oda-hub / deprecated-renku-aqs

renku-aqs

params

$ (cd renku-aqs-test-case/; renku aqs params)
+--------------------------------------+-------------------+--------------+
| Run ID                               | AstroQuery Module | Astro Object |
+--------------------------------------+-------------------+--------------+
| 228555e4-151a-4440-919d-f1269132a0fb |    SimbadClass    |   Mrk 421    |
| 76943a72-30bf-4e9e-ad92-3dd068424968 |    SimbadClass    |   Mrk 421    |
| 0320ea0d-eee2-4b50-aa3e-b64c557b9bf2 |    SimbadClass    |   Mrk 421    |
+--------------------------------------+-------------------+--------------+
@prefix local-renku: <file:///home/savchenk/work/oda/renku/renku-aqs/renku-aqs-test-case/.renku/> .
@prefix oda: <http://odahub.io/ontology#> .
@prefix odas: <https://odahub.io/ontology#> .

local-renku:4ab60eb4-d5e7-11eb-a2dc-b5ff8b3b1162 a oda:Run ;
    oda:isRequestingAstroObject odas:AstroObjectMrk_421 ;
    oda:isUsing odas:AQModuleSimbadClass .

local-renku:53e67e80-d5ea-11eb-a2dc-b5ff8b3b1162 a oda:Run ;
    oda:isRequestingAstroObject odas:AstroObjectMrk_421 ;
    oda:isUsing odas:AQModuleSimbadClass .

local-renku:dd481450-d5e4-11eb-a2dc-b5ff8b3b1162 a oda:Run ;
    oda:isRequestingAstroObject odas:AstroObjectMrk_421 ;
    oda:isUsing odas:AQModuleSimbadClass .

Graphical visualization of the graph

Starting from the knowledge graph generated and enriched during the various executions of the notebooks present within the repository, this is queried to retrieve the needed information, perform some inferring and generate a graphical representation.

In particular, two commands are provided:

• display to generate a representation of the graph over an output image
• show-graph to start an interactive visualization of the graph over the browser

display command

CLI command to generate a graphical representation of the graph over an image.

In particular, the following information are elaborated:

• inputs/arguments/outputs of the notebook execution;
• astroquery modules used and the main query methods called (astroquery api).

Parameters

• --filename The filename of the output file image, until now, only png images are supported (eg --filename graph.png), default is graph.png
• --input-notebook Input notebook to process, if not specified, will query for all the executions from all notebooks
• --no-oda-info Exclude oda related information in the output graph, an output much closer to the lineage graph provided in the renkulab will be generated

$ renku aqs display

Specify executed notebook

$ renku aqs display --input-notebook final-an.ipynb

Do not display oda-related information

$ renku aqs display --input-notebook final-an.ipynb --no-oda-info

show-graph command

CLI command to generate an interactive graphical representation of the graph.

$ renku aqs show-graph

The user can interact with the graph via a single click on one of its nodes: upon clicking, a SPARQL query is dynamically built, and this will retrieve all the nodes and edges directly connected to the clicked node, as shown in the animation below. Once the node has been expanded, the newly added nodes, along with the other leaves nodes that are connected to the previously clicked node, can be re-absorbed by clicking again on the very same node. This is also visible in the animation below.

The interface provides the user with a number of adjustable options:

• Change graph layout: Two possible layouts are at the moment supported

  • random: where nodes and edges are displayed in a random fashion over the dedicated frame (this layout is used in the above picture)
  • hierarchical: where a hierarchical visualization is applied to the nodes and the edges, an example of this is displayed in the image below
  

• Enable/disable selection of subsets of nodes: filtering of certain subset of nodes (eg astroquery-related nodes). This is configurable via a dedicated json file.

• Apply reductions on the graph: allows to enable the display of certain nodes with the relative child ones absorbed within, and viceversa (eg in the example images, the Plan node has a number of child nodes, those can be visualized inside the Plan, left image, as well as regular ones, right image) This is configurable via a dedicated json file.

• Enable/disable graphical configurations for the graph: enable/disable a set of graphical configurations for the graph (nodes and edges), where each configuration is loaded from a dedicated json file. In the image displayed below, two json files have been loaded, and the related checkbox will enable/disable that configuration.

The functionalities for the graph drawing and its behavior are developed in javascript and are avaialble at the following repository.

Installation of the plugin

Currently, the plugin is developed using the version 2.2.0 of renku-python. Please make sure such version is installed by running:

renku --version

The versioning of the dependency is guaranteed during the installation of the plugin, and in addition a dedicated check will be performed during the import.

For the installation of the plugin via pip:

pip install renku_aqs