reach | Wellcome tool to parse references | Machine Learning library

 by   wellcometrust Python Version: Current License: MIT

kandi X-RAY | reach Summary

kandi X-RAY | reach Summary

reach is a Python library typically used in Telecommunications, Media, Advertising, Marketing, Artificial Intelligence, Machine Learning, Deep Learning, Nodejs, Neural Network applications. reach has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Wellcome Reach is an open source service for discovering how research publications are cited in global policy documents, including those produced by policy organizations such as the WHO, MSF, and the UK government. Key parts of it include:. Wellcome Reach is written in Python and developed using docker-compose. It's deployed into Kubernetes. Although parts of the Wellcome Reach have been in use at Wellcome since mid-2018, the project has only been open source since March 2019. Given these early days, please be patient as various parts of it are made accessible to external users. All issues and pull requests are welcome. Contributing guidelines can be found in CONTRIBUTING.md.
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              reach has a low active ecosystem.
              It has 23 star(s) with 5 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 62 open issues and 242 have been closed. On average issues are closed in 72 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of reach is current.

            kandi-Quality Quality

              reach has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              reach is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              reach releases are not available. You will need to build from source code and install.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              It has 16743 lines of code, 409 functions and 173 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed reach and discovered the below as its top functions. This is intended to give you an instant insight into reach implemented functionality, and help decide if they suit your requirements.
            • Sync secrets from secrets_dir
            • Check if the cluster name matches the cluster name
            • Delete a k8s secret
            • Encode a plaintext payload
            • Make plots of negative references
            • Print the percentile of the data
            • Handles GET requests
            • Returns a context manager for the database
            • Handle POST request
            • Create a GitHub issue
            • Parse PDF files
            • Evaluate find section
            • Creates an argument parser
            • Parse a single article page
            • Process a single item
            • Return a list of policy names based on the source title
            • Execute the script
            • Handles GET requests
            • Execute fuzzy search
            • Parse the article
            • Create an API
            • Clean Elasticsearch index
            • Handle GET request
            • Execute the scraper
            • Refparse the references file
            • Handle GET requests
            Get all kandi verified functions for this library.

            reach Key Features

            No Key Features are available at this moment for reach.

            reach Examples and Code Snippets

            No Code Snippets are available at this moment for reach.

            Community Discussions

            QUESTION

            C++ If statement before case in switch
            Asked 2022-Apr-11 at 13:44

            I am tasked to rewrite some old software for my company and found an interesting construct inside the sources.

            ...

            ANSWER

            Answered 2022-Apr-11 at 13:44

            Is there any reason ... why you would write a construct like that?

            Only the author knows for sure (even they might not know). If there is source versioning metadata available, then associated commit message might be useful. Without more information, we can only guess what they were thinking. Some potential answers:

            • The author assumed that the condition of the if-statement would have some effect, but they were wrong and the mistake wasn't tested.
            • It's a vestigial result of some refactoring.
              • Perhaps some code was removed that used to make the statement meaningful.
              • Or perhaps it was copied from elsewhere where it did have a meaning.
              • Or perhaps there used to be a series of if-statements and there was an intention to replace them with a switch, but the change was half-assed.

            Source https://stackoverflow.com/questions/71828383

            QUESTION

            Group numeric vector by predefined maximal group sum
            Asked 2022-Jan-27 at 09:29

            I have a numeric vector like this x <- c(1, 23, 7, 10, 9, 2, 4) and I want to group the elements from left to right with the constrain that each group sum must not exceed 25. Thus, here the first group is c(1, 23), the second is c(7, 10) and the last c(9, 2, 4). the expected output is a dataframe with a second column containing the groups:

            ...

            ANSWER

            Answered 2022-Jan-26 at 08:55

            I think cpp function is the fastest way:

            Source https://stackoverflow.com/questions/70860620

            QUESTION

            How do I disable SSL Requirement in MySQL Workbench?
            Asked 2022-Jan-19 at 15:39

            It seems that SSL connection is required to use MySQL Workbench, and I don't think this is the case with previous versions.

            I remember SSL connections used to be optional. After I updated it, all options are locked to require SSL.

            How do I bypass this? I'm just a student and setting up SSL is out of my reach.

            Screenshot:

            ...

            ANSWER

            Answered 2021-Nov-02 at 19:29

            I don't know if it may be the right approach for you, but what I did is downgrade my version of MySQL Workbench to 6.3 and uninstalled the previous version and it will then give you the "if available" option for SSL. As you are right, it is not the case for previous versions, however you do lose a few more modern features in the process.

            https://downloads.mysql.com/archives/workbench/

            Another solution as well is to connect to connect to the database in 6.3 and since the configuration saves are in same location, upgrade to 8.0 where it will still have the old configuration file and won't use SSL due to backwards compatibility.

            Source https://stackoverflow.com/questions/69769563

            QUESTION

            Memoize multi-dimensional recursive solutions in haskell
            Asked 2022-Jan-13 at 14:28

            I was solving a recursive problem in haskell, although I could get the solution I would like to cache outputs of sub problems since has over lapping sub-problem property.

            The question is, given a grid of dimension n*m, and an integer k, how many ways are there to reach the gird (n, m) from (1, 1) with not more than k change of direction?

            Here is the code without of memoization

            ...

            ANSWER

            Answered 2021-Dec-16 at 16:23

            In Haskell these kinds of things aren't the most trivial ones, indeed. You would really like to have some in-place mutations going on to save up on memory and time, so I don't see any better way than equipping the frightening ST monad.

            This could be done over various data structures, arrays, vectors, repa tensors. I chose HashTable from hashtables because it is the simplest to use and is performant enough to make sense in my example.

            First of all, introduction:

            Source https://stackoverflow.com/questions/70376569

            QUESTION

            jdeps can't print-module-deps due to a MultiReleaseException
            Asked 2021-Dec-13 at 13:36

            We have a JavaFX based application which is not modularized (there are reasons, a legacy library is involved) but we build an custom runtime using jdeps and jlink.

            We've recently rewritten the app and added a couple of new dependencies, as well as removing others. Now the script that is building the application suddenly stopped working during the jdeps call.

            Note: This is happening on Linux – I've yet to test other OS'ses, but I don't expect another result.

            When the script calls

            ...

            ANSWER

            Answered 2021-Dec-13 at 13:36

            Update: These issues have been fixed, and a patched version of jdeps is available as part of the early access build for JDK 18 at: http://jdk.java.net/18/ (starting from build 26)

            Turning my comments into an answer. There seem to be 3 bugs going on here:

            1. The MultiReleaseException seems to be because jdeps can not handle classes in different jars that have the same name, such as module-info.class, but are stored in a different META-INF/versions/xxx directory. (JDK-8277165)
            2. The fact that this exception is sometimes suddenly not occuring seems to be the result of a race condition in the code that checks for the above; classes of the same name having multiple versions. (JDK-8277166)
            3. The MultiReleaseException is missing it's exception message since it's thrown as part of an asynchronous task, which wraps it in an ExecutionException, which then leads to jdeps not reporting the exception correctly. (JDK-8277123)

            As for a workaround, I don't think there's a good one at this point, except maybe for editing all the jars on the class path so that they put the module-info.class in the same META-INF/versions/xxx directory (but, this might have other consequences as well, so you probably don't want to run with the edited jars, and only use them for jdeps).

            Source https://stackoverflow.com/questions/69943899

            QUESTION

            Xcode 13 on iOS 15 Beta 'Untrusted Developer' error on iPhone XS device
            Asked 2021-Oct-28 at 19:25

            I have been testing my iOS app on my physical iPhone XS for quite some time now and all of a sudden it threw an error when I tried to run it saying:

            "APP NAME" is no longer available.

            So I went to re-build via Xcode into my device again to reinstall it. But I was getting an error message saying "Untrusted Developer".

            So I tried to go to the Settings > General > VPN and Device Management screen to see if I need to 'Trust' my own developer profile again. But it's not appearing on that screen or any other new developer profile for that matter.

            Did a bit of research and tried to troubleshoot. One of the solutions I've found and worked was to actually create a new developer account and use that to build and install the app on my device. I does work but I don't want to use another developer account to to build this app as the bundle identifier that I wanted to use was already tied up to that old account. And I have a bunch of other apps tied up to that old account as well.

            The other reason why the above solution also wouldn't be ideal as I already have months worth of data in my device that was saved in that app. If created a new build using a new account it wouldn't be able to access the data of the old app built using the other account.

            Just to note, that old account was formerly a paid account but now it expired. But I didn't have that problem until recently. So I am guessing it has something to do with the recent iOS 15 beta builds.

            I will be filing a bug report for this. But does anyone have any idea or workaround to get rid of this issue? Any information that could potentially point me towards the right direction would be appreciated. Thanks!

            I've filed this as a bug on AppleFeedback Assitant. They've reached out to me to ask for logs and the certificate I used to re-build the project. I'm guessing this this a bug and they are trying to fix it.

            ...

            ANSWER

            Answered 2021-Sep-23 at 00:49

            I managed to fix this issue.

            Xcode -> Preferences -> Accounts -> Manage Certificates -> + -> Apple Development and then make a new certificate

            My situation might be different from yours but here were the symptoms I was seeing. I was able to sign random Github projects and run them on my phone. I also have a paid developer account. I never saw anything related to my app in the VPN & Device Management settings on my iPhone and I still don't.

            Source https://stackoverflow.com/questions/69151276

            QUESTION

            How to run the predicted probabilities (or average marginal effects) for individuals fixed effects in panel data using R?
            Asked 2021-Oct-26 at 18:47

            These are three different ways to run an individual fixed effect method which gives more or less the same results (see below). My main question is how to get predictive probabilities or average marginal effects using the second model (model_plm) or the third model(model_felm). I know how to do it using the first model (model_lm) and show an example below using ggeffects, but that only works when i have a small sample.

            As i have over a million individual, my model only works using model_plm and model_felm. If i use model_lm, it takes a lot of time to run with one million individuals since they are controlled for in the model. I also get the following error: Error: vector memory exhausted (limit reached?). I checked many threads on StackOverflow to work around that error but nothing seems to solve it.

            I was wondering whether there is an efficient way to work around this issue. My main interest is to extract the predicted probabilities of the interaction residence*union. I usually extract predictive probabilities or average marginal effects using one of these packages: ggeffects,emmeans or margins.

            ...

            ANSWER

            Answered 2021-Oct-22 at 17:46

            This potential solution uses biglm::biglm() to fit the lm model and then uses emmeans::qdrg() with a nuisance specified. Does this approach help in your situation?

            Source https://stackoverflow.com/questions/69581584

            QUESTION

            Understanding the point of supply blocks (on-demand supplies)
            Asked 2021-Oct-05 at 23:02

            I'm having trouble getting my head around the purpose of supply {…} blocks/the on-demand supplies that they create.

            Live supplies (that is, the types that come from a Supplier and get new values whenever that Supplier emits a value) make sense to me – they're a version of asynchronous streams that I can use to broadcast a message from one or more senders to one or more receivers. It's easy to see use cases for responding to a live stream of messages: I might want to take an action every time I get a UI event from a GUI interface, or every time a chat application broadcasts that it has received a new message.

            But on-demand supplies don't make a similar amount of sense. The docs say that

            An on-demand broadcast is like Netflix: everyone who starts streaming a movie (taps a supply), always starts it from the beginning (gets all the values), regardless of how many people are watching it right now.

            Ok, fair enough. But why/when would I want those semantics?

            The examples also leave me scratching my head a bit. The Concurancy page currently provides three examples of a supply block, but two of them just emit the values from a for loop. The third is a bit more detailed:

            ...

            ANSWER

            Answered 2021-Oct-05 at 23:02

            Given you mentioned Supply.merge, let's start with that. Imagine it wasn't in the Raku standard library, and we had to implement it. What would we have to take care of in order to reach a correct implementation? At least:

            1. Produce a Supply result that, when tapped, will...
            2. Tap (that is, subscribe to) all of the input supplies.
            3. When one of the input supplies emits a value, emit it to our tapper...
            4. ...but make sure we follow the serial supply rule, which is that we only emit one message at a time; it's possible that two of our input supplies will emit values at the same time from different threads, so this isn't an automatic property.
            5. When all of our supplies have sent their done event, send the done event also.
            6. If any of the input supplies we tapped sends a quit event, relay it, and also close the taps of all of the other input supplies.
            7. Make very sure we don't have any odd races that will lead to breaking the supply grammar emit* [done|quit].
            8. When a tap on the resulting Supply we produce is closed, be sure to close the tap on all (still active) input supplies we tapped.

            Good luck!

            So how does the standard library do it? Like this:

            Source https://stackoverflow.com/questions/69421730

            QUESTION

            Trust issue while sending a post to my API since DST Root CA X3 Expiration
            Asked 2021-Oct-01 at 15:05

            I have a C# api running on a aws S3 with ubuntu. This API is use by a website, a windows application and a xamarin app deployed on Samsung android devices.

            Since today 16:00 (paris time), the android part is not working anymore, I have a "trust issue". Clearly it seems to be related with DST Root CA X3 Expiration (No release on my side and the timing is perfect).

            But I don't understand why...

            1. SSL certificate

            I checked my SSL certificate and regarding let'sencrypt forums, I have one of the path base on "ISRG Root X1". The second one is base on "DST Root CA X3" (expired). I renew them anyway to be sure, but still the same certificate path. (and no problem for chrome to contact them).

            1. Internet with https is working

            I can reach internet with a webview inside the app (to my website in https)

            1. Can't connect using restsharp

            When I use RestSharp to contact my server, I have the trust issue.

            My android devices are all the same: Samsung A7 tab, half up to date, the other half was update in august, all of them with Android 11. So theorically they are "not concerned" with this certificate expiration.

            Can the problem come from Xamarin or RestSharp ? Maybe my server certificate ?

            EDIT Ok half resolved.... If I go to the "Trusted Root Certificates folder" in my android device (don't know the exact name), If I disable the "Digital Signature Trust Co. - DST Root CA X3", it's working again !

            Not a "real solution" since I need to update something like 150 devices... 2 options in my mind

            • Can I force RestSharp to use a certificate more than another ?
            • Is it just because Android know the expiration date is 30/09 and still use it because we are still the 30/09 and everythin will work Tomorow ?

            EDIT 2 resolved.

            Thx to all of you, sorry I should have been able to validate this answer before some post, but stackoverflow was on readonly mode this night and I fall asleep after that.

            What I did (not sure if all step are mandatory).

            1/ I updated the certbot since mine was < 1 (check with certbot --version)

            ...

            ANSWER

            Answered 2021-Sep-30 at 21:09

            We’ve had similar issues today, unfortunately we were using older Amazon Linux on elasticbeanstalks. Upgrading to the latest Ubuntu build in your case should fix your issues.

            The issue we had was the Amazon Linux version trusted certificate service was always adding the expired root certificate.

            The reason restsharp is having problems is probably because it’s trying to do something like a curl request behind the scenes and is doing a handshake to verify the validity of the ssl cert when sending a request. The way it does this is checks it against certs that are trusted on the server, which includes the expired certificate.

            See here for Ubuntu builds that have the latest certs upgrade https://ubuntu.com/security/notices/USN-5089-1

            Source https://stackoverflow.com/questions/69397845

            QUESTION

            Since I'm blind and Visual Studio isn't accessible, can I create C# WPF applications just with plain code?
            Asked 2021-Sep-07 at 11:43

            I am totally blind, I use NVDA screen reader to operate my system, and I am trying to create a Windows desktop application. Visual Studio isn't screen-reader friendly, at least not the forms designer part. VS Code is pretty much accessible, although powershell's protools' designer isn't.

            Whenever I see a question about writing GUI in WPF with pure code I find a lot of "why in the name of God would you want to do that? Use VS!" answers. Well, here is the reason, VS form designer is out of reach to blind programmers, so the least practical approach will have to do.

            So, can it be done? Would you suggest any resources or approaches to this?

            ...

            ANSWER

            Answered 2021-Sep-05 at 23:28

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

            Vulnerabilities

            No vulnerabilities reported

            Install reach

            You can download it from GitHub.
            You can use reach 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.

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            See the Contributing guidelines.
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            https://github.com/wellcometrust/reach.git

          • CLI

            gh repo clone wellcometrust/reach

          • sshUrl

            git@github.com:wellcometrust/reach.git

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