dagr | scala based DSL framework for writing | BPM library
kandi X-RAY | dagr Summary
kandi X-RAY | dagr Summary
A task and pipeline execution system for directed acyclic graphs to support scientific, and more specifically, genomic analysis workflows. We are currently in alpha development; please see the Roadmap. The latest API documentation can be found here.
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Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of dagr
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dagr Examples and Code Snippets
Lines of Code : 24License : Permissive (MIT)
Copy@clp(description="Example FASTQ to BAM pipeline.", group = classOf[Pipelines])
class ExamplePipeline
( @arg(flag="i", doc="Input FASTQ.") val fastq: PathToFastq,
@arg(flag="r", doc="Reference FASTA.") val ref: PathToFasta,
@arg(flag="t" class FastqToSam(fastq1: PathToFastq,
fastq2: Option[PathToFastq] = None,
out: PathToBam,
...)
extends PicardTask with Pipe[Fastq,SamOrBam]
val unmappedBam = output.resolve("unmapped.bam")
val fq import dagr.tasks.ScatterGather.Scatter
val scatterer = new SplitIntervalsForCallingRegions(ref=ref, intervals=intervals, output=Some(dir), maxBasesPerScatter=5e6.toInt)
val scatter = Scatter(scatterer)
val hc = scatter.map(il => new Haplotyp Community Discussions
Trending Discussions on dagr
QUESTION
I have an issue regarding an application that I am working on. I have a button that is triggering 2 function. One of them is a setState which changes the direction of a dagre graph and the other one is a function that React-flow-renderer provides and fits (centers) the instance of the graph in the screen. I think it needs to be done asynchronously, as the 2nd function is executed only if I double click the button or if I set a setTimeOut to execute after f.ex., 3 seconds. So this works:
ANSWER
Answered 2022-Mar-29 at 12:56Try using async/await:
QUESTION
I am using Cytoscape Dagre extension to show hierarchical graph from left to right. It has 14 children and one parent 1 and main parent. I am calculating the height of the container using the number of nodes. Then I am calling fit function after the layout is created but it is not working.
I have added a fit button and if I click on it after the graph is loaded, it works then. What am I doing wrong? I would like fit function to be called after the graph is initialzed.
Here is the stackblitz link: https://stackblitz.com/edit/dagre-childrenconnected-fit?file=src%2Fapp%2Fapp.component.ts
You can try clicking on Fit and see the graph is fitted properly if you click on fit button but it does not work if you refresh the page.
...ANSWER
Answered 2021-Apr-07 at 21:04Your code is not working correctly, there are some errors.
(1) Firstly, your "dynamic height" [ngStyle]="{'height': heightTest + 'px'}" is undefined at graph init and runs into a weird error after that. Just use something like [ngStyle]="{'height': '100vh'}" and go from there.
(2) As the docs say:
If your code resizes the graph’s dimensions or position (i.e. by changing the style of the HTML DOM element that holds the graph, or by changing the DOM element’s position in the DOM tree), you will want to call cy.resize() to have the graph resize and redraw itself.
Your approach is not really ideal, I'd suggest just changing the height of your container and then resizing/fitting your graph:
QUESTION
I am using Cytoscape Dagre extension to show hierarchical graph from left to right. It has 14 children and one parent 1 and main parent. All children are connected to parent 1 but whenever I use draw a graph using dagre extension, it seems like children are connected between each other. They do not have any edges between them but Dagre still shows that. Is Cytoscape with Dagre capable of showing hierarchical graphs with multiple children?
Here is the stackblitz example: https://stackblitz.com/edit/dagre-childrenconnected
...ANSWER
Answered 2021-Apr-06 at 07:39Your edges overlap with your child nodes, that is not a dagre specific problem, your cytoscape-stylesheet is just missing some parameters. With taxi edges, the important thing to understand is, that your edges follow style rules like the layout algorithm you use. For layouts, you use the layout option to specify how the layout should place the nodes. The edges are styled via the stylesheet and they all have some options to play around with.
In your case, you should take a look at this section in the docs. There you can find options like the taxi-direction:
QUESTION
I am trying to use cytoscape with tippy but it is not showing any tool tips. It throws an error that ele.popperRef is not a function.
Here is the stackblitz link: https://stackblitz.com/edit/dagre-tippy?file=src%2Fapp%2Fapp.component.ts
I have added all the packages required which includes popper.js, tippy.js but still it does not work
...ANSWER
Answered 2021-Mar-26 at 12:50Check this https://stackblitz.com/edit/dagre-tippy-wgg8zz
You are not simply importing libraries properly and registering the cytoscape.js extensions.
You should register popper extension with cytoscape.use(popper);
You can use tippy.js with a function like
QUESTION
The problem: Looking for quite some time for a js graph library to create a directed graph (e.g. using dagre layout), with the constrain of non-overlapping edges.
- Started with cytoscape.js but as it seems, such a feature doesn't exist.
- Continued on with an
svgbased solution (considering that all elements are in the DOM), d3.js using the dagre-d3, but still the information in the DOM is the path route.
- Find a way to detect edge overlapping, either
canvasorsvgbased. - Create a custom layout to respect this constrain. Will use this as a metric for my convergence algorithm.
Below a graphical representation of the objective.
I want to detect that edges 0>1 and 2>3 are overlapping.
Any ideas, thoughts are welcome. If there is something wrong with my logic, corrections/suggestions are more than welcome.
...ANSWER
Answered 2021-Feb-19 at 10:12Finding edge crossings (line intersections) is a fairly simple bit of geometry which is explained here --> https://stackoverflow.com/a/18234609/368214
But then minimising such edge crossings in a graph (zero edge crossings are only possible in planar graphs) is one of the great research challenges of graph layout - https://cs.stackexchange.com/questions/14901/how-to-reduce-the-number-of-crossing-edges-in-a-diagram
Some graph layouts for specific graph types like DAGS such as Sugiyama aim to reduce crossings and similar cytoscape layouts are available at yfiles if that helps (i.e. the hierarchic layout) --> http://apps.cytoscape.org/apps/yfileslayoutalgorithms
QUESTION
So after initializing the graph, I want to make it fit to its div by using cy.fit(). I have done this:
ANSWER
Answered 2021-Feb-04 at 18:06Cytoscape.js deals with this via cy.ready(). Just use it like this:
QUESTION
I'm trying to set up very simple example with Vue2 using dagre-d3 for rendering directed graphs.
Unfortunately, even with extremely simple example, it wont work. Examples found elsewhere online are using older version of d3.
Currently, Vue2 app is mostly default template with a router with a typescript as language. Diagram component is in javascript (due to missing types in my code for d3 and dagre-d3).
When running the component mentioned below, following error happens and nothing is shown in the block.
ANSWER
Answered 2020-Oct-31 at 15:48There were two problems with this component:
- Default edge label needs to be set
I was missing a call on the graph instantiation. It should have been
QUESTION
I have a problem with this plugin. I want to double click on nodes and the id of nodes should be displayed in console. I added the link of this extension from https://github.com/fixpoint/cytoscape-dblclick and followed by this post Cytoscape js - Call a function whenever a node is clicked, but still is not working. Is anybody have any idea why it is not working, it would be nice if you share it. You can see my code:
...ANSWER
Answered 2020-May-06 at 07:51Just follow the post you already linked and log the node information instead of fitting the graph to the clicked node. Also, your demo had some static scripts in the header, I removed them for that reason. That way, the qtip works again too:
QUESTION
Given the cytoscape.js snippet below, using the dagre layout, can anyone explain why node number 2 positions itself to the bottom right instead of in order like the rest of them?
...ANSWER
Answered 2020-Mar-24 at 07:50With a little re-arragement, you can easily get this to work. Generally, it is better to group the elements by nodes and edges, also in a ascending order. This improves readability and, in this case, prevents inconsistent layouts.
I think that the issue here stemms from the edges being added to the graph before the corresponding node (node Number 2) is present.
Here is the working code:
QUESTION
In my application I need to support both json and xml response format and want to omit null values from responses. In the json response this works fine, but not in xml response. The result:
...ANSWER
Answered 2020-Mar-21 at 10:21this works fine for me...
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