Package: dtool-lookup-server-dependency-graph-plugin
GitHub:https://github.com/livMatS/dtool-lookup-server-dependency-graph-pluginPyPI:https://pypi.python.org/pypi/dtool-lookup-server-dependency-graph-pluginFree software: MIT LicenseFeaturesUse a dataset UUID to lookup all datasets within the same dependency graphBuild views on dataset dependency trees based on arbitrary connecting keysIntroductiondtoolis 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.Thedtool-lookup-serverprovides a web API for registering datasets’ metadata
and provides functionality to lookup, list and search for datasets.This plugin enables the dtool-lookup-server to directly provide all
datasets within a specific dependency graph.InstallationInstall the dtool lookup server dependency graph plugin$pipinstalldtool-lookup-server-dependency-graph-pluginSetup and configurationConfigure plugin behaviorWithexportDTOOL_LOOKUP_SERVER_ENABLE_DEPENDENCY_VIEW=Truethe 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. WithexportDTOOL_LOOKUP_SERVER_FORCE_REBUILD_DEPENDENCY_VIEW=Truethis view is reestablished at every query. This is required to apply changes to
related options, such as the JSON-formatted listexportDTOOL_LOOKUP_SERVER_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'}]}}SettingexportDTOOL_LOOKUP_SERVER_DYNAMIC_DEPENDENCY_KEYS=Truewill allow the client side to request graphs spanned by arbitrary dependency
keys (see below). The related optionsexportDTOOL_LOOKUP_SERVER_MONGO_DEPENDENCY_VIEW_PREFIX=depexportDTOOL_LOOKUP_SERVER_MONGO_DEPENDENCY_VIEW_BOOKKEEPING=dep_viewsexportDTOOL_LOOKUP_SERVER_MONGO_DEPENDENCY_VIEW_CACHE_SIZE=10control 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 APIThe 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 thecurlcommands$TOKEN=$(flaskusertokenolssont)$HEADER="Authorization: Bearer$TOKEN"Standard user usageLooking up dependency graphs based on a dataset’s UUIDA dataset can be derived from one or several source datasets, usually
by machine-generated annotations attached via the Python API at dataset
creation time, or manually by recording the UUIDs of parent datasets in some
arbitrary fields within the README.yml. If configured appropriately,
querying the server directly for all datasets within the same dependency
graph by UUID is possible, i.e.$UUID=41a2e3e2-0c01-444f-bd7d-f9bb45512373$curl-H"$HEADER"http://localhost:5000/graph/lookup/$UUIDLooking up a dependency graph by UUID will result in unique per-UUID hits.
As it is possible for a dataset to be registered in more than one base
URI, the query will yield one arbitrary hit in such a case.Looking up graphs spanned by arbitrary dependency keysIfDTOOL_LOOKUP_SERVER_DYNAMIC_DEPENDENCY_KEYS=True, then the client may
ask the server to explore a graph spanned by dependency keys differing from
the server-side defaults inDTOOL_LOOKUP_SERVER_DEPENDENCY_KEYS. This
happens as above, but with via aPOSTrequest with a JSON-formatted list
of desired dependency keys attached$curl-H"$HEADER"-H"Content-Type: application/json"\-XPOST-d\'["annotations.source_dataset_uuid","readme.derived_from.uuid"]'http://localhost:5000/graph/lookup/$UUIDIf 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$mongo>showdbsadmin0.000GBconfig0.000GBdtool_info0.020GBlocal0.000GB>usedtool_infoswitchedtodbdtool_info>showcollectionsdatasetsdep:2020-10-05T01:22:39.581592dep:2020-10-06T21:45:00.525410dep:2020-10-06T21:45:28.495903dep_viewsdependenciessystem.viewsHere, alldep-prefixed collections are dependency views for distinct sets
of keys. The bookkeeping collection``dep_views`` holds records of all
dependency view - key set mappings together with the latest access>db.dep_views.find(){"_id":ObjectId("5f7a755faea9fcf239f68dba"),"name":"dep:2020-10-05T01:22:39.581592","keys":["annotations.source_dataset_uuid","readme.derived_from.uuid"],"accessed_on":ISODate("2020-10-07T12:24:32.724Z")}{"_id":ObjectId("5f7ce55caea9fcf239f68dbb"),"name":"dep:2020-10-06T21:45:00.525410","keys":["readme.derived_from.uuid"],"accessed_on":ISODate("2020-10-06T21:45:00.538Z")}{"_id":ObjectId("5f7ce578aea9fcf239f68dbc"),"name":"dep:2020-10-06T21:45:28.495903","keys":["bla"],"accessed_on":ISODate("2020-10-06T21:45:28.498Z")}and querying with a specific set of keys for the first time$curl-H"$HEADER"-H"Content-Type: application/json"\-XPOST-d\'["another.possibly_nested.dependency_key"]'\http://localhost:5000/graph/lookup/$UUIDwill 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.viewsand an according entry withindep_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 inDTOOL_LOOKUP_SERVER_MONGO_DEPENDENCY_VIEW_CACHE_SIZE, then
the view accessed least recently is dropped.