Tag: json

parallel-fastq-dump install failed 0 Good morning, I am trying to install parallel-fastq-dump but I failed. And here is what ssh sever say: conda install parallel-fastq-dump Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current…

It’s a little hard to know what your goal is here based on the sample code, but I do find that your JSON snippet does not match any spec. I was able to edit it to add brackets to make the entries elements of a list: [ { “biosample_ontology”: {…

Hi guys, I need an help to understand the server side code generation pattern that I should use with the openapi-generator while exposing my REST endpoints: <plugin>                <groupId>org.openapitools</groupId>                <artifactId>openapi-generator-maven-plugin</artifactId>              …

When you work on a React & TypeScript project that fetches data from a REST API, keeping your data types in sync can be problematic. You obviously can create all the types on your frontend by hand. But this is a tedious and error-prone process. You might get a type…

I am using the openapi-generator to create a multipart/form-data. In an ideal situation I should be able to upload a file, and specify in the options what should happen with the file. I would like the options to be an object. For one or another reason, this does not seem…

Leadership role:- You will be responsible for supporting the system design and conducting the development to deliver the business solution for the project according to the requirements and engineering standards. He/she will perform system analysis, application development, unit testing, trouble-shooting, and operations support work. Client Details We are an forward…

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP155.GRCh37     This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh37; to use it, please install the devel version of Bioconductor. Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly Bioconductor version: Development (3.16) The 929,496,192 SNPs in this package were extracted from…

The isolate is a qualifier of the source feature that you can access like so: from Bio import SeqIO from pprint import pprint # Read genbank file for rec in SeqIO.parse(“genome.gb”, “genbank”): source = rec.features[0] pprint(source.qualifiers) will print: OrderedDict([(‘organism’, [‘Amauroderma calcitum’]), (‘mol_type’, [‘genomic DNA’]), (‘isolate’, [‘FLOR 50931’]), (‘db_xref’, [‘taxon:1774182’]), (‘country’,…

1. Overview In this article, we’ll write an API specification that allows returning two different objects for the same response code. We’ll demonstrate how we can use that specification to generate Java code and the Swagger documentation. 2. Presentation of the Problem Let’s define two objects. A Car has an…

什么是openapi 3.0 OpenAPI 3.0.0 是 OpenAPI The first official version of the specification,因为它是由 SmartBear Software 捐赠给 OpenAPI Initiative,并在2015年从 Swagger 规范重命名为 OpenAPI 规范. 介绍: OpenAPI 规范（OAS）,is to define a standard、programming language-independentRESTful API的规范.OpenAPI Specifications enable both humans and computers to“Do not contact with any program source code and documentation、Does not monitor network…

OpenAPI: combine JAXB and JSON (WRAPPER_OBJECT) correctly? Dear community, I’m a beginner with swagger/openapi. I want write Java classes with annotations and generate documentation by OpenAPI library. In my gradle project I use: implementation “io.swagger.core.v3:swagger-core:2.2.2” implementation ‘io.swagger.core.v3:swagger-annotations:2.2.2’ implementation “io.swagger.core.v3:swagger-jaxrs2:2.2.2” implementation ‘com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.2’ implementation ‘com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.13.2’ implementation ‘com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.13.2’ My demo class is: @XmlRootElement(name…

Rapini is a new tool that can generate custom React Query hooks using OpenAPI (Swagger) files. The Command Line Interface (CLI) tool will take a path to an Open API file and generate a package that includes react hooks, typescript types and axios http requests – and this package is…

dint May 9, 2022, 1:33pm #1 i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster o the UKB RAP? From the hail website, the following command can be used on your matrix file to annotate with these features: db =…

Transcript Lane: I’d like to share with you a high level view of why API specifications matter. How OpenAPI, AsyncAPI, JSON Schema and others are helping us standardize and deliver API lifecycle in a way that the machines understand. Also, allows us humans to better communicate, collaborate, and move forward…

I don’t see where you’re actually reading from the file in the first place. You have to actually read your path_text.txt before you can format it correctly right? with open(‘path_text.txt’,’r’,encoding=’utf-8′) as myfile: content = myfiel.read().splitlines() Which will give you [‘/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam’, ‘/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam’] in content. Now if you want to write this…

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I trying to install vina using pip and get this error: C:\Users\chase>pip install vina Collecting vina Using cached vina-1.2.3.tar.gz (95 kB) Installing build dependencies … done Getting requirements to build wheel … error ERROR: Command errored out with exit status 1: command: ‘D:\Anaconda\python.exe’ ‘D:\Anaconda\lib\site- packages\pip\_vendor\pep517\in_process\_in_process.py’ get_requires_for_build_wheel ‘C:\Users\chase\AppData\Local\Temp\tmpo4147jnr’ cwd: C:\Users\chase\AppData\Local\Temp\pip-install- x0_x1cyl\vina_418ca6103711445caf359fdf3574d54b…

You’ve in all probability heard of Kaggle knowledge science competitions, however do you know that Kaggle has many different options that may allow you to together with your subsequent machine studying challenge? For folks on the lookout for datasets for his or her subsequent machine studying challenge, Kaggle means that…

The following is a minimal OpenAPI description that describes how to call the /me endpoint on Microsoft Graph. This description is used in the following guides. openapi: 3.0.3 info: title: Microsoft Graph get user API version: 1.0.0 servers: – url: graph.microsoft.com/v1.0/ paths: /me: get: responses: 200: description: Success! content: application/json:…

How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…

I’m a relatively new qiime2 (bioinformatics tool based on python language) and python user. So far, I have been using qiime2 inside a virtual machine, which is ok but not great. Since I’m taking a python course and have gotten used to work with pycharm, I’m trying to install the…

goa version 3.7.2 Design The field name anyobject with Attribute MapOf(String, Any) should describe a map of string to any unknown value. For HTTP requests, the field anyobject can be sent like the following (i.e. any json object): { “anyobject”: { “testkey”: 10, “test1”: “testval”, “myarr”: [ { “nestedk”: {…

GitHub – ebi-wp/sss_json_schema: JSON schema for EBI’s Job Dispatcher sequence similarity search outputs This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window….

Steps: Open a terminal in dev cloud (+ on top left corner) Type following in the terminal pip install kaggle To use Kaggle API, create an account in kaggle official page(www.kaggle.com). Then, go to “My Account” tab of user’s profile and select “create new API token“. This will download the…

A new version of pins is available on CRAN today, which adds support for versioning your datasets and DigitalOcean Spaces boards! As a quick recap, the pins package allows you to cache, discover and share resources. You can use pins in a wide range of situations, from downloading a dataset…

Want to improve this question? Update the question so it’s on-topic for Cross Validated. Closed 11 hours ago. I have a code that has a data module and a model and I am training my model with Ray trainer, here is my code: class…

OpenAPI Generator team implemented jackson-databind-nullable module which you should include to your project. The newest version is 0.2.1. <dependency> <groupId>org.openapitools</groupId> <artifactId>jackson-databind-nullable</artifactId> <version>0.2.1</version> </dependency> If module will not be detected automatically you need to do it manually by: ObjectMapper mapper = new ObjectMapper(); mapper.registerModule(new JsonNullableModule()); Or if you using Jackson in…

Source: golang-github-albenik-go-serial Version: 2.5.0-1 Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of golang-github-albenik-go-serial the autopkgtest of golang-github-albenik-go-serial fails in testing when that autopkgtest is run with the binary packages of golang-github-albenik-go-serial from unstable. It passes when run with only packages from testing. In tabular form:…

I’m currently enrolled with a spring-boot project, and they are using an API first approach which I think is great… except that this approach leads to us generating our ingoing API clients + input models, and the chosen tool org.openapi.generator 5.3.0 is really bad at it. I have an API…

Tutorial to learn the steps involve in the installation of Jupyter Notebook on Debian 11 Bullseye using command terminal. What is Jupyter Notebook? The Jupyter Project is a non-profit initiative that aims to develop and provide open-source software and open standards for interactive work. One of the most famous products…

Koa intends to be a fully functional DSL for OpenAPI in Kotlin, including a Ktor plugin to add OpenAPI to your server Kotlin applications. install(Koa) { title = “Koa example” description = “Ktor + OpenAPI (+ Swagger UI) = Koa!” version = “1.2.3” } install(KoaSwaggerUi) // Optional, you can remove…

Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

GitHub – EvanBacon/App-Store-Connect-OpenAPI-Spec: Automatically tracks every copy of the App Store Connect OpenAPI JSON Spec This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab…

REST (Representational State Transfer) is an architectural style that can be used to communicate with web services. REST has a lot in common with protocols such as SOAP. It is used as a communication mechanism between two applications, or between an application and an online service. Many mobile…

I’ve got a Blazor WebAssembly project with an ASP.NET WebAPI hosted service. If I use the auto-generated code in the “Connected Services” in Visual Studio to retrieve the OpenAPI definition, I get a nice proxy representing all of the HTTP endpoints, complete with request and reply objects. But the generated…

0.8.0 • Published 1 year ago Share package openapi-apigee-node-utility openapi2apigee module converts a standard Open API spec (previously known as Swagger) into an Apigee API Proxy bundle and deploys into an Apigee Edge Organization. Now supports OAS v3 as well Pre-requisite Installation You can install openapi2apigee either through npm or…

This depends on the OpenAPI version. OpenAPI 3.1 Your example is valid in OpenAPI 3.1, which is fully compatible with JSON Schema 2020-12. type: – ‘null’ # Note the quotes around ‘null’ – string # same as type: [‘null’, string] The above is equivalent to: oneOf: – type: ‘null’ #…

Hi Rijan, Just to be sure I understand what you want: you have a list of species and you would like to get the accession numbers for the reference genomes for each one of them, is that correct? If so, you could try using the command datasets summary in combination…

In this weblog, you’ll learn to generate server code utilizing the OpenAPI Generator based mostly on an OpenAPI specification. The code will likely be generated for a Spring Boot Application, however OpenAPI helps many different languages which can be utilized. 1. Introduction In November I attended JFall, the biggest sooner…

Ok. So I’m doing this in a computing cluster for reference, and before doing anything I can see these conda environments: (base) [cjone228@jhu.edu@bc-login01 ~]$ conda env list # conda environments: # base * /home-1/cjone228@jhu.edu/miniconda3 picrust2 /home-1/cjone228@jhu.edu/miniconda3/envs/picrust2 qiime2-2019.10 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2019.10 qiime2-2019.7 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2019.7 qiime2-2020.2 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2020.2 qiime2-2020.6 /home-1/cjone228@jhu.edu/miniconda3/envs/qiime2-2020.6 Now when I try and install…

Need a little help. Cant get docs for any of my andpoints on swager-ui except default /api/schema/ and several endpoints from djoser library. I have created file with one simple service like: def auth2(request): json_dict = dict( _id=’2′, toc=”xyztoc”, name=”John”, mail=”[email protected]“, perm=’rwx’, important=”true”, moretok=’mrt’ ) return JsonResponse(json_dict) and in urls:…

I have a simple Spring Boot application with some routes and OpenAPI maps them and I can see the docs, play around with it when the project is running and so on. But what I am trying to figure out is, how to import an existing OpenAPI JSON schema and…

I’m trying to install Autodock Vina with pip command. But when I run the command pip install -U numpy vina: I get a the following error: Collecting vina Using cached vina-1.2.3.tar.gz (95 kB) Installing build dependencies … done Getting requirements to build wheel … error error: subprocess-exited-with-error × Getting requirements…

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…

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>…

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…

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…

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…

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…

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…

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…

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…

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, }), ); /* … */…

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”: […

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….

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” } ],…

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…

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:…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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=””)…

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,…

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…