- GitHub: https://github.com/livMatS/dserver-dependency-graph-plugin
- PyPI: https://pypi.python.org/pypi/dserver-dependency-graph-plugin
- Free software: MIT License
- Use a dataset UUID to lookup all datasets within the same dependency graph
- Build views on dataset dependency trees based on arbitrary connecting keys
dtool is a command line tool for packaging data and metadata into a dataset. A dtool dataset manages data and metadata without the need for a central database.
However, if one has to manage more than a hundred datasets it can be helpful to have the datasets' metadata stored in a central server to enable one to quickly find datasets of interest.
The dserver provides a web API for registering datasets' metadata and provides functionality to lookup, list and search for datasets.
This plugin enables the dserver to directly provide all datasets within a specific dependency graph.
Install the dtool lookup server dependency graph plugin
$ pip install dserver-dependency-graph-plugin
With
export DSERVER_ENABLE_DEPENDENCY_VIEW=True
the underlying database will offer a view on the default collection. This view offers an on-the-fly-generated collection of undirected per-dataset adjacency lists in order to facilitate searching dataset dependeny graphs in both directions. With
export DSERVER_FORCE_REBUILD_DEPENDENCY_VIEW=True
this view is reestablished at every query. This is required to apply changes to related options, such as the JSON-formatted list
export DSERVER_DEPENDENCY_KEYS='["readme.derived_from.uuid", "annotations.source_dataset_uuid"]'
which indicates at which keys to look for source dataset(s) by UUID. The example above illustrates the default. All keys are treated equivalently and nested fields are separated by the dot (.). The actual nesting hierarchy does not matter. This means, for example, both structures evaluate equivalently in the following
{'readme': {'derived_from': {'uuid':
['8ecd8e05-558a-48e2-b563-0c9ea273e71e',
'faa44606-cb86-4877-b9ea-643a3777e021']}}}
{'readme': {'derived_from':
[{'uuid': '8ecd8e05-558a-48e2-b563-0c9ea273e71e'},
{'uuid': 'faa44606-cb86-4877-b9ea-643a3777e021'}]}}
Setting
export DSERVER_DYNAMIC_DEPENDENCY_KEYS=True
will allow the client side to request graphs spanned by arbitrary dependency keys (see below). The related options
export DSERVER_MONGO_DEPENDENCY_VIEW_PREFIX=dep
export DSERVER_MONGO_DEPENDENCY_VIEW_BOOKKEEPING=dep_views
export DSERVER_MONGO_DEPENDENCY_VIEW_CACHE_SIZE=10
control internal behavior. See source code and examples below.
Note that the above exports containing JSON syntax are formatted for usage in bash. Enclosing single quotes are not to be part of the actual variable value when environment variables are configured elsewhere.
The dtool lookup server makes use of the Authorized header to pass through the
JSON web token for authorization. Below we create environment variables for the
token and the header used in the curl
commands
$ TOKEN=$(flask user token olssont)
$ HEADER="Authorization: Bearer $TOKEN"
A dataset can be derived from one or several source datasets, usually by machine-generated annotations attached via the Python API at dataset creation time, or manually by recording the UUIDs of parent datasets in some arbitrary fields within the README.yml. If configured appropriately, querying the server directly for all datasets within the same dependency graph by UUID is possible, i.e.
$ UUID=41a2e3e2-0c01-444f-bd7d-f9bb45512373
$ curl -H "$HEADER" http://localhost:5000/graph/lookup/$UUID
Looking up a dependency graph by UUID will result in unique per-UUID hits. As it is possible for a dataset to be registered in more than one base URI, the query will yield one arbitrary hit in such a case.
If DSERVER_DYNAMIC_DEPENDENCY_KEYS=True
, then the client may
ask the server to explore a graph spanned by dependency keys differing from
the server-side defaults in DSERVER_DEPENDENCY_KEYS
. This
happens as above, but with via a POST
request with a JSON-formatted list
of desired dependency keys attached
$ curl -H "$HEADER" -H "Content-Type: application/json" \
-X POST -d \
'["annotations.source_dataset_uuid","readme.derived_from.uuid"]'
http://localhost:5000/graph/lookup/$UUID
If a view for this particular set of keys does not exist yet, the server will generate and cache it on-the-fly. This can be observed in the mongo shell
$ mongo
> show dbs
admin 0.000GB
config 0.000GB
dtool_info 0.020GB
local 0.000GB
> use dtool_info
switched to db dtool_info
> show collections
datasets
dep:2020-10-05T01:22:39.581592
dep:2020-10-06T21:45:00.525410
dep:2020-10-06T21:45:28.495903
dep_views
dependencies
system.views
Here, all dep
-prefixed collections are dependency views for distinct sets
of keys. The bookkeeping collection``dep_views`` holds records of all
dependency view - key set mappings together with the latest access
> db.dep_views.find()
{ "_id" : ObjectId("5f7a755faea9fcf239f68dba"), "name" : "dep:2020-10-05T01:22:39.581592", "keys" : [ "annotations.source_dataset_uuid", "readme.derived_from.uuid" ], "accessed_on" : ISODate("2020-10-07T12:24:32.724Z") }
{ "_id" : ObjectId("5f7ce55caea9fcf239f68dbb"), "name" : "dep:2020-10-06T21:45:00.525410", "keys" : [ "readme.derived_from.uuid" ], "accessed_on" : ISODate("2020-10-06T21:45:00.538Z") }
{ "_id" : ObjectId("5f7ce578aea9fcf239f68dbc"), "name" : "dep:2020-10-06T21:45:28.495903", "keys" : [ "bla" ], "accessed_on" : ISODate("2020-10-06T21:45:28.498Z") }
and querying with a specific set of keys for the first time
$ curl -H "$HEADER" -H "Content-Type: application/json" \
-X POST -d \
'["another.possibly_nested.dependency_key"]' \
http://localhost:5000/graph/lookup/$UUID
will result in an additional view named uniquely by the current UTC time:
> show collections datasets dep:2020-10-05T01:22:39.581592 dep:2020-10-06T21:45:00.525410 dep:2020-10-06T21:45:28.495903 dep:2020-10-07T17:03:58.831223 dep_views dependencies system.views
and an according entry within dep_views
> db.dep_views.find()
{ "_id" : ObjectId("5f7a755faea9fcf239f68dba"), "name" : "dep:2020-10-05T01:22:39.581592", "keys" : [ "annotations.source_dataset_uuid", "readme.derived_from.uuid" ], "accessed_on" : ISODate("2020-10-07T16:59:12.467Z") }
{ "_id" : ObjectId("5f7ce55caea9fcf239f68dbb"), "name" : "dep:2020-10-06T21:45:00.525410", "keys" : [ "readme.derived_from.uuid" ], "accessed_on" : ISODate("2020-10-06T21:45:00.538Z") }
{ "_id" : ObjectId("5f7ce578aea9fcf239f68dbc"), "name" : "dep:2020-10-06T21:45:28.495903", "keys" : [ "bla" ], "accessed_on" : ISODate("2020-10-06T21:45:28.498Z") }
{ "_id" : ObjectId("5f7df4feaea9fcf239f68dbd"), "name" : "dep:2020-10-07T17:03:58.831223", "keys" : [ "another.possibly_nested.dependency_key" ], "accessed_on" : ISODate("2020-10-07T17:03:58.833Z") }
If the total number of such cached views exceeds the allowed maximum value
configured in DSERVER_MONGO_DEPENDENCY_VIEW_CACHE_SIZE
, then
the view accessed least recently is dropped.