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Function update_loop has a Cognitive Complexity of 14 (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_adapter.py - About 1 hr 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

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            if line.strip().startswith("git_date ="):
                mo = re.search(r'=\s*"(.*)"', line)
                if mo:
                    keywords["date"] = mo.group(1)
Severity: Major
Found in python/src/odin_data/_version.py and 2 other locations - About 1 hr to fix
python/src/odin_data/_version.py on lines 143..146
python/src/odin_data/_version.py on lines 147..150

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 47.

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

Function configure has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

    def configure(self, request):
        """Handle a configuration message

        Args:
            request(IpcMessage): The request message
Severity: Minor
Found in python/src/odin_data/meta_writer/meta_listener.py - About 1 hr 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

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            if line.strip().startswith("git_full ="):
                mo = re.search(r'=\s*"(.*)"', line)
                if mo:
                    keywords["full"] = mo.group(1)
Severity: Major
Found in python/src/odin_data/_version.py and 2 other locations - About 1 hr to fix
python/src/odin_data/_version.py on lines 143..146
python/src/odin_data/_version.py on lines 151..154

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 47.

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

Method refreshImage has a Cognitive Complexity of 14 (exceeds 5 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: Minor
Found in tools/imagej/src/LiveViewSocket.java - About 1 hr 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

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

        elif path in self._status_parameters:
            response["value"] = self._status_parameters[path]
        elif path in self._config_parameters:
            response["value"] = self._config_parameters[path]
        else:
Severity: Major
Found in python/src/odin_data/control/meta_listener_adapter.py and 1 other location - About 1 hr to fix
python/src/odin_data/control/frame_processor_adapter.py on lines 108..111

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 47.

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

Function process_reconnection has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

    def process_reconnection(self, client):
        # We have been notified that a client has reconnected.
        # Loop over all stored configuration, sending any that needs to be processed
        logging.debug("Processing reconnection for client: %d", client)
        # First load the configuration file
Severity: Minor
Found in python/src/odin_data/control/odin_data_adapter.py - About 1 hr 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

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            if line.strip().startswith("git_refnames ="):
                mo = re.search(r'=\s*"(.*)"', line)
                if mo:
                    keywords["refnames"] = mo.group(1)
Severity: Major
Found in python/src/odin_data/_version.py and 2 other locations - About 1 hr to fix
python/src/odin_data/_version.py on lines 147..150
python/src/odin_data/_version.py on lines 151..154

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 47.

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

        if (clip_array[0] is None) or isinstance(clip_array[0], int):
            self.clip_min = clip_array[0]
Severity: Major
Found in python/src/odin_data/control/live_view_adapter.py and 1 other location - About 1 hr to fix
python/src/odin_data/control/live_view_adapter.py on lines 344..345

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 45.

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

        if (clip_array[1] is None) or isinstance(clip_array[1], int):
            self.clip_max = clip_array[1]
Severity: Major
Found in python/src/odin_data/control/live_view_adapter.py and 1 other location - About 1 hr to fix
python/src/odin_data/control/live_view_adapter.py on lines 341..342

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 45.

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

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

        if target is not None:
            msg.set_param(target, content)
        else:
            for parameter, value in content.items():
                msg.set_param(parameter, value)
Severity: Major
Found in python/src/odin_data/control/ipc_tornado_client.py and 1 other location - About 1 hr to fix
python/src/odin_data/control/ipc_client.py on lines 81..85

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 44.

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

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

        if target is not None:
            msg.set_param(target, content)
        else:
            for parameter, value in content.items():
                msg.set_param(parameter, value)
Severity: Major
Found in python/src/odin_data/control/ipc_client.py and 1 other location - About 1 hr to fix
python/src/odin_data/control/ipc_tornado_client.py on lines 94..98

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 44.

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

Identical blocks of code found in 5 locations. Consider refactoring.
Open

        try:
            self._client.send_configuration(config_message)
        except Exception as err:
            logging.debug(OdinDataAdapter.ERROR_FAILED_TO_SEND)
            logging.error("Error: %s", err)
Severity: Major
Found in python/src/odin_data/control/meta_listener_adapter.py and 4 other locations - About 1 hr to fix
python/src/odin_data/control/odin_data_adapter.py on lines 397..409
python/src/odin_data/control/odin_data_adapter.py on lines 432..440
python/src/odin_data/control/odin_data_adapter.py on lines 448..454
python/src/odin_data/control/odin_data_adapter.py on lines 457..464

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 43.

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

Function handle_data_message has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def handle_data_message(self, socket, endpoint):
        """Handle a data message on the given socket

        Args:
            socket(zmq.Socket): The socket to receive a message on
Severity: Minor
Found in python/src/odin_data/meta_writer/meta_listener.py - About 1 hr 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

Function _send_message has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def _send_message(self, msg, timeout):
        msg.set_msg_id(self.message_id)
        self.message_id = (self.message_id + 1) % self.MESSAGE_ID_MAX
        self.logger.debug("Sending control message:\n%s", msg.encode())
        with self._lock:
Severity: Minor
Found in python/src/odin_data/control/ipc_client.py - About 1 hr 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

Identical blocks of code found in 5 locations. Consider refactoring.
Open

        try:
            if client_index == -1:
                # We are sending the value to all clients
                for client in self._clients:
                    client.send_request(command)
Severity: Major
Found in python/src/odin_data/control/odin_data_adapter.py and 4 other locations - About 1 hr to fix
python/src/odin_data/control/meta_listener_adapter.py on lines 153..159
python/src/odin_data/control/odin_data_adapter.py on lines 432..440
python/src/odin_data/control/odin_data_adapter.py on lines 448..454
python/src/odin_data/control/odin_data_adapter.py on lines 457..464

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 43.

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

Identical blocks of code found in 5 locations. Consider refactoring.
Open

                try:
                    command, parameters = OdinDataAdapter.uri_params_to_dictionary(request_command, parameters)
                    self._clients[client_index].send_configuration(parameters, command)
                except Exception as err:
                    logging.debug(OdinDataAdapter.ERROR_FAILED_TO_SEND)
Severity: Major
Found in python/src/odin_data/control/odin_data_adapter.py and 4 other locations - About 1 hr to fix
python/src/odin_data/control/meta_listener_adapter.py on lines 153..159
python/src/odin_data/control/odin_data_adapter.py on lines 397..409
python/src/odin_data/control/odin_data_adapter.py on lines 432..440
python/src/odin_data/control/odin_data_adapter.py on lines 448..454

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 43.

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

Function __del__ has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def __del__(self):

        for mapped_ctype_name in ('manager_id', 'num_buffers', 'buffer_size'):
            mapped_ctype = getattr(self, mapped_ctype_name, None)
            if mapped_ctype is not None:
Severity: Minor
Found in python/src/odin_data/shared_buffer_manager.py - About 1 hr 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

Identical blocks of code found in 5 locations. Consider refactoring.
Open

                        try:
                            command, parameters = OdinDataAdapter.uri_params_to_dictionary(request_command,
                                                                                           param_set)
                            client.send_configuration(parameters, command)
                        except Exception as err:
Severity: Major
Found in python/src/odin_data/control/odin_data_adapter.py and 4 other locations - About 1 hr to fix
python/src/odin_data/control/meta_listener_adapter.py on lines 153..159
python/src/odin_data/control/odin_data_adapter.py on lines 397..409
python/src/odin_data/control/odin_data_adapter.py on lines 448..454
python/src/odin_data/control/odin_data_adapter.py on lines 457..464

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 43.

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

class SharedBufferManagerException(Exception):

    def __init__(self, msg, errno=None):
        self.msg = msg
        self.errno = errno
Severity: Major
Found in python/src/odin_data/shared_buffer_manager.py and 1 other location - About 1 hr to fix
python/src/odin_data/control/ipc_message.py on lines 12..18

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 43.

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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