savu.data.plugin_list.PluginList._get_plugin_group() - Code Metrics - Inspection of "Iterative plugins API" - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed
Pull Request — master (#888)

by Daniil
created 2022-02-03 21:08 UTC
PluginList._get_plugin_group() A

↳ Parent: savu.data.plugin_list
Complexity

Conditions
Size

Total Lines	17
Code Lines	8
Duplication

Lines	0
Ratio	0 %
Importance

Changes
Metric	Value
cc	3
eloc	8
nop	4
dl	0
loc	17
rs	10
c	0
b	0
f	0
# Copyright 2014 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""
.. module:: plugin_list
   :platform: Unix
   :synopsis: Contains the PluginList class, which deals with loading and \
   saving the plugin list, and the CitationInformation class. An instance is \
   held by the MetaData class.

.. moduleauthor:: Nicola Wadeson <[email protected]>

"""
import ast
import copy
import inspect
import json
import logging
import os
import re
from collections import defaultdict

import h5py
import numpy as np

import savu.data.framework_citations as fc
import savu.plugins.docstring_parser as doc
import savu.plugins.loaders.utils.yaml_utils as yu
import savu.plugins.utils as pu
from savu.data.meta_data import MetaData

NX_CLASS = "NX_class"


class PluginList(object):
    """
    The PluginList class handles the plugin list - loading, saving and adding
    citation information for the plugin
    """

    def __init__(self):
        self.plugin_list = []
        self.n_plugins = None
        self.n_loaders = 0
        self.n_savers = 0
        self.loader_idx = None
        self.saver_idx = None
        self.datasets_list = []
        self.saver_plugin_status = True
        self._template = None
        self.version = None
        self.iterate_plugin_groups = []

    def add_template(self, create=False):
        self._template = Template(self)
        if create:
            self._template.creating = True

    def _get_plugin_entry_template(self):
        template = {"active": True, "name": None, "id": None, "data": None}
        return template

    def __get_json_keys(self):
        return ["data"]

    def _populate_plugin_list(
        self, filename, active_pass=False, template=False
    ):
        """ Populate the plugin list from a nexus file. """
        with h5py.File(filename, "r") as plugin_file:
            if "entry/savu_notes/version" in plugin_file:
                self.version = plugin_file["entry/savu_notes/version"][()]
                self._show_process_list_version()

            plugin_group = plugin_file["entry/plugin"]
            self.plugin_list = []
            single_val = ["name", "id", "pos", "active"]
            exclude = ["citation"]
            ordered_pl_keys = pu.sort_alphanum(list(plugin_group.keys()))
            for group in ordered_pl_keys:
                plugin = self._get_plugin_entry_template()
                entry_keys = plugin_group[group].keys()
                parameters = [
                    k
                    for k in entry_keys
                    for e in exclude
                    if k not in single_val and e not in k
                ]

                if "active" in entry_keys:
                    plugin["active"] = plugin_group[group]["active"][0]

                if plugin['active'] or active_pass:
                    plugin['name'] = plugin_group[group]['name'][0].decode("utf-8")
                    plugin['id'] = plugin_group[group]['id'][0].decode("utf-8")
                    plugin_tools = None
                    try:
                        plugin_class = pu.load_class(plugin["id"])()
                        # Populate the parameters (including those from it's base classes)
                        plugin_tools = plugin_class.get_plugin_tools()
                        if not plugin_tools:
                            raise OSError(f"Tools file not found for {plugin['name']}")
                        plugin_tools._populate_default_parameters()
                    except ImportError:
                        # No plugin class found
                        logging.error(f"No class found for {plugin['name']}")

                    plugin['doc'] = plugin_tools.docstring_info if plugin_tools else ""
                    plugin['tools'] = plugin_tools if plugin_tools else {}
                    plugin['param'] = plugin_tools.get_param_definitions() if \
                        plugin_tools else {}
                    plugin['pos'] = group.strip()

                    for param in parameters:
                        try:
                            plugin[param] = json.loads(plugin_group[group][param][0])
                        except ValueError as e:
                            raise ValueError(
                                f"Error: {e}\n Could not parse key '{param}' from group '{group}' as JSON"
                            )
                    self.plugin_list.append(plugin)

            # add info about groups of plugins to iterate over into
            # self.iterate_plugin_groups
            self.clear_iterate_plugin_group_dicts()
            try:
                iterate_groups = plugin_file['entry/iterate_plugin_groups']
                for key in list(iterate_groups.keys()):
                    iterate_group_dict = {
                        'start_index': iterate_groups[key]['start'][()],
                        'end_index': iterate_groups[key]['end'][()],
                        'iterations': iterate_groups[key]['iterations'][()]
                    }
                    self.iterate_plugin_groups.append(iterate_group_dict)
            except Exception as e:
                err_str = f"Process list file {filename} doesn't have the " \
                          f"iterate_plugin_groups internal hdf5 path"
                print(err_str)

            if template:
                self.add_template()
                self._template.update_process_list(template)

    def _show_process_list_version(self):
        """If the input process list was created using an older version
        of Savu, then alert the user"""
        from savu.version import __version__
        pl_version = float(self.version)
        if float(__version__) > pl_version:
            separator = "*" * 53
            print(separator)
            print(f"*** This process list was created using Savu "
                  f"{pl_version}  ***")
            print(separator)
            print(f"The process list has been updated, the incorrect \n"
                  f"parameter values have been reverted to default. \n"
                  f"Any warnings below point to the problematic parameters.\n"
                  f"Save this process list to save the updated values.")
            print(separator)

    def _save_plugin_list(self, out_filename):
        with h5py.File(out_filename, "a") as nxs_file:

            entry = nxs_file.require_group("entry")

            self._save_framework_citations(self._overwrite_group(
                entry, 'framework_citations', 'NXcollection'))

            self.__save_savu_notes(self._overwrite_group(
                entry, 'savu_notes', 'NXnote'))

            plugins_group = self._overwrite_group(entry, 'plugin', 'NXprocess')

            count = 1
            for plugin in self.plugin_list:
                plugin_group = self._get_plugin_group(
                    plugins_group, plugin, count
                )
                self.__populate_plugins_group(plugin_group, plugin)

            self.__save_iterate_plugin_groups(self._overwrite_group(
                entry, 'iterate_plugin_groups', 'NXnote'))

        if self._template and self._template.creating:
            fname = os.path.splitext(out_filename)[0] + ".savu"
            self._template._output_template(fname, out_filename)

    def _overwrite_group(self, entry, name, nxclass):
        if name in entry:
            entry.pop(name)
        group = entry.create_group(name.encode("ascii"))
        group.attrs[NX_CLASS] = nxclass.encode("ascii")
        return group

    def add_iterate_plugin_group(self, start, end, iterations):
        """Add an element to self.iterate_plugin_groups"""
        group_new = {
            'start_index': start,
            'end_index': end,
            'iterations': iterations
        }
        list_new_indices = list(range(start, end+1))

        if iterations <= 0:
            print("The number of iterations should be larger than zero and nonnegative")
            return
        elif start <= 0 or start > len(self.plugin_list) or end <= 0 or end > len(self.plugin_list):
            print("The given plugin indices are not within the range of existing plugin indices")
            return

        # crosscheck with the existing iterative loops
        if len(self.iterate_plugin_groups) != 0:
            noexactlist = True
            nointersection = True
            for count, group in enumerate(self.iterate_plugin_groups, 1):
                start_int = int(group['start_index'])
                end_int = int(group['end_index'])
                list_existing_indices = list(range(start_int, end_int+1))
                if bool(set(list_new_indices).intersection(list_existing_indices)):
                    # check if the intersection of lists is exact (number of iterations to change)
                    nointersection = False
                    if list_new_indices == list_existing_indices:
                        print(f"The number of iterations of loop group no. {count}, {list_new_indices} has been set to: {iterations}")
                        self.iterate_plugin_groups[count-1]["iterations"] = iterations
                        noexactlist = False
                    else:
                        print(f"The plugins of group no. {count} are already set to be iterative: {set(list_new_indices).intersection(list_existing_indices)}")
            if noexactlist and nointersection:
                self.iterate_plugin_groups.append(group_new)
        else:
            self.iterate_plugin_groups.append(group_new)
        self.print_iterative_loops()

    def remove_iterate_plugin_groups(self, indices):
        """ Remove elements from self.iterate_plugin_groups """
        if len(indices) == 0:
            # remove all iterative loops in process list
            prompt_str = 'Are you sure you want to remove all iterative ' \
                'loops? [y/N]'
            check = input(prompt_str)
            should_remove_all = check.lower() == 'y'
            if should_remove_all:
                self.clear_iterate_plugin_group_dicts()
        else:
            # remove specified iterative loops in process list
            sorted_indices = sorted(indices)

            if sorted_indices[0] <= 0:
                print('The iterative loops are indexed starting from 1')
                self.print_iterative_loops()
                return

            for i in reversed(sorted_indices):
                try:
                    # convert the one-based index to a zero-based index
                    del self.iterate_plugin_groups[i - 1]
                except IndexError as e:
                    info_str = f"There doesn't exist an iterative loop with " \
                               f"number {i}"
                    print(info_str)

        self.print_iterative_loops()

    def clear_iterate_plugin_group_dicts(self):
        """
        Reset the list of dicts representing groups of plugins to iterate over
        """
        self.iterate_plugin_groups = []

    def get_iterate_plugin_group_dicts(self):
        """
        Return the list of dicts representing groups of plugins to iterate over
        """
        return self.iterate_plugin_groups

    def print_iterative_loops(self):
        if len(self.iterate_plugin_groups) == 0:
            print('There are no iterative loops in the current process list')
        else:
            print('Iterative loops in the current process list are:')
            for count, group in enumerate(self.iterate_plugin_groups, 1):
                number = f"({count}) "
                start_str = f"start plugin index: {group['start_index']}"
                end_str = f"end index: {group['end_index']}"
                iterations_str = f"iterations number: {group['iterations']}"
                full_str = number + start_str + ', ' + end_str + ', ' + \
                    iterations_str
                print(full_str)

    def remove_associated_iterate_group_dict(self, pos, direction):
        """
        Remove an iterative loop associated to a plugin index
        """
        operation = 'add' if direction == 1 else 'remove'
        for i, iterate_group in enumerate(self.iterate_plugin_groups):
            if operation == 'remove':
                if iterate_group['start_index'] <= pos and \
                    pos <= iterate_group['end_index']:
                    # remove the loop if the plugin being removed is at any
                    # position within an iterative loop
                    del self.iterate_plugin_groups[i]
                    break
            elif operation == 'add':
                if iterate_group['start_index'] != iterate_group['end_index']:
                    # remove the loop only if the plugin is being added between
                    # the start and end of the loop
                    if iterate_group['start_index'] < pos and \
                        pos <= iterate_group['end_index']:
                        del self.iterate_plugin_groups[i]
                        break

    def check_pos_in_iterative_loop(self, pos):
        """
        Check if the given plugin position is in an iterative loop
        """
        is_in_loop = False
        for iterate_group in self.iterate_plugin_groups:
            if iterate_group['start_index'] <= pos and \
                pos <= iterate_group['end_index']:
                is_in_loop = True
                break

        return is_in_loop

    def __save_iterate_plugin_groups(self, group):
        '''
        Save information regarding the groups of plugins to iterate over
        '''
        for count, iterate_group in enumerate(self.iterate_plugin_groups):
            grp_name = str(count)
            grp = group.create_group(grp_name.encode('ascii'))
            shape = () # scalar data
            grp.create_dataset('start'.encode('ascii'), shape, 'i',
                iterate_group['start_index'])
            grp.create_dataset('end'.encode('ascii'), shape, 'i',
                iterate_group['end_index'])
            grp.create_dataset('iterations'.encode('ascii'), shape, 'i',
                iterate_group['iterations'])

    def shift_subsequent_iterative_loops(self, pos, direction):
        """
        Shift all iterative loops occurring after a given plugin position
        """
        # if removing a plugin that is positioned before a loop, the loop should
        # be shifted down by 1; but if removing a plugin that is positioned at
        # the start of the loop, it will be removed instead of shifted (ie, both
        # < or <= work for this case)
        #
        # if adding a plugin that will be positioned before a loop, the loop
        # should be shifted up by 1; also, if adding a plugin to be positioned
        # where the start of a loop currently exists, this should shift the loop
        # up by 1 as well (ie, only <= works for this case, hence the use of <=)
        for iterate_group in self.iterate_plugin_groups:
            if pos <= iterate_group['start_index']:
                self.shift_iterative_loop(iterate_group, direction)

    def shift_range_iterative_loops(self, positions, direction):
        """
        Shift all iterative loops within a range of plugin indices
        """
        for iterate_group in self.iterate_plugin_groups:
            if positions[0] <= iterate_group['start_index'] and \
                iterate_group['end_index'] <= positions[1]:
                self.shift_iterative_loop(iterate_group, direction)

    def shift_iterative_loop(self, iterate_group, direction):
        """
        Shift an iterative loop up or down in the process list, based on if a
        plugin is added or removed
        """
        if direction == 1:
            iterate_group['start_index'] += 1
            iterate_group['end_index'] += 1
        elif direction == -1:
            iterate_group['start_index'] -= 1
            iterate_group['end_index'] -= 1
        else:
            err_str = f"Bad direction value given to shift iterative loop: " \
                      f"{direction}"
            raise ValueError(err_str)

    def __save_savu_notes(self, notes):
        """ Save the version number

        :param notes: hdf5 group to save data to
        """
        from savu.version import __version__

        notes["version"] = __version__

    def __populate_plugins_group(self, plugin_group, plugin):
        """Populate the plugin group information which will be saved

        :param plugin_group: Plugin group to save to
        :param plugin: Plugin to be saved
        """
        plugin_group.attrs[NX_CLASS] = "NXnote".encode("ascii")
        required_keys = self._get_plugin_entry_template().keys()
        json_keys = self.__get_json_keys()

        self._save_citations(plugin, plugin_group)

        for key in required_keys:
            # only need to apply dumps if saving in configurator
            if key == "data":
                data = {}
                for k, v in plugin[key].items():
                    #  Replace any missing quotes around variables.
                    data[k] = pu._dumps(v)
            else:
                data = plugin[key]

            # get the string value
            data = json.dumps(data) if key in json_keys else plugin[key]
            # if the data is string it has to be encoded to ascii so that
            # hdf5 can save out the bytes
            if isinstance(data, str):
                data = data.encode("ascii")
            data = np.array([data])
            plugin_group.create_dataset(
                key.encode("ascii"), data.shape, data.dtype, data
            )

    def _get_plugin_group(self, plugins_group, plugin, count):
        """Return the plugin_group, into which the plugin information
         will be saved

        :param plugins_group: Current group to save inside
        :param plugin: Plugin to be saved
        :param count: Order number of the plugin in the process list
        :return: plugin group
        """
        if "pos" in plugin.keys():
            num = int(re.findall(r"\d+", str(plugin["pos"]))[0])
            letter = re.findall("[a-z]", str(plugin["pos"]))
            letter = letter[0] if letter else ""
            group_name = "%i%s" % (num, letter)
        else:
            group_name = count
        return plugins_group.create_group(group_name.encode("ascii"))

    def _add(self, idx, entry):
        self.plugin_list.insert(idx, entry)
        self.__set_loaders_and_savers()

    def _remove(self, idx):
        del self.plugin_list[idx]
        self.__set_loaders_and_savers()

    def _save_citations(self, plugin, group):
        """Save all the citations in the plugin

        :param plugin: dictionary of plugin information
        :param group: Group to save to
        """
        if "tools" in plugin.keys():
            citation_plugin = plugin.get("tools").get_citations()
            if citation_plugin:
                count = 1
                for citation in citation_plugin.values():
                    group_label = f"citation{count}"
                    if (
                        not citation.dependency
                        or self._dependent_citation_used(plugin, citation)
                    ):
                        self._save_citation_group(
                            citation, citation.__dict__, group, group_label
                        )
                        count += 1

    def _dependent_citation_used(self, plugin, citation):
        """Check if any Plugin parameter values match the citation
        dependency requirement.

        :param plugin: dictionary of plugin information
        :param citation: A plugin citation
        :return: bool True if the citation is for a parameter value
            being used inside this plugin
        """
        parameters = plugin["data"]
        for (
            citation_dependent_parameter,
            citation_dependent_value,
        ) in citation.dependency.items():
            current_value = parameters[citation_dependent_parameter]
            if current_value == citation_dependent_value:
                return True
        return False

    def _exec_citations(self, cite, citation):
        """Execute citations to variable
        :param cite: citation dictionary
        """
        for key, value in cite.items():
            exec("citation." + key + "= value")

    def _save_framework_citations(self, group):
        """Save all the citations in dict

        :param group: Group for nxs file
        """
        framework_cites = fc.get_framework_citations()
        for cite in framework_cites.values():
            label = cite.short_name_article
            del cite.short_name_article
            self._save_citation_group(cite, cite.__dict__, group, label)


    def _save_citation_group(self, citation, cite_dict, group, group_label):
        """Save the citations to the provided group label

        :param citation: Citation object
        :param cite_dict: Citation dictionary
        :param group: Group
        :param group_label: Group label
        :return:
        """
        citation_group = group.require_group(group_label.encode("ascii"))
        self._exec_citations(cite_dict, citation)
        citation.write(citation_group)

    def _get_docstring_info(self, plugin):
        plugin_inst = pu.plugins[plugin]()
        tools = plugin_inst.get_plugin_tools()
        tools._populate_default_parameters()
        return plugin_inst.docstring_info

    # def _byteify(self, input):
    #     if isinstance(input, dict):
    #         return {self._byteify(key): self._byteify(value)
    #                 for key, value in input.items()}
    #     elif isinstance(input, list):
    #         temp = [self._byteify(element) for element in input]
    #         return temp
    #     elif isinstance(input, str):
    #         return input.encode('utf-8')
    #     else:
    #         return input

    def _set_datasets_list(self, plugin):
        in_pData, out_pData = plugin.get_plugin_datasets()
        in_data_list = self._populate_datasets_list(in_pData)
        out_data_list = self._populate_datasets_list(out_pData)
        self.datasets_list.append({'in_datasets': in_data_list,
                                   'out_datasets': out_data_list})

    def _populate_datasets_list(self, data):
        data_list = []
        for d in data:
            name = d.data_obj.get_name()
            pattern = copy.deepcopy(d.get_pattern())
            pattern[list(pattern.keys())[0]]['max_frames_transfer'] = \

                d.meta_data.get('max_frames_transfer')
            pattern[list(pattern.keys())[0]]['transfer_shape'] = \
                d.meta_data.get('transfer_shape')
            data_list.append({'name': name, 'pattern': pattern})
        return data_list

    def _get_datasets_list(self):
        return self.datasets_list

    def _reset_datasets_list(self):
        self.datasets_list = []

    def _get_n_loaders(self):
        return self.n_loaders

    def _get_n_savers(self):
        return self.n_savers

    def _get_loaders_index(self):
        return self.loader_idx

    def _get_savers_index(self):
        return self.saver_idx

    def _get_n_processing_plugins(self):
        return len(self.plugin_list) - self._get_n_loaders()

    def __set_loaders_and_savers(self):
        """Get lists of loader and saver positions within the plugin list and
        set the number of loaders.

        :returns: loader index list and saver index list
        :rtype: list(int(loader)), list(int(saver))
        """
        from savu.plugins.loaders.base_loader import BaseLoader
        from savu.plugins.savers.base_saver import BaseSaver

        loader_idx = []
        saver_idx = []
        self.n_plugins = len(self.plugin_list)

        for i in range(self.n_plugins):
            pid = self.plugin_list[i]["id"]
            bases = inspect.getmro(pu.load_class(pid))
            loader_list = [b for b in bases if b == BaseLoader]
            saver_list = [b for b in bases if b == BaseSaver]
            if loader_list:
                loader_idx.append(i)
            if saver_list:
                saver_idx.append(i)
        self.loader_idx = loader_idx
        self.saver_idx = saver_idx
        self.n_loaders = len(loader_idx)
        self.n_savers = len(saver_idx)

    def _check_loaders(self):
        """Check plugin list starts with a loader."""
        self.__set_loaders_and_savers()
        loaders = self._get_loaders_index()

        if loaders:
            if loaders[0] != 0 or loaders[-1] + 1 != len(loaders):
                raise Exception("All loader plugins must be at the beginning "
                                "of the process list")
        else:
            raise Exception("The first plugin in the process list must be a "
                            "loader plugin.")

    def _add_missing_savers(self, exp):
        """ Add savers for missing datasets. """
        data_names = exp.index["in_data"].keys()
        saved_data = []

        for i in self._get_savers_index():
            saved_data.append(self.plugin_list[i]["data"]["in_datasets"])
        saved_data = set([s for sub_list in saved_data for s in sub_list])

        for name in [data for data in data_names if data not in saved_data]:
            pos = exp.meta_data.get("nPlugin") + 1
            exp.meta_data.set("nPlugin", pos)
            process = {}
            plugin = pu.load_class("savu.plugins.savers.hdf5_saver")()
            ptools = plugin.get_plugin_tools()
            plugin.parameters["in_datasets"] = [name]
            process["name"] = plugin.name
            process["id"] = plugin.__module__
            process["pos"] = str(pos + 1)
            process["data"] = plugin.parameters
            process["active"] = True
            process["param"] = ptools.get_param_definitions()
            process["doc"] = ptools.docstring_info
            process["tools"] = ptools
            self._add(pos + 1, process)

    def _update_datasets(self, plugin_no, data_dict):
        n_loaders = self._get_n_loaders()
        idx = self._get_n_loaders() + plugin_no
        self.plugin_list[idx]["data"].update(data_dict)

    def _get_dataset_flow(self):
        datasets_idx = []
        n_loaders = self._get_n_loaders()
        n_plugins = self._get_n_processing_plugins()
        for i in range(self.n_loaders, n_loaders + n_plugins):
            datasets_idx.append(self.plugin_list[i]["data"]["out_datasets"])
        return datasets_idx

    def _contains_gpu_processes(self):
        """ Returns True if gpu processes exist in the process list. """
        try:
            from savu.plugins.driver.gpu_plugin import GpuPlugin

            for i in range(self.n_plugins):
                bases = inspect.getmro(
                    pu.load_class(self.plugin_list[i]["id"])
                )
                if GpuPlugin in bases:
                    return True
        except ImportError as ex:
            if "pynvml" in ex.message:
                logging.error(
                    "Error while importing GPU dependencies: %s", ex.message
                )
            else:
                raise

        return False


class Template(object):
    """A class to read and write templates for plugin lists."""

    def __init__(self, plist):
        super(Template, self).__init__()
        self.plist = plist
        self.creating = False

    def _output_template(self, fname, process_fname):
        plist = self.plist.plugin_list
        index = [i for i in range(len(plist)) if plist[i]["active"]]

        local_dict = MetaData(ordered=True)
        global_dict = MetaData(ordered=True)
        local_dict.set(["process_list"], os.path.abspath(process_fname))

        for i in index:
            params = self.__get_template_params(plist[i]["data"], [])
            name = plist[i]["name"]
            for p in params:
                ptype, isyaml, key, value = p
                if isyaml:
                    data_name = isyaml if ptype == "local" else "all"
                    local_dict.set([i + 1, name, data_name, key], value)
                elif ptype == "local":
                    local_dict.set([i + 1, name, key], value)
                else:
                    global_dict.set(["all", name, key], value)

        with open(fname, "w") as stream:
            local_dict.get_dictionary().update(global_dict.get_dictionary())
            yu.dump_yaml(local_dict.get_dictionary(), stream)

    def __get_template_params(self, params, tlist, yaml=False):
        for key, value in params.items():
            if key == "yaml_file":
                yaml_dict = self._get_yaml_dict(value)
                for entry in list(yaml_dict.keys()):
                    self.__get_template_params(
                        yaml_dict[entry]["params"], tlist, yaml=entry
                    )
            value = pu.is_template_param(value)
            if value is not False:
                ptype, value = value
                isyaml = yaml if yaml else False
                tlist.append([ptype, isyaml, key, value])
        return tlist

    def _get_yaml_dict(self, yfile):
        from savu.plugins.loaders.yaml_converter import YamlConverter

        yaml_c = YamlConverter()
        template_check = pu.is_template_param(yfile)
        yfile = template_check[1] if template_check is not False else yfile
        yaml_c.parameters = {"yaml_file": yfile}
        return yaml_c.setup(template=True)

    def update_process_list(self, template):
        tdict = yu.read_yaml(template)
        del tdict["process_list"]

        for plugin_no, entry in tdict.items():
            plugin = list(entry.keys())[0]
            for key, value in list(entry.values())[0].items():
                depth = self.dict_depth(value)
                if depth == 1:
                    self._set_param_for_template_loader_plugin(
                        plugin_no, key, value
                    )
                elif depth == 0:
                    if plugin_no == "all":
                        self._set_param_for_all_instances_of_a_plugin(
                            plugin, key, value
                        )
                    else:
                        data = self._get_plugin_data_dict(str(plugin_no))
                        data[key] = value
                else:
                    raise Exception("Template key not recognised.")

    def dict_depth(self, d, depth=0):
        if not isinstance(d, dict) or not d:
            return depth
        return max(self.dict_depth(v, depth + 1) for k, v in d.items())

    def _set_param_for_all_instances_of_a_plugin(self, plugin, param, value):
        # find all plugins with this name and replace the param
        for p in self.plist.plugin_list:
            if p["name"] == plugin:
                p["data"][param] = value

    def _set_param_for_template_loader_plugin(self, plugin_no, data, value):
        param_key = list(value.keys())[0]
        param_val = list(value.values())[0]
        pdict = self._get_plugin_data_dict(str(plugin_no))["template_param"]
        pdict = defaultdict(dict) if not pdict else pdict
        pdict[data][param_key] = param_val

    def _get_plugin_data_dict(self, plugin_no):
        """ input plugin_no as a string """
        plist = self.plist.plugin_list
        index = [plist[i]["pos"] for i in range(len(plist))]
        return plist[index.index(plugin_no)]["data"]


class CitationInformation(object):
    """
    Descriptor of Citation Information for plugins
    """

    def __init__(
        self,
        description,
        bibtex="",
        endnote="",
        doi="",
        short_name_article="",
        dependency="",
    ):
        self.description = description
        self.short_name_article = short_name_article
        self.bibtex = bibtex
        self.endnote = endnote
        self.doi = doi
        self.dependency = dependency
        self.name = self._set_citation_name()
        self.id = self._set_id()

    def _set_citation_name(self):
        """Create a short identifier using the short name of the article
        and the first author
        """
        cite_info = True if self.endnote or self.bibtex else False

        if cite_info and self.short_name_article:
            cite_name = (
                self.short_name_article.title()
                + " by "
                + self._get_first_author()
                + " et al."
            )
        elif cite_info:
            cite_name = (
                self._get_title()
                + " by "
                + self._get_first_author()
                + " et al."
            )
        else:
            # Set the tools class name as the citation name causes overwriting
            # module_name = tool_class.__module__.split('.')[-1].replace('_', ' ')
            # cite_name = module_name.split('tools')[0].title()
            cite_name = self.description
        return cite_name

    def _set_citation_id(self, tool_class):
        """Create a short identifier using the bibtex identification"""
        # Remove blank space
        if self.bibtex:
            cite_id = self._get_id()
        else:
            # Set the tools class name as the citation name
            module_name = tool_class.__module__.split(".")[-1]
            cite_id = module_name
        return cite_id

    def _set_id(self):
        """ Retrieve the id from the bibtex """
        cite_id = self.seperate_bibtex("@article{", ",")
        return cite_id

    def _get_first_author(self):
        """ Retrieve the first author name """
        if self.endnote:
            first_author = self.seperate_endnote("%A ")
        elif self.bibtex:
            first_author = self.seperate_bibtex("author={", "}", author=True)
        return first_author


    def _get_title(self):
        """ Retrieve the title """
        if self.endnote:
            title = self.seperate_endnote("%T ")
        elif self.bibtex:
            title = self.seperate_bibtex("title={", "}")
        return title


    def seperate_endnote(self, seperation_char):
        """Return the string contained between start characters
        and a new line

        :param seperation_char: Character to split the string at
        :return: The string contained between start characters and a new line
        """
        item = self.endnote.partition(seperation_char)[2].split("\n")[0]
        return item

    def seperate_bibtex(self, start_char, end_char, author=False):
        """Return the string contained between provided characters

        :param start_char: Character to split the string at
        :param end_char: Character to end the split at
        :return: The string contained between both characters
        """
        plain_text = doc.remove_new_lines(self.bibtex)
        item = plain_text.partition(start_char)[2].split(end_char)[0]
        if author:
            # Return one author only
            if " and " in item:
                item = item.split(" and ")[0]

        return item

    def write(self, citation_group):
        # classes don't have to be encoded to ASCII
        citation_group.attrs[NX_CLASS] = "NXcite"
        # Valid ascii sequences will be encoded, invalid ones will be
        # preserved as escape sequences
        description_array = np.array([self.description.encode('ascii','backslashreplace')])
        citation_group.create_dataset('description'.encode('ascii'),
                                      description_array.shape,
                                      description_array.dtype,
                                      description_array)
        doi_array = np.array([self.doi.encode('ascii')])
        citation_group.create_dataset('doi'.encode('ascii'),
                                      doi_array.shape,
                                      doi_array.dtype,
                                      doi_array)
        endnote_array = np.array([self.endnote.encode('ascii','backslashreplace')])
        citation_group.create_dataset('endnote'.encode('ascii'),
                                      endnote_array.shape,
                                      endnote_array.dtype,
                                      endnote_array)
        bibtex_array = np.array([self.bibtex.encode('ascii','backslashreplace')])
        citation_group.create_dataset('bibtex'.encode('ascii'),
                                      bibtex_array.shape,
                                      bibtex_array.dtype,
                                      bibtex_array)

DiamondLightSource / Savu

Pull Request — master (#888)

PluginList._get_plugin_group() A

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