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JUDI | repository contains the source code | BPM library

 by   ncbi Python Version: 0.0.0.4 License: MIT

 by   ncbi Python Version: 0.0.0.4 License: MIT

kandi X-RAY | JUDI Summary

JUDI is a Python library typically used in Automation, BPM, Deep Learning applications. JUDI 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 JUDI' or download it from GitHub, PyPI.
judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings.
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Quality
Quality
Security
Security
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kandi-support Support

  • JUDI has a low active ecosystem.
  • It has 25 star(s) with 9 fork(s). There are 17 watchers for this library.
  • It had no major release in the last 12 months.
  • There are 1 open issues and 0 have been closed. On average issues are closed in 426 days. There are 1 open pull requests and 0 closed requests.
  • It has a neutral sentiment in the developer community.
  • The latest version of JUDI is 0.0.0.4
JUDI Support
Best in #BPM
Average in #BPM
JUDI Support
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quality kandi Quality

  • JUDI has 0 bugs and 0 code smells.
JUDI Quality
Best in #BPM
Average in #BPM
JUDI Quality
Best in #BPM
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securitySecurity

  • JUDI has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
  • JUDI code analysis shows 0 unresolved vulnerabilities.
  • There are 0 security hotspots that need review.
JUDI Security
Best in #BPM
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JUDI Security
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license License

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

  • JUDI releases are not available. You will need to build from source code and install.
  • Deployable package is available in PyPI.
  • Build file is available. You can build the component from source.
  • Installation instructions, examples and code snippets are available.
  • It has 806 lines of code, 57 functions and 13 files.
  • It has medium code complexity. Code complexity directly impacts maintainability of the code.
JUDI Reuse
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JUDI Reuse
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Top functions reviewed by kandi - BETA

kandi has reviewed JUDI and discovered the below as its top functions. This is intended to give you an instant insight into JUDI implemented functionality, and help decide if they suit your requirements.

  • This function creates the tasks for the class
    • Return a configuration string
  • Pastes PDFs
    • Pastes PDF files
  • Query parameter db
    • Returns a copy of the file
  • Mask the given parameters from the DB
    • Return a copy of this ParamDB instance
  • Show the parameter database
    • Print the dataframe
  • Combine csv files
    • Combine csv files
  • Merge two PDFs files
    • Merge PDFs
  • Add a JUDI parameter
    • Add a parameter to the main dataframe
  • Creates a PDF matrix
    • Takes a string and converts it to latex
  • Show the dataframe
    • Merge csv files
      • Return a copy of the file
        • Subset query string into a single query string
          • Merge two PDFs
            • Make a copy of self df
              • Tile PDFs

                Get all kandi verified functions for this library.

                Get all kandi verified functions for this library.

                JUDI Key Features

                This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!

                JUDI Examples and Code Snippets

                See all related Code Snippets

                Community Discussions

                Trending Discussions on JUDI
                • mongoimport displaying error: E11000 duplicate key error
                • How can I remove last 1 in json?
                • How to grouping an sub array in one column php
                • contentful documentHtmlToString format links
                • Cannot convert a list of "strings" to a tf.Dataset.from_tensor_slicer() - ValueError: Can't convert non-rectangular Python sequence to Tensor
                Trending Discussions on JUDI

                QUESTION

                mongoimport displaying error: E11000 duplicate key error

                Asked 2021-Feb-26 at 14:47

                I'm doing a tutorial on Flask. I'm trying to add some information from a json file into a MongoDB database

                users.json

                [{"id":1,"first_name":"Jacques","last_name":"Blazewicz","email":"jblazewicz0@posterous.com","password":"k9doaly"},
                {"id":2,"first_name":"Budd","last_name":"Zellick","email":"bzellick1@uol.com.br","password":"kik8N0cyKG"},
                {"id":3,"first_name":"Simone","last_name":"Brenston","email":"sbrenston2@squarespace.com","password":"9BO7nEvdci8"},
                {"id":4,"first_name":"Waneta","last_name":"Stading","email":"wstading3@google.es","password":"GpzWY536X"},
                {"id":5,"first_name":"Barbey","last_name":"Corder","email":"bcorder4@csmonitor.com","password":"BXFkbgEz"},
                {"id":6,"first_name":"Becca","last_name":"Hartington","email":"bhartington5@wsj.com","password":"ijh3RfxcGB"},
                {"id":7,"first_name":"Elyse","last_name":"Eddy","email":"eeddy6@archive.org","password":"QJHg5Gc0V"},
                {"id":8,"first_name":"Reggie","last_name":"Souster","email":"rsouster7@4shared.com","password":"nmCeQGRC"},
                {"id":9,"first_name":"Brnaby","last_name":"Abrahmson","email":"babrahmson8@digg.com","password":"BqOgwfIMJmTx"},
                {"id":10,"first_name":"Yuma","last_name":"Graine","email":"ygraine9@tmall.com","password":"4VpkAWyL"},
                {"id":11,"first_name":"Quinton","last_name":"Chater","email":"qchatera@squarespace.com","password":"7x6IYp"},
                {"id":12,"first_name":"Raymund","last_name":"Moorman","email":"rmoormanb@indiatimes.com","password":"aRgaXm1"},
                {"id":13,"first_name":"Boycey","last_name":"Ferrelli","email":"bferrellic@cnet.com","password":"VCKtIJEUi"},
                {"id":14,"first_name":"Ty","last_name":"Raffeorty","email":"traffeortyd@cnet.com","password":"wVOd2oi"},
                {"id":15,"first_name":"Judie","last_name":"Penella","email":"jpenellae@psu.edu","password":"0WP0F6516"},
                {"id":16,"first_name":"Alden","last_name":"Gemlett","email":"agemlettf@independent.co.uk","password":"3rAW4wlTsCWz"},
                {"id":17,"first_name":"Josephina","last_name":"MacLeod","email":"jmacleodg@livejournal.com","password":"gQ7ytj7CtA6"},
                {"id":18,"first_name":"Lorene","last_name":"Lindeberg","email":"llindebergh@chron.com","password":"Q4WU8aHkm"},
                {"id":19,"first_name":"Lamar","last_name":"Sotham","email":"lsothami@rediff.com","password":"5yyhnYPTDs"},
                {"id":20,"first_name":"Derek","last_name":"Breakey","email":"dbreakeyj@home.pl","password":"jrz2kl2jeX"}]
                

                I run this command in the terminal:

                mongoimport --jsonArray --db UTA_Enrollment --collection user --file users.json
                

                Instead of getting all 20 rows in the database, I only get the first row, and these error messages are displaying in the command line.

                2021-02-25T17:47:40.654-0800    connected to: mongodb://localhost/
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    continuing through error: E11000 duplicate key error collection: UTA_Enrollment.user index: user_id_1 dup key: { user_id: null }
                2021-02-25T17:47:40.658-0800    1 document(s) imported successfully. 19 document(s) failed to import.
                

                I had previously ran these lines of code in python and have since deleted the two entries, that are commented, from the database.

                class User(db.Document):
                    user_id     =   db.IntField( unique=True )
                    first_name  =   db.StringField( max_length=50 )
                    last_name   =   db.StringField( max_length=50 )
                    email       =   db.StringField( max_length=30 )
                    password    =   db.StringField( max_length=30 )
                
                @app.route("/user")
                def user():
                    # User(user_id=1, first_name="Frank", last_name="Ho", email="frank.ho@uta.com", password="password123").save()
                    # User(user_id=2, first_name="Mary", last_name="Jane", email="mary.jane@uta.com", password="abc1234").save()
                    users = User.objects.all()
                    return render_template("user.html", users=users)
                

                I have no idea why this is happening, since the id is different for each entry. Thanks for the help

                ANSWER

                Answered 2021-Feb-26 at 14:47

                user_id seems to have an index that forces the field values to be unique

                But in your users.json file, there is no user_id field. So when importing the data it creates the field with a null value for all the users. And since the field, as to be unique you have this error dup key:

                So to fix this, you have to remove the index on the user_id field. The identifier of a document is named _id in mongodb

                Source https://stackoverflow.com/questions/66379042

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

                Vulnerabilities

                No vulnerabilities reported

                Install JUDI

                judi is tested on python 3.6.

                Support

                docs folder contains ReST documentation based on Sphinx.

                Find more information at:

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                Install
                • pip install judi

                Clone
                • https://github.com/ncbi/JUDI.git

                • gh repo clone ncbi/JUDI

                • git@github.com:ncbi/JUDI.git

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