Tag: json

Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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spring boot – Centralized Swagger/OpenAPI UI for all the different microservices on a single swagger URL i.e accessing all the URLs through one

If all you µservices use the same host, you can create a Spring Boot µservice which acts as a openAPI gateway using spring-doc. (If they are not using the same host, you will have to deal with CORS issues) First, add the following dependencies to your new gateway µservice <dependency>…

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Read bam/cram file with IGV from aws s3

Hi all, We store our alignment files on aws s3. I would like to be able to open them with IGV without needing to download them completely, but I can’t find an optimal solution. If I get a pre-signed url it works but it’s not convenient. I try to follow…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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php-openapi make implementations of built-in interfaces PHP 8.1 friendly

Problem Unfortunately, PHP 8.1 throws Fatal Error if the built-in interface implementation is incompatible with the new, type enhanced interfaces. Example error: Fatal error: During inheritance of ArrayAccess: Uncaught Return type of cebeopenapispecResponses::offsetExists($offset) should either be compatible with ArrayAccess::offsetExists(mixed $offset): bool, or the #[ReturnTypeWillChange] attribute should be used to temporarily…

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java – OpenApi Generator to generate parameter with @RequestBody as String

I have the following OpenApi specs: paths: /student: post: requestBody: required: true content: application/json: schema: $ref: “#/components/schemas/Student” responses: 204: components: schemas: Student: type: object properties: name: type: string school: type: string With org.openapitools.generator, it generates a controller with function like below void addStudent(@RequestBody Student student) { } Is there any…

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Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

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[META] Drop dependency on schemata for something more json:api specific/lighter [#3258301]

Per conversation with a number of api-first maintainers/OGs as reflected on #3258113: [META] Future of Schemata/Compatibility with other ecosystem modules: @richgerdes: …maybe the openapi side of the house could just work off of the jsonapi_schema system instead and schemata can be left for more general entity schema and rest? I…

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biojs – Github Plus

Try to be as detailed as possible. Why do you need it? What data does it use? What should the user experience? ABI file parser –> read .abi files into JSON. We have chromatogram files. Would be great to be able to view these in the browser. Some other .abi…

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node.js – OpenAPI: “request should have required property ‘body'”

I am building out a new endpoint in my application which uses express-openapi-validator as validator middleware. /* index.ts */ import * as OpenApiValidator from ‘express-openapi-validator’; const whitelistedPaths = [/* regex tested paths */]; app.use( OpenApiValidator.middleware({ apiSpec: ‘./schema/api.json’, validateRequests: true, validateResponses: true, ignorePaths: whitelistedPaths, validateSecurity: true, }), ); /* … */…

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make Pyspark working inside jupyterhub

You need to configure the pyspark kernel. On my server jupyter kernels are located at: /usr/local/share/jupyter/kernels/ You can create a new kernel by making a new directory: mkdir /usr/local/share/jupyter/kernels/pyspark Then create the kernel.json file – I paste my as a reference: { “display_name”: “pySpark (Spark 1.6.0)”, “language”: “python”, “argv”: […

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drf-spectacular support OpenAPI 3.1 | GitAnswer

Are there any plans to support OpenAPI v3.1? If yes when can we expect it? If nothing else it will allow exploded arrays for multipart/form-data requests which is the default behavior of MultipartParser. spec.openapis.org/oas/v3.1.0#fixed-fields-12 Asked May 7 ’21 at 08:43 BorisBeast 2 Answers: hi @BorisBeast, the plan is definitely there….

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swagger – How to define this array of objects in OpenAPI?

How to write an OpenAPI definition for the following JSON? Bazically it is an array consisting of two objects with similar attributes but different fields. [ { “studentname”: “somename”, “studentrollno”: “somerollno”, “studentsubjects”: [ { “level”: “third”, “physics”: “xyz”, “maths”: “somevalue” }, { “level”: “second”, “physics”: “abc”, “maths”: “somevalue11” } ],…

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Introducing CreateAPI | kean.blog

If you’ve tried OpenAPI spec generators, you know how it goes. They get you about 60-80% there, but you end up having to modify the code by hand. For one of the specs (GitHub REST API spec), a popular code generator I tried produced more than 300 compile-time errors. With…

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fairtracks/fairtracks_validator_python: FAIRification of Genomic Data Tracks JSON Schema validator, Python edition

GitHub – fairtracks/fairtracks_validator_python: FAIRification of Genomic Data Tracks JSON Schema validator, Python edition You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here:…

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Quick questions about Alevin and AlevinQC

I have just started using Alevin and I have few basic queries. And I am asking this because I couldn’t find it in the documentation How to know how many reads are uniquely mapping and how many are multi mapping when doing quantification with Alevin. The alevin_meta_info.json says Number of…

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Install alphafold on the local machine, get out of docker.

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

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How can I get PHRED score?

How can I get PHRED score? 1 Hi, all. I am trying to get the assembly stat(Table S1.) according to the following paper about de novo assembly. [www.ncbi.nlm.nih.gov/pmc/articles/PMC7266049/%5D%5B1] In the table, there is an item “Mean read PHRED score after filtering and trimming”. How can I get this? Is there…

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MiXCR error with the complied cat TCR library

MiXCR error with the complied cat TCR library 0 Dear great helpers, I compiled json library for cat’s TCR using ‘repseqio’ as attached file. The command lines were as followed: $MIXCR analyze amplicon –threads 20 –library imgt –species “cat” –starting-material rna –5-end v-primers –3-end j-primers –adapters adapters-present –receptor-type tcr –region-of-interest…

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Downloading Files In Kaggle Gives

What if the grid variables in the source dataset DON’T share the same axis variables? Projected Gridded Data; Data Types; Media Files; AWS S3 Files; NcML; NCO. We use cookies on Kaggle to deliver our services analyze web traffic and improve your experience on the site. By using Kaggle you…

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How to install hisat2 on Mac OS Big Sur

How to install hisat2 on Mac OS Big Sur 0 I’d like to install HISAT2 on Mac OS Big Sur ver.11.5.2. I have tried to install HISAT2 by using bioconda (Hisate2 :: Anaconda), and the installation seemed to be successful, but when I tried to start hisat2, I’m getting the…

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kaggle datasets for tableau

The homepage is full of small visualizations telling stories about each data set. This is the default Tableau location (if you’ve not changed) so far. Transformation processes can also be referred to as data wrangling, or data munging, transforming and mapping data from one raw data form into another format…

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GitHub – anitaokoh/Automating_kaggle_dataset_download

GitHub – anitaokoh/Automating_kaggle_dataset_download Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time This .sh script helps to switch to root directory Install kaggle create a .kaggle directory and move the kaggle.json file to .kaggle (.kaggle must be created in the root directory) get the…

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Getting Started With Kaggle #1: Text Data (Quora Question Pairs, Spam SMSes)

Getting Started With Kaggle #1: Text Data (Quora Question Pairs, Spam SMSes) | Jessica Yung Exciting Kaggle Competitions With Cash Prizes In Data Science Kaggle Text Data Dating lofconf.ristoranteallacacciatora.it 24.8.2021 If you are a data science professional or a machine learning…

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Metadata for splice variant VCF

Metadata for splice variant VCF 0 Hi all, I am making manual VCF for splice site Variant using IGV tool.. I can make the VCF fine but I don’t know that meta data required for splice variants VCF . Small variant vcf metadata is not working as I am not…

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How do I start clue GO in R using the cytoscape REST API?

How do I start clue GO in R using the cytoscape REST API? 0 Hi there, I am trying to connect to open the Clue GO application in R using cytoscape REST API. I have the following code: port.number = 1234 host.address <- “localhost” cytoscape.base.url = paste(“http://”,host.address,”:”, toString(port.number), “/v3.11.1″, sep=””)…

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Pybedtools error sans

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

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graph datasets kaggle

This graph is pretty big, for global graph queries you’d need a page-cache of 6G and heap of 16G to work with it. bar_chart Datasets. Found insideWith this practical book, you’ll learn how to design and implement a graph database that brings the power of graphs to bear on a…

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