dipper | Data Ingestion Pipeline for Monarch | Genomics library

 by   monarch-initiative Python Version: 0.2.32 License: BSD-3-Clause

kandi X-RAY | dipper Summary

kandi X-RAY | dipper Summary

dipper is a Python library typically used in Manufacturing, Utilities, Energy, Utilities, Artificial Intelligence, Genomics, Kafka applications. dipper has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install dipper' or download it from GitHub, PyPI.

The Dipper data pipeline was born out of the need for a uniform representation of human and model organism genotype-to-phenotype data, and an Extract-Transform-Load (ETL) pipeline to process it all. It became too cumbersome to first get all of these data into a relational schema; so, we decided to go straight from each source into triples that are semantically captured, using standard modeling patterns. We are currently working on tooling around defining, documenting, and constraining our schema as biolink models.
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            kandi-support Support

              dipper has a low active ecosystem.
              It has 42 star(s) with 22 fork(s). There are 39 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 231 open issues and 341 have been closed. On average issues are closed in 454 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of dipper is 0.2.32

            kandi-Quality Quality

              dipper has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              dipper 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.

            kandi-Reuse Reuse

              dipper releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              dipper saves you 10201 person hours of effort in developing the same functionality from scratch.
              It has 20754 lines of code, 797 functions and 124 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed dipper and discovered the below as its top functions. This is intended to give you an instant insight into dipper implemented functionality, and help decide if they suit your requirements.
            • Parse command line arguments
            • Create a spo representation of a subject
            • Generate a unique id
            • Construct a Biolink category
            • Transform an NCBI entry
            • Adds a triples
            • Add an individual to the ontology
            • Add association to the graph
            • Parse the drugbank output file
            • Process gene interaction associations
            • Parses the G2p_clean output file
            • Fetch the most recent files from the system
            • Process a single phene phenotype row
            • Make a property graph from the given properties
            • Add triples
            • Write the graph to a file
            • Add property axioms to the graph
            • Return a mapping of uniprot IDs to Entrez IDs
            • Process a breeding phene row
            • Convert KEGG disease to Gene object
            • Populate the OMIM type
            • Process a disease2gene
            • Process pheno envirom
            • Fetch data from udp
            • Parse the genotype files
            • Process OMIM to KEGG gene
            Get all kandi verified functions for this library.

            dipper Key Features

            No Key Features are available at this moment for dipper.

            dipper Examples and Code Snippets

            Dipper,Building locally
            Pythondot img1Lines of Code : 4dot img1License : Permissive (BSD-3-Clause)
            copy iconCopy
                pip3 install -r requirements.txt
                pip3 install -r requirements/mgi.txt
            
                pip3 install -r requirements.txt
                pip3 install -r requirements/all-sources.txt
              
            Python 3: read file of names, create new file with first names and last names reverse
            Pythondot img2Lines of Code : 6dot img2License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            def reverse_list(lst):
                    new = []
                    for name in lst:
                            temp = name.split(" ")
                            new += [temp[1]+" "+temp[0]]
            

            Community Discussions

            QUESTION

            Get-AzureRmStorageAccount, Dig into Container files and get "Modified" property
            Asked 2020-Mar-16 at 02:44

            I need to get all Storage Accounts which last modified date is 6 months ago with PS script. I didn't found any cmdlet or function which could provide such information. I thought it would be enough to sort by 'LastModifiedTime' but then I dig dipper, I saw that I have a lot of new files inside containers with the parameter "Modified". Question is how can I access these files with Powershell? Any cmdlet, function, etc?

            Here is what I used to get SA before:

            ...

            ANSWER

            Answered 2020-Mar-16 at 02:44

            Not sure if you just want to get the blobs which LastModifiedTime (aka: LMT) is in 180 days. If so, you don't need to check the container LMT, since it is not related with blob last modify time. (container LMT is for container properties modification).

            Following script works with pipeline. If you don't need to check container LMT, just remove the check:

            Source https://stackoverflow.com/questions/60671233

            QUESTION

            Merging elements in a CSS selector
            Asked 2020-Feb-05 at 00:08

            I already have a CSS/HTML mockup that makes it look like WhatsApp messaging, but only for conversations between 2 people. I want to add the group-chat feature, which means the names.

            It's based on a

            list, so the HTML looks like this:

            ...

            ANSWER

            Answered 2020-Feb-04 at 04:26

            From what I understand,

            1. You need the full name + text to come in one bubble. For that you can give background and styling to the .in and .out divs. Same goes for the pointing arrow.

            2. You need to have some width, so the bubble has some width. For this remove the float left/right given to dd.

            Rest you can fix using margin and padding.

            Source https://stackoverflow.com/questions/60048294

            QUESTION

            Images not showing in GridView even though asset specified in pubspec.yaml Flutter
            Asked 2020-Jan-30 at 13:45

            I am developing a menu kiosk app right now, and I have some problems loading the images on my app, I made sure to specify each image in my pubspec.yaml but the images still does not show. The error i'm getting is this: ════════ Exception caught by image resource service ════════════════════════════ Unable to load asset: assets/images/sideDesserts/Dippers with Choco Dip.png ════════════════════════════════════════════════════════════════════════════════

            Here is what my pubspec.yaml contains

            ...

            ANSWER

            Answered 2020-Jan-30 at 13:14

            Rename your image. Your image name has space. In android image not load with space name. so Refactor your image name Dippers with Choco Dip to Dippers_with_Choco_Dip

            Source https://stackoverflow.com/questions/59986333

            QUESTION

            Calling external API and parsing JSON Object
            Asked 2019-Sep-18 at 01:55

            I am trying to fetch JSON from external API and parse it so that I can access JSON object values in order to avoid values(fields) that I do not need.

            I have studied JSONOBject library a little and parsed the objects, however, it feels that I am doing too much hard coding and not doing it correctly at all, feedback is much appreciated.

            Output result after user input :

            Sending 'GET' request to URL: https://api.coindesk.com/v1/bpi/currentprice/(user input currency)

            Data fetched at UTC time/date : Sep 17, 2019 22:51:00 UTC Description: Ukrainian Hryvnia Rate float: 253737.6633

            ...

            ANSWER

            Answered 2019-Sep-18 at 01:55

            I wrote a sample code to demonstrate what I said in comment by using ObjectMapper to transform response json string into POJO.

            First, create a class, says CoinDeskResponse to store the transformation result.

            Source https://stackoverflow.com/questions/57983506

            QUESTION

            Align a button at the bottom of a grid
            Asked 2019-Aug-29 at 08:54

            I am trying to assign the button : called 'go to form' right at the bottom of the grid i have done in CSS.

            I have messed around with the relative position but this seems not to want to work. Any ideas guys ?

            ...

            ANSWER

            Answered 2019-Aug-29 at 08:30

            QUESTION

            $addFields where condition
            Asked 2019-Aug-01 at 05:01

            I want to add extra field to lookup result but i need a condition here. Every user has a relationship status (local field) and it should be added to lookup result for each user, but It's adding every 'status' to every user.

            ...

            ANSWER

            Answered 2019-Aug-01 at 04:48

            You need $unwind to get single document per relationship:

            Source https://stackoverflow.com/questions/57301928

            QUESTION

            creating conditions for recieving partial delivery of products in laravel
            Asked 2019-Mar-16 at 09:37

            Its my 2nd day of trying to make my "receiving of partial delivery" for my app. I am trying my luck here with you masters.

            I have these two tables, the first one is the order_items table,

            This table holds the items from the purchase order. and the other table is warehouse1

            which hold the partially receive items.

            I get the logic, I have to group the warehouse1.order_item_id so that I could get the sum of the items from let say order_number_id=22 which is the id from order_items table. to show you, here's my code doing the GROUP

            ...

            ANSWER

            Answered 2019-Mar-15 at 21:52

            If you are asking why the quantity on your quantity column is not giving you a form, or why the return from that input is not correct, you have a few problems that I can see. The first issue is that you are creating n+1 number of number input form items in the same space with the same ID. This will likely prevent them from showing up, and will never produce a usable form. This:

            Source https://stackoverflow.com/questions/55188695

            QUESTION

            ggplot2 heatmap not arranging values from high to low
            Asked 2019-Jan-21 at 19:52

            I'm trying to arrange my heatmap so that values with higher "Overall" will appear at the top and values with a lower "Overall" will appear at the bottom. The issue is that the data (mydata) is already arranged like this, but this arrangement isn't being applied to the end.

            Any idea how I can fix this?

            Thanks.

            ...

            ANSWER

            Answered 2019-Jan-21 at 19:52

            You need to get the order that you want track_name to be in, and then use that order to create a factor.

            Source https://stackoverflow.com/questions/54296609

            QUESTION

            Set waypoints on multipule elements
            Asked 2018-Apr-14 at 06:44

            I have a div tag with the class "dipper"

            ...

            ANSWER

            Answered 2018-Apr-14 at 06:44

            QUESTION

            Only classes that inherit from NSObject can be declared @objc
            Asked 2017-Nov-07 at 12:50

            I have to set value to property by string name representation.

            ...

            ANSWER

            Answered 2017-Nov-07 at 12:50

            Documentation

            Swift without the Objective-C Runtime: Swift on Linux does not depend on the Objective-C runtime nor includes it. While Swift was designed to interoperate closely with Objective-C when it is present, it was also designed to work in environments where the Objective-C runtime does not exist.

            https://swift.org/blog/swift-linux-port/

            Which is clear, provided that it states:

            value of type 'A' has no member 'setValue'

            It basically tells that there is no KVC mechanism underneath. setValue method comes from Objective-C runtime, which is absent on Linux. Thus, it's a no-go and what you're trying to accomplish is simply not possible.

            Other than that, the following rule is applied on systems with Obj-C runtime environment:

            Key-Value Coding with Swift

            Swift objects that inherit from NSObject or one of its subclasses are key-value coding compliant for their properties by default. Whereas in Objective-C, a property’s accessors and instance variables must follow certain patterns, a standard property declaration in Swift automatically guarantees this. On the other hand, many of the protocol’s features are either not relevant or are better handled using native Swift constructs or techniques that do not exist in Objective-C. For example, because all Swift properties are objects, you never exercise the default implementation’s special handling of non-object properties.

            Also: Requiring Dynamic Dispatch

            Swift APIs that are callable from Objective-C must be available through dynamic dispatch. However, the availability of dynamic dispatch doesn’t prevent the Swift compiler from selecting a more efficient dispatch approach when those APIs are called from Swift code.

            You use the @objc attribute along with the dynamic modifier to require that access to members be dynamically dispatched through the Objective-C runtime. Requiring this kind of dynamic dispatch is rarely necessary. However, it is necessary when using APIs like key–value observing or the method_exchangeImplementations function in the Objective-C runtime, which dynamically replace the implementation of a method at runtime.

            Declarations marked with the dynamic modifier must also be explicitly marked with the @objc attribute unless the @objc attribute is implicitly added by the declaration’s context. For information about when the @objc attribute is implicitly added, see Declaration Attributes in The Swift Programming Language (Swift 4).

            Elements must also be declared dynamic in order to be KVO-compatible (for KVC, inheriting from NSObject is enough):

            Source https://stackoverflow.com/questions/46849486

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

            Vulnerabilities

            No vulnerabilities reported

            Install dipper

            You can install using 'pip install dipper' or download it from GitHub, PyPI.
            You can use dipper 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

            The full documentation, including API docs, can be found on read the docs.
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            Install
          • PyPI

            pip install dipper

          • CLONE
          • HTTPS

            https://github.com/monarch-initiative/dipper.git

          • CLI

            gh repo clone monarch-initiative/dipper

          • sshUrl

            git@github.com:monarch-initiative/dipper.git

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