biolink-model-toolkit | useful python functions for looking up information | JSON Processing library

by biolink Python Version: v1.0.15 License: BSD-3-Clause

X-Ray Key Features Code Snippets(3)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | biolink-model-toolkit Summary

biolink-model-toolkit is a Python library typically used in Utilities, JSON Processing applications. biolink-model-toolkit has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However biolink-model-toolkit build file is not available. You can install using 'pip install biolink-model-toolkit' or download it from GitHub, PyPI.

Biolink Model Toolkit (BMT): A Python API for working with the Biolink Model. BMT provides utility functions to look up Biolink Model for classes, relations, and properties based on Biolink CURIEs or external CURIEs that have been mapped to Biolink Model. Note: Each release of BMT is pinned to a specific version of the Biolink Model to ensure consistency.

Support

Quality

Security

License

Reuse

Support

biolink-model-toolkit has a low active ecosystem.

It has 15 star(s) with 10 fork(s). There are 5 watchers for this library.

There were 2 major release(s) in the last 12 months.

There are 4 open issues and 58 have been closed. On average issues are closed in 70 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of biolink-model-toolkit is v1.0.15

Quality

biolink-model-toolkit has no bugs reported.

Security

biolink-model-toolkit has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

biolink-model-toolkit is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

biolink-model-toolkit releases are available to install and integrate.

Deployable package is available in PyPI.

biolink-model-toolkit has no build file. You will be need to create the build yourself to 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 biolink-model-toolkit and discovered the below as its top functions. This is intended to give you an instant insight into biolink-model-toolkit implemented functionality, and help decide if they suit your requirements.

Gets all predicates with the given class
Format all elements
Returns an element object corresponding to an element
Format an element
Set slot definition
Visit the given element
Fixes aliases
Returns True if name is in subset
Return whether the given name is a relationship
Visit the class definition
Visit the type definition
Visit a subset
Returns a list of all the ancestors of the mixin

Get all kandi verified functions for this library.

biolink-model-toolkit Key Features

No Key Features are available at this moment for biolink-model-toolkit.

biolink-model-toolkit Examples and Code Snippets

Biolink Model Toolkit,Usage,Using the Toolkit class

Python

Lines of Code : 25

License : Permissive (BSD-3-Clause)

Copy

from bmt import Toolkit
t = Toolkit()
element = t.get_element('gene') # This returns the element for 'biolink:Gene'

from bmt import Toolkit
t = Toolkit()
element_name = t.get_element_by_mapping('SEMMEDDB:CAUSES') # This returns 'causes'
element = t.

Biolink Model Toolkit,For developers

Python

Lines of Code : 8

License : Permissive (BSD-3-Clause)

Copy

# clone the repo
git clone https://github.com/biolink/biolink-model-toolkit

# cd into the folder
cd biolink-model-toolkit

# install
python setup.py install

Biolink Model Toolkit,Usage,Using the Toolkit class with different versions of Biolink Model

Python

Lines of Code : 2

License : Permissive (BSD-3-Clause)

Copy

from bmt import Toolkit
t = Toolkit('/path/to/biolink-model.yaml')

Community Discussions

Trending Discussions on JSON Processing

st_read path for shinyapp in R

How to write jsonb inside WHERE without JSON Processing Functions

Renumerating indexed JSON

How to get values from array of JSON in C#

SSIS Script Task Fails with NewtonSoft.Json

Is there an automated way to split a JSON(B) column into multiple columns in PostgreSQL?

A simple way to parse XML with repeated element using Jackson

Shiny.io cannot deploy the application

How to deploy shiny app to shinyapps.io from drake plan

QUESTION

st_read path for shinyapp in R

Asked 2021-Oct-03 at 00:33

Usually when st_read is used you put path in dsn, but in case of shiny if you put a full path inside dsn it will give an error as that file path does not exist on the server. So, now I put the shapefile in the www folder, but I don't know what path to put in dsn so that the app picks up the shapefile.

How can I fix this?

Current function code in the app:

...

ANSWER

Answered 2021-Oct-03 at 00:33

Thanks to Guillaumme for his comment, so I was able to fix the problem by first moving the shiny app to a R project. Then in the app code write st_read as follows, and the app is able to pick up the shapefile when its published on shinyapps.io.

Source https://stackoverflow.com/questions/69415642

QUESTION

How to write jsonb inside WHERE without JSON Processing Functions

Asked 2021-Aug-17 at 05:22

This is my query and it works. I store the list of dictionaries inside my jsonb column.

...

ANSWER

Answered 2021-Aug-17 at 05:22

The evaluation of the JSON path is a bit different between the jsonb_path_xxx() functions and the equivalent operator. Most importantly you do not need the ? (...) condition as that is implied when using the operator.

The following should be equivalent:

Source https://stackoverflow.com/questions/68809993

QUESTION

Renumerating indexed JSON

Asked 2021-Jun-30 at 15:27

I have data stored in a JSON - and one of the fields is an index that determines the order in which the other data is done. Imagine

...

ANSWER

Answered 2021-Jun-30 at 15:27

Use any programing language, With java script, use Array.splice

Source https://stackoverflow.com/questions/68182592

QUESTION

How to get values from array of JSON in C#

Asked 2021-Jun-23 at 20:23

I am new to JSON processing by NewtonSoft on C#. I have the following JSON and trying to get all orderIds and orderNumbers. I tried the following code. But in both cases, I am getting can't access child items error. I also tried using JObject.Parse(json) and tried to get the two values, but got similar errors.

...

ANSWER

Answered 2021-Jun-23 at 19:49

The for loop statement seems to be wrong since dynJson is an object and not an array. You need to loop through the dynJson.orders, like below.

Source https://stackoverflow.com/questions/68106071

QUESTION

SSIS Script Task Fails with NewtonSoft.Json

Asked 2021-Jan-26 at 19:47

I have a C# code embedded in a script task in SSIS, and I installed NewtonSoft.Json for some json processing. When I run the package, below error shows up:

Could not load file or assembly 'Newtonsoft.Json, Version=12.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The system cannot find the file specified.

Despite trying all solutions and recommendations (uninstall & re-install the package, both from NuGet manager and through console, or adding the reference manually, etc.. ), whenever I run the SSIS package I still get the same error and the script task component fails.

I am using Visual Studio 2017 (SSDT).

How to solve the issue permanently?

...

ANSWER

Answered 2021-Jan-26 at 17:24

With SSIS, you can only reference assemblies installed on the GAC. Use gacutil, from Windows SDK to install the required assembly to the GAC

Source https://stackoverflow.com/questions/65906096

QUESTION

Is there an automated way to split a JSON(B) column into multiple columns in PostgreSQL?

Asked 2020-Sep-07 at 16:54

So I have a PostgreSQL (TimescaleDB) table that looks like this:

...

ANSWER

Answered 2020-Sep-07 at 16:54

There is no way to make this dynamic. The number (and types) of all columns of a query must be known to the database when parsing the statement, long before it's actually executed.

If you always have the same structure you can create a type:

Source https://stackoverflow.com/questions/63779087

QUESTION

Asked 2020-Aug-23 at 22:02

I am running my Fat Jar in Flink Cluster which reads Kafka and saves in Cassandra, the code is,

...

ANSWER

Answered 2020-Aug-23 at 22:02

I solved the problem, there was LocalDateTime which was emitting from and when i was converting with same type, there was above error. I changed the type into java.util Date type then it worked.

Source https://stackoverflow.com/questions/63494496

QUESTION

A simple way to parse XML with repeated element using Jackson

Asked 2020-Aug-23 at 14:42

I am looking for a simple way to parse an XML structure with a repeated element using Jackson. Here is a simplified example:

...

ANSWER

Answered 2020-Aug-23 at 14:42

The problem mentioned here is described in this Github issue: https://github.com/FasterXML/jackson-dataformat-xml/issues/187

Basically what is happening is that Jackson is translating XML tree structure in JsonNode data model and this will not work as it's not supported.

There is 2 options described in that Github issue:

Fully transform this XML to JSON (answer from @cawena on Github)
Or if you know your data structure to just use answer from p0sitron which is:

Code:

Source https://stackoverflow.com/questions/63539315

QUESTION

Shiny.io cannot deploy the application

Asked 2020-Jul-28 at 21:34

I was trying to create an interactive map with the Shiny web application, however, after I published it to my shiny.io account, clicking the URL will only yield: shiny.io application page

...

ANSWER

Answered 2020-Jul-28 at 21:15

I am thinking you mean shinyapps.io. To get to the logs:

Click on the dashboard view (the left-side panel).
Click on the name of your app (a hyperlink)
Click on the logs button at the top of the screen

Source https://stackoverflow.com/questions/63142711

QUESTION

How to deploy shiny app to shinyapps.io from drake plan

Asked 2020-Jul-16 at 18:20

This is a follow-on question from closing the loop on passing the app and data to a Shiny deployment function:

How to use shiny app as a target in drake

I would like to deploy a Shiny app directly from a drake plan as below.

...

ANSWER

Answered 2020-Jul-16 at 18:20

Now that I see how you are deploying the app, I can say that this is expected behavior. Yes, your custom_shiny_deployment() has access to the data, but the deployed app does not because rsconnect::deployApp() does not ship objects from the calling environment. If you want the data to be available to the app, I recommend saving it (and tracking it with file_in() and file_out()) then passing it to the appFiles argument of deployApp() via custom_shiny_deployment().

EDIT

Your app.R can stay like it is.

app.R is the same as what you wrote.

Source https://stackoverflow.com/questions/62903543

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

Vulnerabilities

No vulnerabilities reported

Install biolink-model-toolkit

You can install using 'pip install biolink-model-toolkit' or download it from GitHub, PyPI.
You can use biolink-model-toolkit 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.