PubData | Smart search engine for all bioinformatics databases | Database library

 by   Bohdan-Khomtchouk Python Version: Current License: No License

kandi X-RAY | PubData Summary

kandi X-RAY | PubData Summary

PubData is a Python library typically used in Institutions, Learning, Education, Database applications. PubData has no bugs, it has no vulnerabilities and it has low support. However PubData build file is not available. You can download it from GitHub.

PubData is a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical FTP data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is hosted as both a web application and a standalone graphical user interface (GUI) software program, while PubMed is hosted as an online web server. PubData is built on novel network programming and natural language processing algorithms that can patch into the FTP servers of any user-specified bioinformatics database, query its contents, and retrieve files for download. PubData is written in the Python programming language (specifically, Django and PyQt4). PubData can remotely search, access, view, and retrieve files from the deeply nested directory trees of any major bioinformatics database via a local computer network. By assembling all major bioinformatics databases under the roof of one software program, PubData allows the user to avoid the unnecessary hassle and non-standardized complexities inherent to accessing databases one-by-one using an Internet browser. More importantly, it allows a user to query multiple databases simultaneously for user-specified keywords (e.g., human, cancer, transcriptome). As such, PubData allows researchers to search, access, view, and download files from the FTP servers of any major bioinformatics database directly from one centralized location. By using only a GUI or web application, PubData allows the user to simultaneously surf multiple bioinformatics FTP servers directly from the comfort of their local computer. Please cite: "Khomtchouk et al.: 'PubData: search engine for bioinformatics databases worldwide', 2016: within any source that makes use of any methods inspired by PubData.
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            kandi-support Support

              PubData has a low active ecosystem.
              It has 23 star(s) with 5 fork(s). There are 8 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 0 open issues and 9 have been closed. On average issues are closed in 5 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of PubData is current.

            kandi-Quality Quality

              PubData has 0 bugs and 0 code smells.

            kandi-Security Security

              PubData has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              PubData code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              PubData does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              PubData releases are not available. You will need to build from source code and install.
              PubData has no build file. You will be need to create the build yourself to build the component from source.
              PubData saves you 19061 person hours of effort in developing the same functionality from scratch.
              It has 37641 lines of code, 142 functions and 42 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed PubData and discovered the below as its top functions. This is intended to give you an instant insight into PubData implemented functionality, and help decide if they suit your requirements.
            • Helper function to traverse a single file
            • Recursively walk recursively
            • Recursively walk directory
            • List the contents of a directory
            • Checks the server state
            • Process the dispatcher
            • Exit the server
            • Double clicked slot
            • Add an item to the list
            • Update the ftp command
            • Enable the download button
            • Updates the status of an ftp server
            • Refiner of words
            • Create a JSON file with the tag
            • Start manual update
            • Create a wordnet file
            • Stop the unix daemon
            • Start the service
            • Create the recommender system tables
            • Start a Unix daemon process
            • Create the server names table
            • Start the server
            • Update all servers
            • Add a new server
            • Create the WordNet table
            • Creates the database
            Get all kandi verified functions for this library.

            PubData Key Features

            No Key Features are available at this moment for PubData.

            PubData Examples and Code Snippets

            No Code Snippets are available at this moment for PubData.

            Community Discussions

            QUESTION

            I got connection refused for python TCP HolePunching
            Asked 2020-Dec-07 at 09:46

            This is the code in serverside:

            ...

            ANSWER

            Answered 2020-Dec-07 at 09:46

            in util.py the ip should be public not private

            Source https://stackoverflow.com/questions/64805071

            QUESTION

            Adding a key-value pair to an object inside loop using React useState hook
            Asked 2020-Jun-30 at 02:24

            I'm trying to add a key-value pair to an object using useState inside map function. However, the spread operation in setContainer({...container, [data.pk]: data.name}); seems to be ineffective.

            The code snippet below exactly illustrates the problem that I'm trying to solve. In fact, in my original code container is declared at another ContextProvider component and referenced using useContext, but I replaced it with useState for simpliticy.

            I guess it has to do with the asynchronous nature of setState hook, but I don't fully understand what's going on under the hood.

            Please let me know what is causing this issue and how to yield the outcome I expected. Thank you.

            ...

            ANSWER

            Answered 2020-Jun-26 at 15:34

            You're right, it's because of asynchronous nature of setState hook, it basically runs in batch.

            From react docs:

            setState() does not immediately mutate this.state but creates a pending state transition. Accessing this.state after calling this method can potentially return the existing value. There is no guarantee of synchronous operation of calls to setState and calls may be batched for performance gains.

            You can create an object first and set it once the loop is completed. Also you shouldn't use map here. Since you're not creating a new array.

            Source https://stackoverflow.com/questions/62597448

            QUESTION

            Reorder FlatList based on a value in the contents
            Asked 2020-May-09 at 13:31

            I'm passing data to my FlatList using the following code

            ...

            ANSWER

            Answered 2020-May-08 at 07:18

            You can sort Data Source State and re-render FlatList, but it's better to do all calculations before rendering data.

            Source https://stackoverflow.com/questions/61673822

            QUESTION

            Right way to loop and amend an object without re-render loops
            Asked 2020-Apr-30 at 07:47

            My main App component calls in a JSON object of venues with their lat / long data.

            I am rendering this JSON object out using FlatList and this all works fine. The app is also pulling the device's location so that I can sort this data into distance sorted information.

            I'm currently trying to modify this JSON object to add in the distance from the device to the venue and put this back into the FlatList but this seems to be throwing an infinite re-render loop and I don't actually think it's able to trigger my distance checks.

            This is my component here. I've commented out the distance work which I thought was the cause but it's still appearing to throw a re-render infinite loop

            ...

            ANSWER

            Answered 2020-Apr-30 at 07:45

            Your useEffect in Fulllist is being causing the re-renders.

            To make it run only once when component is mounted (like componentDidMount lifecycle), add an empty dependency array as a second parameter

            Source https://stackoverflow.com/questions/61518200

            QUESTION

            Output SecKeyCopyExternalRepresentation
            Asked 2020-Apr-24 at 17:34

            I'm trying to pass around a public key from my iPhone to other parties, however I am unable to use the output from iOS.

            ...

            ANSWER

            Answered 2018-Apr-23 at 14:15

            I havent quite found the answer to the question as I still don't know what exactly the output is that Apple provides, however, I came up with a solution found in this key import export manager.

            Source https://stackoverflow.com/questions/49967723

            QUESTION

            Retrieve entire document as array of entries
            Asked 2019-Mar-24 at 16:31

            I have a collection in Firestore with the following structure:

            ...

            ANSWER

            Answered 2019-Mar-24 at 16:17

            QUESTION

            TextField will not load from RealmSwift
            Asked 2018-Nov-15 at 13:31

            So here is the problem that I have been going crazy with. I have an app that uses Realm as its Database. I have used Realm in the past with tableviews and it works properly. I can't seem to get the textField data that I saved to load into my view on viewDidLoad. With tableViews there is a reloadData method, but that isn't the case with textFields. I need the data that is in my data base to load into the view on viewDidLoad and I have confirmed several times that data has been saved and is sitting in the dataBase just waiting to load into the view, but it will not load.

            ...

            ANSWER

            Answered 2018-Nov-15 at 13:31

            Thanks to Mrkrisher on Discord here is the answer on how to display the last saved textViews and textFields from Realm into your viewDidLoad

            Source https://stackoverflow.com/questions/53272085

            QUESTION

            How to use an onItemClickListener to expand a listView when clicked?
            Asked 2018-Mar-10 at 07:11

            I am currently completing a piece of coursework whereby I need to parse an XML file using android and display its data in a useful format on an android phone.

            I have used XmlPullParser and have successfully parsed the file into a listView. Here is the result:

            To improve the layout above I have set the program to display the title alone (i.e. A78 Seamill etc) and when the user clicks on the title I would like info relating to the works to appear as a drop down.

            In my MainActivity.java class I have a setOnItemClickListener that looks like the following:

            ...

            ANSWER

            Answered 2018-Mar-10 at 04:26

            You should use a RecyclerView instead of a ListView. Then you will have ItemAnimator available to handle the insertion animations. Then all you have to do is call notifyItemInserted to produce the desired effect.

            Tutorial: http://frogermcs.github.io/recyclerview-animations-androiddevsummit-write-up/

            Source https://stackoverflow.com/questions/49203436

            QUESTION

            How to get variables from another script C#
            Asked 2018-Mar-07 at 06:23

            I am completely stuck, and I feel like it's a simple issue too. Basically, I have two strings pubKey and privKey in one script called WalletGen.cs and I want to display them in Loader.cs. In my search for an answer, all I could find is how to do it in Unity, which doesn't exactly help since I'm not using Unity.

            Here is the code for WalletGen.cs

            ...

            ANSWER

            Answered 2018-Mar-07 at 05:00

            As your code stands you cannot access pubKey or privKey because they exist only in the scope of the method WalletHash.

            To expose them you could return them from WalletHash, eg.

            Source https://stackoverflow.com/questions/49144104

            QUESTION

            XSLT: Value of element attribute gets lost when applying a select template
            Asked 2017-Jul-11 at 13:56

            I'm having a problem when I apply a to my xml document.

            The extract of XML is:

            ...

            ANSWER

            Answered 2017-Jul-10 at 18:21

            It seems that your (EDIT: see below) templates don't copy attribute values correctly.

            So add an identity template

            Source https://stackoverflow.com/questions/45017449

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

            Vulnerabilities

            No vulnerabilities reported

            Install PubData

            You can download it from GitHub.
            You can use PubData like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            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 .
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            https://github.com/Bohdan-Khomtchouk/PubData.git

          • CLI

            gh repo clone Bohdan-Khomtchouk/PubData

          • sshUrl

            git@github.com:Bohdan-Khomtchouk/PubData.git

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