atlas | Expression Atlas is made up of a collection of web services

 by   ebi-gene-expression-group Java Version: v28.0.2 License: Apache-2.0

kandi X-RAY | atlas Summary

kandi X-RAY | atlas Summary

atlas is a Java library typically used in Healthcare, Pharma, Life Sciences applications. atlas has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can install using 'npm i @ebi-gene-expression-group/expression-atlas-disclaimers' or download it from GitHub, npm.

Expression Atlas is made up of a collection of web services, online resources and software to explore gene expression patterns associated or in response to experimental conditions. At its core, it is a Java EE 7 application built with several components from the Spring framework. It specifically depends on modules from the Data Access/Integration, Web and Core Container groups. If in doubt, refer to the section in the parent POM file of the project. All the code, resources and static assets are packaged with Maven using the WAR plugin; the end result is a file with extension .war which is actually a zipped archive that follows the conventions and directory layout of Java EE applications. This WAR file is later then mounted by Apache Tomcat. Other servlet containers might work although none other but Tomcat 7 have been tested.
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            kandi-support Support

              atlas has a highly active ecosystem.
              It has 25 star(s) with 4 fork(s). There are 15 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 0 open issues and 5 have been closed. On average issues are closed in 105 days. There are no pull requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of atlas is v28.0.2

            kandi-Quality Quality

              atlas has no bugs reported.

            kandi-Security Security

              atlas has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              atlas is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              atlas releases are available to install and integrate.
              Deployable package is available in npm.
              Build file is available. You can build the component from source.

            Top functions reviewed by kandi - BETA

            kandi has reviewed atlas and discovered the below as its top functions. This is intended to give you an instant insight into atlas implemented functionality, and help decide if they suit your requirements.
            • Extracts the results as JSON object
            • Creates a card which contains all the images of the experiment .
            • Fetches the profiles for the given gene ids .
            • Compares two profiles .
            • Populate the factor definitions for the given runs .
            • Reads the next contrast analytics and returns the results .
            • Attempt to perform a stateful operation .
            • Get the bioentity identifiers of the experiment .
            • Creates the description for an experiment .
            • Converts the query to a query plan .
            Get all kandi verified functions for this library.

            atlas Key Features

            No Key Features are available at this moment for atlas.

            atlas Examples and Code Snippets

            No Code Snippets are available at this moment for atlas.

            Community Discussions

            QUESTION

            How to properly connect to MongoDB using Cloud functions?
            Asked 2022-Mar-25 at 16:08

            I would like to connect to my Atlas cluster only once per instance running Cloud Functions.

            Here is my code for an instance :

            ...

            ANSWER

            Answered 2022-Mar-25 at 16:08

            You can store your database client as a global variable. From the documentation,

            Cloud Functions often recycles the execution environment of a previous invocation. If you declare a variable in global scope, its value can be reused in subsequent invocations without having to be recomputed.

            Try refactoring the code as shown below:

            Source https://stackoverflow.com/questions/71353766

            QUESTION

            Phaser 3: Spritesheet doesn't load correctly
            Asked 2022-Feb-23 at 05:57

            I tried to add a spritesheet to my Phaser game the same way I've done it a few times before, however this time it seems to not load the images correctly, causing it to display a black & green square instead and causing it to throw an error when trying to play an animation.

            Can anyone tell what is causing this issue?

            (Warning: Playing the Code here seems to freeze up your browser for a few seconds, alternatively view on JSFiddle: https://jsfiddle.net/cak3goru/4/ )

            ...

            ANSWER

            Answered 2022-Feb-23 at 05:57

            The problem is, that you are using the wrong function, you should use this.anims.generateFrameNames, and not this.anims.generateFrameNumbers.

            And set the correct key clean for the sprite.
            the line should be:

            Source https://stackoverflow.com/questions/71225698

            QUESTION

            curl to fetch with digest flag
            Asked 2022-Feb-19 at 15:18

            There has been other questions on the subject, but nothing seems working for me.
            I have a functional CURL, but I want to translate to JS (with Node).

            CURL ...

            ANSWER

            Answered 2022-Feb-19 at 13:04
            PHP

            You need to specify that it's a digest:

            Source https://stackoverflow.com/questions/71148572

            QUESTION

            Connect mongodb compass with node.js
            Asked 2022-Feb-19 at 08:53

            I'm trying to connect a nodejs with mongodb using mongo db compass and im getting the following error:

            ...

            ANSWER

            Answered 2021-Nov-21 at 14:18

            For first, you have double quotes in the connection variable. Secondly: it seems to me that mongoUri should include the username and password in the query string, right?

            Source https://stackoverflow.com/questions/70055282

            QUESTION

            pymongo [SSL: CERTIFICATE_VERIFY_FAILED]: certificate has expired on Mongo Atlas
            Asked 2022-Jan-29 at 22:03

            I am using MongoDB(Mongo Atlas) in my Django app. All was working fine till yesterday. But today, when I ran the server, it is showing me the following error on console

            ...

            ANSWER

            Answered 2021-Oct-03 at 05:57

            This is because of a root CA Let’s Encrypt uses (and Mongo Atals uses Let's Encrypt) has expired on 2020-09-30 - namely the "IdentTrust DST Root CA X3" one.

            The fix is to manually install in the Windows certificate store the "ISRG Root X1" and "ISRG Root X2" root certificates, and the "Let’s Encrypt R3" intermediate one - link to their official site - https://letsencrypt.org/certificates/

            Copy from the comments: download the .der field from the 1st category, download, double click and follow the wizard to install it.

            Source https://stackoverflow.com/questions/69397039

            QUESTION

            MongoDB - How to use substitute value when there is missing field-and-value pair
            Asked 2022-Jan-23 at 13:14

            I have a documents in MongoDB Atlas with this structure:

            ...

            ANSWER

            Answered 2022-Jan-21 at 20:00

            QUESTION

            Unable to copy a database from one mongodb account to another
            Asked 2022-Jan-22 at 21:25

            I usually create a copy of a database in the same cluster in the same account like this:

            1. DUMP THE ORIGINAL DATABASE

            mongodump --uri 'mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --forceTableScan

            1. RESTORE THE DATABASE FROM THE DUMP FILE

            mongorestore --uri 'mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --nsFrom='ORIGINAL_DATABASE_NAME.' --nsTo='NEW_DATABASE_NAME.'

            And that works perfectly.

            Now, I created a new MongoDB atlas account, and I am trying to copy the original database into the new account.

            So the first step is similar:

            1. DUMP THE ORIGINAL DATABASE

            mongodump --uri 'mongodb+srv://ORIGINAL_ACC_USER_NAME:ORIGINAL_ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --forceTableScan

            1. RESTORE THE DATABASE FROM THE DUMP FILE

            Here I could not find which params to use.
            In the first example, in the second step, the URI is like this:

            mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME

            So I obviously should replace

            ACC_USER_NAME:ACC_USER_PASSWORD

            with

            NEW_ACC_USER_NAME:NEW_ACC_USER_PASSWORD

            But, what about the ORIGINAL_DATABASE_NAME, I could not find an equivalent to put there. The rest of the params:

            --archive="DUMP_FILE_NAME" --nsFrom='ORIGINAL_DATABASE_NAME.' --nsTo='NEW_DATABASE_NAME.'

            should remain the same.

            ...

            ANSWER

            Answered 2022-Jan-22 at 21:25
            Step 1

            First, you should do mongodump. You already did that correctly.

            Source https://stackoverflow.com/questions/70785706

            QUESTION

            Azure Static Web App: transform Blazor webassembly appsettings.json in Azure DevOps
            Asked 2022-Jan-06 at 09:09

            I have a static blazor web app that has the following structure:

            and the following setting in appsettings.json:

            ...

            ANSWER

            Answered 2021-Dec-01 at 07:57

            I don't think it's possible to manipulate the configuration file during the build/deployment that happens within the Oryx-container. What you could do is to manipulate the file during the pipeline run by, for example, tokenizing the environment-specific configuration values and replacing the tokens during the pipeline run. To achieve this with single json-file (ie. having just a file with the localhost-value stored in version control) you could use tokenizer- and replace tokens -task from Colin's ALM Corner extension collection (https://marketplace.visualstudio.com/items?itemName=colinsalmcorner.colinsalmcorner-buildtasks). Another option would be to have multiple environment-specific configuration files in version control and just copying a specific one over the appsettings.json during the pipeline run.

            Not sure if Static Web App environment variables could be utilized here, but adding it here if someone using GitHub Actions is looking for this - they are not yet supported by Azure Pipelines.

            https://docs.microsoft.com/en-us/azure/static-web-apps/build-configuration?tabs=github-actions#environment-variables

            Source https://stackoverflow.com/questions/70162453

            QUESTION

            Clamp geodesic to min/max latitude with d3
            Asked 2021-Dec-04 at 08:19

            I am using d3 to plot a route on a map:

            ...

            ANSWER

            Answered 2021-Dec-04 at 07:31

            A clipping function won't achieve the correct effect as it will cut your features not coerce them to follow that line.

            Instead, we can combine your projection with a geotransform to force the line to adhere to rules within the projected space:

            Source https://stackoverflow.com/questions/70220638

            QUESTION

            Can't install Matplotlib on Python 3.10 after its release (2021-10-05)
            Asked 2021-Nov-06 at 23:20

            After the release of Python 3.10, I reinstalled my modules for the newest version and I'm getting some trouble. First of all I tried to pip Numpy as it's the required one for matplotlib. But I got this problem:

            ...

            ANSWER

            Answered 2021-Nov-06 at 23:20

            As others have stated, Python 3.10 is not currently compatible with Matplotlib. You need to install and use Python 3.9 until it is supported. Until then you have a few options:

            Windows

            You can use the Python Launcher for Windows (py.exe) script to choose which Python version to run like so:

            py.exe script help: py -h

            List all installed versions py -0

            Use a specified version py -3.9

            e.g. 1 Create a virtual environment using python 3.9 py -3.9 venv .venv

            e.g. 2 install matplotlib with pip using python 3.9 py -3.9 -m pip install matplotlib

            Linux

            On Linux you can run whatever Python version you like like so:

            python3.9

            You can set up a local (your working directory and all sub-directories) virtual environment that will use your specified version like so:

            python3.9 -m venv .venv

            Which will set the version of python used to 3.9 while in the local directory, and allow you to type python instead of python3.9 each time you need it.

            Another relevant and helpful post by Rotareti here.

            Please note that I have not described how to activate and use Python Virtual Environments here in detail, for more information on using them read the python docs.

            Reference this answer if you're interested in installing a matplotlib release candidate.

            Source https://stackoverflow.com/questions/69466552

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install atlas

            You can install using 'npm i @ebi-gene-expression-group/expression-atlas-disclaimers' or download it from GitHub, npm.
            You can use atlas like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the atlas component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

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            https://github.com/ebi-gene-expression-group/atlas.git

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            gh repo clone ebi-gene-expression-group/atlas

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            git@github.com:ebi-gene-expression-group/atlas.git

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