ReQue | Benchmark Workflow and Dataset Collection | Genomics library

 by   hosseinfani Python Version: v0.1.0 License: Non-SPDX

kandi X-RAY | ReQue Summary

kandi X-RAY | ReQue Summary

ReQue is a Python library typically used in Artificial Intelligence, Genomics applications. ReQue has no bugs, it has no vulnerabilities, it has build file available and it has low support. However ReQue has a Non-SPDX License. You can download it from GitHub.

A Benchmark Workflow and Dataset Collection for Query Refinement
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              ReQue has a low active ecosystem.
              It has 16 star(s) with 3 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 13 open issues and 17 have been closed. On average issues are closed in 32 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of ReQue is v0.1.0

            kandi-Quality Quality

              ReQue has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              ReQue has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              ReQue releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed ReQue and discovered the below as its top functions. This is intended to give you an instant insight into ReQue implemented functionality, and help decide if they suit your requirements.
            • Run build function
            • Read expanded queries from file
            • Perform aggregation on expanders
            • Return model name
            • Validate examples
            • Forward a single document
            • Apply pooling to encodings
            • Encodes a list of queries into a query
            • Create a sequence mask
            • Compute an embedding
            • Prepare batch of examples
            • Decodes source_rep
            • Predict the prediction
            • Performs decoding
            • Compute attention
            • Compute the decision loss
            • Expand expanded queries in QExpander
            • Compute the classification loss
            • Update the model
            • Load examples from a file
            • Runs the encoder
            • Forward embedding
            • Convert csv to json
            • Aggregate expanders
            • Get model name
            • Stem a string
            • Predict for given examples
            • Gets the expanded query string
            • Validate the given model with the given arguments
            Get all kandi verified functions for this library.

            ReQue Key Features

            No Key Features are available at this moment for ReQue.

            ReQue Examples and Code Snippets

            No Code Snippets are available at this moment for ReQue.

            Community Discussions

            QUESTION

            Rasterio " does not exist in the file system, and is not recognized as a supported dataset name."
            Asked 2021-Jun-03 at 14:53

            ANSWER

            Answered 2021-Jun-03 at 01:54

            QUESTION

            How to post the data in api fom Android java?
            Asked 2021-May-25 at 21:41

            This is my API:

            https://www.postman.com/collections/ebbe318b42c68fc7740f

            I want upload/post the data inside this path in api

            ...

            ANSWER

            Answered 2021-May-25 at 05:48

            The response string is in the format of JSONObject and not JSONArray. You need to parse it.

            Source https://stackoverflow.com/questions/67682300

            QUESTION

            Parsing error message using substr and indexOf not working
            Asked 2021-May-18 at 08:08

            I'm trying to extract a substring from an error message I receive and parse it to JSON. However it seems something with the indexOf or the substring method is not working as expected.

            Here's the full error message I'm trying to parse:

            ...

            ANSWER

            Answered 2021-May-18 at 08:08

            The javascript substr function takes 2 params.

            First being the start index and second being the length of the string from the start index that you want to take.

            Check the snippet.

            Source https://stackoverflow.com/questions/67582029

            QUESTION

            How to get data from API based on other values types
            Asked 2021-May-08 at 10:38

            I have a question, that i can't resolve. I have a API reques fere i need to get Image from that API. I have Images section fhere i have something like this:

            ...

            ANSWER

            Answered 2021-May-08 at 10:27

            If it is indeterminate that always FRAME is the first element or not, you'll need to find it in array.

            e.g. :

            Source https://stackoverflow.com/questions/67446431

            QUESTION

            Dependency Injection conceptual problem: where to instantiate new object to save to the db?
            Asked 2021-May-06 at 18:32

            I am working on a small toy program to learn some basics about DI and IoC on .Net Core 3.1.

            I have several questions, mostly consisting on where and when to perform certain actions.

            I have created the following architecture for my project:

            A DAL layer, Database First, that has the db entities, context, and extensions for the entities, along with a generic implementation of a repository:

            ...

            ANSWER

            Answered 2021-May-06 at 18:32

            Dependency Injection is the concept of passing depended on objects into the object itself. In this case passing the IRepository repository into the AnonymousLoginService means that AnonmyousLoginService is dependent upon IRepository. It has nothing to do with the parameters passed into the methods.

            If you feel it is best to have the separation of concerns and instantiating new db models in the method to verify that it is valid, instead of accepting user input as a db model and passing it in. It is okay.

            Having the Domain Layer in a separate application is not wrong at all. Especially if you don't want to have to create a new Domain Layer for every application built. The Domain Layer could be used this way to loosely couple the code and have one single Domain Layer for multiple applications. Assuming that method return types, method names, and method parameters don't change, a change to the Domain Layer should not break any project depending on it.

            As far as having the api know about both types of models (db and api models) sounds a lot better than having the Domain Layer know about both types of models. The Domain Layer would probably be better served to only know about Domain Models, then every application that uses the Domain Layer could also have access to the Domain Models. Instead of having the Domain Layer understand models from multiple projects, the only thing to consider is how secure the domain models should be? Maybe have set of dummy domain models (public facing db models) and a set of private db models (actual db models) and the Domain Layer gives access to the dummy models and then from there instantiates the actual db models. Ensuring that the actual logic and code is encapsulated.

            Source https://stackoverflow.com/questions/67423753

            QUESTION

            NPM Login without manually entering the username, password & email
            Asked 2021-Apr-19 at 07:53

            I have been able to login to my npm registry manually, ie: on my local machine - but for some reason it's not working when it goes through the CI. The problem here is that after I execute the npm login command, the program is waiting for the manual user input (username, password, email) and I couldn't find a way to send these inputs in the pipeline (where I can't make manual user input):

            These different approaches I tried:

            1. Copy the npm auth token from my local machine into the environment variables of the gitlab CI/CD Settings, and then just copy them into the global .npmrc at the root directory: This results in an error (unauthenticated):

            ...

            ANSWER

            Answered 2021-Apr-19 at 07:53

            The methods above were maybe not wrong at all, but somehow it only worked for me after using _auth instead of _authToken value in the .npmrc file.

            This is described here: https://gruchalski.com/posts/2020-09-09-authenticate-to-private-jfrog-npm-registry/

            After running this curl command I received everything that I needed to put into my global .npmrc file:

            Source https://stackoverflow.com/questions/66442046

            QUESTION

            Safari does not prompt for basic authentication credentials for cross-origin script and link tags even with crossorigin attribute set
            Asked 2021-Apr-05 at 18:42
            SO Questions Reviewed

            I'm aware of the following questions:

            Safari: "Blocked https://... from asking for credentials because it is a cross-origin request." after updating to Angular 8
            How to use Angular behind Basic Auth protection?
            Safari blocks URL from asking for credentials because it's a cross-origin request

            But I've not been able to solve my issue.

            The use case

            I have some CSS and JS files that cannot be made openly public and therefore are protected by Basic Authentication. These files are located in a different origin (Let's say under Basic Auth-protected https://mycdn.com/) from where they're requested (Let's say https://myapp.com/).

            Expectation

            When I try to render a simple HTML page at https://myapp.com that includes these files from https://mycdn.com/ I expect to be prompted for Basic Auth-credentials and for the browser to parse and execute them correctly.

            Results Chromium and Firefox

            Latest Chromium-like and Firefox browsers behave as I expect, if my page is behind Basic Auth, then they prompt me for the app's site credentials and then they prompt me a second time for the "CDN" credentials (Not the most convenient thing UX-wise, but it serves the purpose). After that the page renders without issues.

            Safari

            Safari, (either desktop [14.0.3] or mobile [iOS 14]) on the other hand, behaves different. If my page is behind Basic Auth, it prompts me for credentials and starts rendering its contents, but when the engine reaches my files, it does NOT prompt me for credentials and it logs some error messages in the console stating a 401 Unauthorized HTTP error occurred and depending on the script, the console will also contain an error saying:

            ...

            ANSWER

            Answered 2021-Apr-05 at 18:42

            Per https://trac.webkit.org/changeset/228486/webkit/, the Safari behavior described in the question is intentional. Specifically, Safari blocks cross-origin requests for page subresources, and logs this:

            Blocked from asking for credentials because it is a cross-origin request.

            The https://trac.webkit.org/changeset/228486/webkit/ commit message gives this rationale:

            Prompts for credentials to load cross-origin subresources are typically seen as unexpected by a person that navigates to- or interacts with- a web page. The cross-origin and implicit loading nature of these subresources makes asking for credentials questionable because they are not being served by the same origin of the page a person explicitly loaded and are not guaranteed to correspond to an explicit user interaction other than the initial load of the page. We know that subresources that ask for credentials can be abused as part of a phishing attack. It seems reasonable to disallow cross-origin subresources from asking for credentials due to their questionable nature and the risk for abuse.

            That commit message, written in 2018, also makes this claim:

            This will also make the behavior of WebKit match the behavior of Chrome.

            But while it’s possible that in 2018 Chrome may have also blocked subresources from prompting for credentials, it’s not true for Chrome 89. However, it does seems to be true for Chrome 91. So it may be that Chrome is in the process of changing its behavior to do the same blocking Safari does.

            So I think the bottom line is: It isn’t possible to make Safari prompt for credentials for subresources, and it’s also not safe to build web applications on the assumption that prompting for credentials for subresources will continue to work in Chrome (nor in Firefox either, over the long term).

            Source https://stackoverflow.com/questions/66945903

            QUESTION

            How to access the last child tag in a parent tag?
            Asked 2021-Mar-28 at 20:34

            how will I access the last span element in my p tag? I have 4 span tags in my p tag I want to access the last one and do changes to it!! I've added styling to the p span body{} but they all are changing I want the last span tag to be accessible.

            for example here is the code!

            ...

            ANSWER

            Answered 2021-Mar-28 at 20:23

            Use the last-of-type selector

            Source https://stackoverflow.com/questions/66845831

            QUESTION

            pymongo + flask + gunicorn: "Authentication failed" before first operation when "connect=False"
            Asked 2021-Mar-23 at 18:19

            I'm using MongoDB Atlas. I'm have this URL for connecting: mongodb+srv://:@/?retryWrites=true&w=majority&authSource=admin.

            I'm using this stack: flask, gunicorn, pymongo, mongoengine (i don't think that it is related, because mongoengine actually uses pymongo).

            gunicorn config:

            • sync workers,
            • threads = 1,
            • workers count = 8

            When connecting, i'm using connect=False because pymongo itself is not fork-safe. With connect=False it will connect to the DB before first operation. It need to be set to False, because gunicorn uses pre-fork model.

            But I am faced with the following situation:

            1. On first request (endpoint makes some DB operations) i'm getting this error: pymongo.errors.OperationFailure: Authentication failed., full error: {'ok': 0, 'errmsg': 'Authentication failed.', 'code': 8000, 'codeName': 'AtlasError'}
            2. On second request everything is fine (i.e., DB operations were successfully completed).
            3. If you press many times on F5, then sometimes you will occur a "Authentication failed" error, and sometimes everything will be fine.

            If i'm set connect=True, everything will be fine. I'm never seen this "Authentication failed" error.

            But then i'm getting this warning message: UserWarning: MongoClient opened before fork. Create MongoClient only after forking. See PyMongo's documentation for details: https://pymongo.readthedocs.io/en/stable/faq.html#is-pymongo-fork-safe.

            So, obviously, connect need to be set to False.

            I'm tested with two workers. Looks like this situation occurs:

            1. Let's say i have two gunicorn sync workers with following pid's: 22429 and 22430.
            2. I'm getting request. Worker 22429 handles it. Everything is fine, because it is first worker and looks like it successfully made a DB connection.
            3. I'm pressing F5, worker 22429 again handles it and everything is fine.
            4. I'm pressing F5 again, and now worker 22430 handles it. It throws an error "Authentication failed."
            5. I'm pressing F5 again, worker 22430 handles it. Now everything is fine, because that worker has made a connection.
            6. Now, all my workers (i have only two) were connected to the DB. Doesn't matter how many times i'm press on F5, every request will be successfully completed.

            But why it happens on first reques? From pymongo: "if connect=False, then connect on the first operation.". If i'm understanding it right, pymongo should connect before actual first operation, successfully completed the connection, and only then perform that operation.

            Then why my first DB operation fails for each worker? How i should handle this?

            ...

            ANSWER

            Answered 2021-Mar-23 at 18:19

            Actually, the problem was with Mongoengine, not PyMongo. On Mongoengine GitHub I didn't find anything that is related to this issue. I tried many things with Mongoengine to fix this issue, but nothing has worked. The only solution was to refuse Mongoengine and use only PyMongo.

            I rewrote my project to use only PyMongo. Fortunately, it was only beginning of the project, so, it didn't take much time. After rewriting everything worked as expected with exact same configuration.

            Unrelated to this question:

            For those who thinking about using Mongoengine or PyMongo. Use PyMongo. It is much easier to work with PyMongo directly, because it implements actual MongoDB documentation. Mongoengine changes some concepts, and eventually it is becoming hard to read both official MongoDB documentation and Mongoengine documentation which implements some concepts from MongoDB documentation in a different manner. And yes, by refusing one more abstraction you will avoid problems like my question.

            Source https://stackoverflow.com/questions/66044376

            QUESTION

            Symfony / api-platform PATCH NotEncodableValueException: "Syntax error"
            Asked 2021-Mar-19 at 16:01

            I use api-platform, GET and POST work's fine , i need to patch "isFinished" in my entity but i have an error : REQUES Uncaught PHP Exception Symfony\Component\Serializer\Exception\NotEncodableValueException: "Syntax error"

            Do you think my entity have bad configuration ? Thank you for help.

            ...

            ANSWER

            Answered 2021-Mar-19 at 16:01

            I think the problem is about your Content-Type, check it. It should be application/json change it if it was somethings else

            Source https://stackoverflow.com/questions/66711541

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

            Vulnerabilities

            No vulnerabilities reported

            Install ReQue

            You can download it from GitHub.
            You can use ReQue 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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            gh repo clone hosseinfani/ReQue

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