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Function create_demand_config has a Cognitive Complexity of 46 (exceeds 5 allowed). Consider refactoring.
Open

    def create_demand_config(self, new_params, old_params):
        config = None
        for item in new_params:
            logging.debug("Param: {}".format(item))
            logging.debug("   Type: {}".format(type(new_params[item])))
Severity: Minor
Found in python/src/odin_data/control/odin_data_controller.py - About 7 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

File meta_writer.py has 438 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Implementation of odin_data Meta Writer

This module is passed meta data messages for a single acquisition which it writes to disk.
Will need to be subclassed by detector specific implementation.
Severity: Minor
Found in python/src/odin_data/meta_writer/meta_writer.py - About 6 hrs to fix

    File hdf5dataset.py has 390 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    import logging
from time import time
from typing import Optional

import h5py as h5
    Severity: Minor
    Found in python/src/odin_data/meta_writer/hdf5dataset.py - About 5 hrs to fix

      File _version.py has 377 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      # This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains the computed version number.
      Severity: Minor
      Found in python/src/odin_data/_version.py - About 5 hrs to fix

        Function update_loop has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
        Open

            def update_loop(self):
        """Handle background update loop tasks.
        This method handles background update tasks executed periodically in the tornado
        IOLoop instance. This includes requesting the status from the underlying application
        and preparing the JSON encoded reply in a format that can be easily parsed.
        Severity: Minor
        Found in python/src/odin_data/control/odin_data_controller.py - About 4 hrs to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Method buildGUI has 111 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            private Panel buildGUI()
    {
        panel = new Panel();
        panel.setLayout(new GridBagLayout());
        Severity: Major
        Found in tools/imagej/src/Live_View.java - About 4 hrs to fix

          File Live_View.java has 341 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          import java.awt.*;
import java.awt.event.*;

import java.text.SimpleDateFormat;
import java.util.Date;
          Severity: Minor
          Found in tools/imagej/src/Live_View.java - About 4 hrs to fix

            Function __init__ has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
            Open

                def __init__(self, shared_mem_name, shared_mem_size=0, buffer_size=0,
                 remove_when_deleted=False, boost_mmap_mode=False):

        self.remove_when_deleted = remove_when_deleted
        self.shared_mem = None
            Severity: Minor
            Found in python/src/odin_data/shared_buffer_manager.py - About 3 hrs to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            MetaWriter has 31 functions (exceeds 20 allowed). Consider refactoring.
            Open

            class MetaWriter(object):
    """This class handles meta data messages and writes parameters to disk"""

    FILE_SUFFIX = "_meta.h5"
    CONFIGURE_PARAMETERS = [
            Severity: Minor
            Found in python/src/odin_data/meta_writer/meta_writer.py - About 3 hrs to fix

              File live_view_adapter.py has 325 lines of code (exceeds 250 allowed). Consider refactoring.
              Open

              """ODIN data live view adapter.

This module implements an odin-control adapter capable of rendering odin-data live
view images to users.
              Severity: Minor
              Found in python/src/odin_data/control/live_view_adapter.py - About 3 hrs to fix

                File meta_listener.py has 318 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                """Implementation of odin_data Meta Listener

This module listens on one or more ZeroMQ sockets for meta messages which it then passes
on to a MetaWriter to write. Also handles odin Ipc control messages.
                Severity: Minor
                Found in python/src/odin_data/meta_writer/meta_listener.py - About 3 hrs to fix

                  File LiveViewSocket.java has 293 lines of code (exceeds 250 allowed). Consider refactoring.
                  Open

                   import java.nio.*;
import java.util.Date;
import java.util.HashMap;
import java.util.Observable;
                  Severity: Minor
                  Found in tools/imagej/src/LiveViewSocket.java - About 3 hrs to fix

                    Method refreshImage has 71 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                        private void refreshImage(ByteBuffer data, String dtype, int[] shape)
    {
        int bitdepth = dtype_map.get(dtype);
        ImageProcessor ip = img.getProcessor();
        Object img_pixels = null;
                    Severity: Major
                    Found in tools/imagej/src/LiveViewSocket.java - About 2 hrs to fix

                      Similar blocks of code found in 4 locations. Consider refactoring.
                      Open

                          def do_request_command_cmd(self):
        """Send a request commands command to odin-data"""
        status_msg = IpcMessage('cmd', 'request_commands', id=self._next_msg_id())
        self.logger.info("Sending command request to the odin-data application")
        self.ctrl_channel.send(status_msg.encode())
                      Severity: Major
                      Found in python/src/odin_data/client.py and 3 other locations - About 2 hrs to fix
                      python/src/odin_data/client.py on lines 125..130
                      python/src/odin_data/client.py on lines 132..137
                      python/src/odin_data/client.py on lines 146..151

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 60.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 4 locations. Consider refactoring.
                      Open

                          def do_shutdown_cmd(self):
        """Send a shutdown command to odin-data."""
        shutdown_msg = IpcMessage('cmd', 'shutdown', id=self._next_msg_id())
        self.logger.info("Sending shutdown command to the odin-data application")
        self.ctrl_channel.send(shutdown_msg.encode())
                      Severity: Major
                      Found in python/src/odin_data/client.py and 3 other locations - About 2 hrs to fix
                      python/src/odin_data/client.py on lines 125..130
                      python/src/odin_data/client.py on lines 132..137
                      python/src/odin_data/client.py on lines 139..144

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 60.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 4 locations. Consider refactoring.
                      Open

                          def do_request_config_cmd(self):
        """Send a request configuration command to odin-data."""
        status_msg = IpcMessage('cmd', 'request_configuration', id=self._next_msg_id())
        self.logger.info("Sending configuration request to the odin-data application")
        self.ctrl_channel.send(status_msg.encode())
                      Severity: Major
                      Found in python/src/odin_data/client.py and 3 other locations - About 2 hrs to fix
                      python/src/odin_data/client.py on lines 125..130
                      python/src/odin_data/client.py on lines 139..144
                      python/src/odin_data/client.py on lines 146..151

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 60.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                      def cast_bytes(s, encoding="utf8", errors="strict"):
    """Cast unicode or bytes to bytes

    :param obj: the dictionary, list, or unicode string
    :param encoding: encoding to use
                      Severity: Major
                      Found in python/src/odin_data/util.py and 1 other location - About 2 hrs to fix
                      python/src/odin_data/util.py on lines 40..56

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 60.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                      def cast_unicode(s, encoding="utf8", errors="strict"):
    """Cast bytes or unicode to unicode

    :param s: string to cast
    :param encoding: encoding to use
                      Severity: Major
                      Found in python/src/odin_data/util.py and 1 other location - About 2 hrs to fix
                      python/src/odin_data/util.py on lines 20..37

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 60.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 4 locations. Consider refactoring.
                      Open

                          def do_status_cmd(self):
        """Send a status command to odin-data."""
        status_msg = IpcMessage('cmd', 'status', id=self._next_msg_id())
        self.logger.info("Sending status request to the odin-data application")
        self.ctrl_channel.send(status_msg.encode())
                      Severity: Major
                      Found in python/src/odin_data/client.py and 3 other locations - About 2 hrs to fix
                      python/src/odin_data/client.py on lines 132..137
                      python/src/odin_data/client.py on lines 139..144
                      python/src/odin_data/client.py on lines 146..151

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 60.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                          def stop_when_detector_finished(self):
        """Register that it is OK to stop when all detector-specific logic is complete

        By default, detector_finished is set to True initially so that this check always
        passes. Child classes that need to do their own checks can set this to False in
                      Severity: Major
                      Found in python/src/odin_data/meta_writer/meta_writer.py and 1 other location - About 2 hrs to fix
                      python/src/odin_data/meta_writer/meta_writer.py on lines 356..367

                      Duplicated Code

                      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                      Tuning

                      This issue has a mass of 58.

                      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                      Refactorings

                      Further Reading

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