scheme, hostname and catalog number.



In [2]:

    
scheme = 'https'
hostname = 'synapse-dev.isrd.isi.edu'
catalog_number = 1

Use DERIVA-Auth to get a credential or use None if your catalog allows anonymous access.



In [3]:

    
credential = get_credential(hostname)

Get a handle representing your server.



In [4]:

    
server = DerivaServer(scheme, hostname, credential)

Connect to a catalog, and list its schemas.



In [5]:

    
catalog = server.connect_ermrest(catalog_number)
pb = catalog.getPathBuilder()
list(pb.schemas)









    Out[5]:





['Synapse', 'public', 'Zebrafish']

The current catalog handle can return a handle to the latest snapshot.



In [6]:

    
latest = catalog.latest_snapshot()
pb = latest.getPathBuilder()
list(pb.schemas)









    Out[6]:





['Synapse', 'public', 'Zebrafish']

Print the snaptime of this catalog snapshot.



In [7]:

    
print(latest.snaptime)









    



2PS-ERRT-HD8E

Here we pass the snaptime parameter explicitly in the connect_ermrest method.



In [8]:

    
snapshot = server.connect_ermrest('1', '2PM-DGYP-56Z4')
pb = snapshot.getPathBuilder()
list(pb.schemas)









    Out[8]:





['Synapse', 'public', 'Zebrafish']

Alternatively, we could pass a "versioned" catalog_id to the connect_ermrest method.



In [9]:

    
snapshot = server.connect_ermrest('1@2PM-DGYP-56Z4')
pb = snapshot.getPathBuilder()
list(pb.schemas)









    Out[9]:





['Synapse', 'public', 'Zebrafish']

Finally, we can poke around at schemas and tables as they existed at the specified snaptime.



In [10]:

    
subject = pb.schemas['Zebrafish'].tables['Subject']
print(subject.uri)









    



https://synapse-dev.isrd.isi.edu/ermrest/catalog/1@2PM-DGYP-56Z4/entity/Subject:=Zebrafish:Subject

Data may be read from the snapshot. Here, we will see how many subjects existed at that point in time.



In [11]:

    
e = subject.entities()
len(e)









    Out[11]:





486

However, mutation operations on a catalog snapshot are disabled.



In [12]:

    
try:
    subject.insert([{'foo': 'bar'}])
except ErmrestCatalogMutationError as e:
    print(e)









    



Catalog snapshot is immutable



In [ ]: