GSoC17 Final Report

• Summary
• Notebook week reports
• Merged pull requests
• What was not done and why
• What needs to be done yet

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Summary

This is my final report for the Google Summer of Code aka GSoC. I started this GSoC by first getting a feel from the user perspective of bionode-watermill and as the time passed (and I was starting to get more comfortable with the code), I start learning how the API works and how it can be improved. The following reports clarify the progress that was made and have a detailed explanation on why and how modifications were being added to the previous API.

Below, I also made a list of all pull requests made, and a list of issues still needs work to improve current bionode-watermill API.

Notebook week reports

During my GSoC progress was tracked in weekly reports. Here you can find the 12 reports:

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12

Merged pull requests

• PR #48 - Correct path to home folder

PR #48 corrects pipelines path to properly get bionode-watermill lib, which was previously broken.

• PR #53 - Adds a new example pipeline and edits existing example pipeline

PR #53 added a new pipeline used in the bionode-watermill tutorial. This is a pipeline that fetches some sequence data, as well as reference, and maps using two different mappers (bwa and bowtie2) and them performs some operations using samtools. The tutorial was something necessary in order to attract users and to get familiar with bionode-watermill. Also a docker image was added in order to experiment this pipeline.

Also, in the scope of this PR a simpler bionode-watermill tutorial was added to a new repo, called bionode-watermill-tutorial, which targets new users. Then, this pipeline is, in fact, part of a more advanced tutorial, in which users understanding the basics of bionode-watermill can see in action what it can make.

• PR #55 - Added a tutorial on how to run "two-mappers" example

This PR adds the more advanced tutorial referenced above, in which users are challenged to continue assembling the pipeline given their previous knowledge on the work of bionode-watermill. Also, a solution is provided for the challenge in pipeline_lazy.js, which is described in the REAMDE.md available in bionode-watermill tutorials or it can be checked here.

• PR #56 - Updated docker related links and added link to tutorial in README

This PR updates main bionode-watermill README.md to include tutorial information.

• PR #58 - Fixed issue with logging of task name to stdout

This is a small PR that fixed a logging of the task name.

• PR #59 - Transferred experimental branch for development of graph

This PR adds a manifest file implementation that logs graph structure to a file and started implementing graphson like structure to graph.

• PR #61 - Implemented redux-logger given an environmental variable

This PR adds redux-logger to be easier to debug issues regarding actions and states. Now we can use REDUX_LOGGER=1 node pipeline.js to log redux related actions and states to console. This is particularly cool with chrome nodejs V8 inspector.

• PR #62 - Implemented a graph visualization

This PR added a d3 visualization for pipeline shape in which graphson vertices are represented as d3 nodes and graphson edges are represented as links. This visualization is available when pipeline is executed and final graphson visualization can be obtained at the end of the run. d3 visualization nodes also have some metadata regarding tasks definition and execution, such as uid, resolvedInput, resolvedOutput, name and params. Visualization used socket.io to emit data to localhost:8084.

• PR #64 - Added operation command to graphson

This PR added operationString to d3 visualization.

• PR #67 - Edits to two-mappers pipeline and removed of redundant defaultTask

This PR edited two-mappers pipeline to follow bionode-watermill philosophy (removed pipes from commands passed to shell and removed hardcoded file names from input). Also, removed duplicated definition of defaultTask that was not being executed under lib/reducers/task.js.

• PR #70 - Orchestrators refactoring and fork handling other orchestrators

This PR handles orchestrators working inside other orchestrators, implements merkle tree like task uid generation which allows for tasks to be duplicated within the scope of a pipeline. Orchestrators get a similar structure with uid. Also a couple of new tests were added in order to test pipeline shape given different combinations of orchestrators.

• PR #72 - Going deeper on fork orchestration

This PR increases the cases where fork work, because until this PR fork just worked with other level of fork (e.g. fork(fork())). Also some other examples were added on how to handle multiple inputs and concurrency between multiple inputs, which allow to have some control over CPU and memory resources.

• PR #73 - Add another test for fork within fork wrapped in join

This PR fixed a case where fork inside other forks nested in joins and adds tests for travis and codecov.

• PR #76 - Docs update

This PR updates current documentation in bionode-watermill gitbook

What was not done and why

Unfortunately time grew short and definition of directed acyclic graph (DAG) took longer than previously expected. For instance, complex combination of orchestrators were never previously tested and they needed to be properly ruled for the tool to be usable in the maximum number of possible use cases.

Moreover, the tool has to become usable by anyone that shows interest in joining our community and thus documentation was required, both updating the existing docs as well as adding new pipelines that are well documented (e.g. two-mappers pipeline) and bionode-watermill tutorial. Before adding more complexity to the tool we now aimed to make it more accessible to users.

Therefore, there was no time to implement:

• Streams between tasks - this required that all orchestrators behaved more similarl to each other. Therefore a similar structure was made for the three orchestrators (as reported in Week 9). Also fork needed to be more consistent before adding more complexity to the API, since in many example pipelines that I experimented in examples/pipelines/tests it did not worked has expected and thus some handling of fork rules had to be performed (check Week 9 and Week 10 and Week 11 and Week 12 ).

• Metrics to control the workflow - although this may have workarounds using bluebird module as exemplified in Week 12 report.

• Improved validation - Although some validators already exist in current API, we could pass new custom validators that allow the user to contror, for example, file size and extension (Issue #80).

What needs to be done yet

• Issue #74 - Refactor pipeline parsing

This issue is important in order to get pipeline shape before running the pipeline itself within bionode-watermill. We can then check pipeline proper execution using visualization, improve the visualization itself to show what have ran (green node), is running (yellow node), not run yet (blue node) and failed running (red node).

• Issue #75 - Refactor task definition

This issue suggests that task definition becomes more javascript independent and more user friendly. The ultimate goal would be to abstract the users from javascript at all when assembling their pipelines.

• Issue #77 - Improvements to visualization tool

This issue was added since current visualization tool is still a first implementation and may be further developed. Despite being already useful for debugging pipelines execution, it can be improved if we had success/failure checks on tasks and input/output flow to the visualization.

• Issue #78 - Tasks as npm modules

This is a proposal for tasks being transformed into npm modules that require bionode-watermill module and that could be imported into new bionode-watermill pipelines.

• Issue #79 - Streaming Between Tasks

As referenced above this goal was delayed because of orchestrators control but this is a must have feature for the project and thus we opened a new issue that addresses this topic.

• Issue #80 - Improve validators over input/output files

This issue opens a new discussion on how to pass custom file validators.

• Issue #81 - Through tasks not properly logging

This issue raises aweareness to a very experimental feature in bionode-watermill and that despite working well for a single task renders some odd behavior in logging to both graphson.json and for the d3 visualization tool available at localhost:8084.

• Issue #82 - Execution of a pipeline following other pipeline

This was something that I was trying to accomplish at the very end of my GSoC but could not do. For now, I just know that files used in other pipelines that are .then run in the next pipeline seem to be unable to properly be executed in the downstream pipeline.