fred-metadata 0.0.15__tar.gz

fred_metadata-0.0.15/LICENSE

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+MIT License
+
+Copyright (c) 2025 MPI for Heart and Lung Research
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

fred_metadata-0.0.15/MANIFEST.in

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+include fred/config/*
+include fred/structure/*
+include fred/images/*
+include fred/src/*.py
+include fred/src/web_interface/*.py
+include fred/src/heatmap/*.py
+include fred/*

fred_metadata-0.0.15/PKG-INFO

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+Metadata-Version: 2.4
+Name: fred-metadata
+Version: 0.0.15
+Summary: Metadata generation, validation, search and visualization.
+Author-email: Jasmin Walter <Jasmin.Walter@mpi-bn.mpg.de>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Dist: PyYAML>=5.1
+Requires-Dist: pytz
+Requires-Dist: python-dateutil
+Requires-Dist: tabulate
+Requires-Dist: seaborn
+Requires-Dist: biopython
+Requires-Dist: plotly<=6.2.0
+Requires-Dist: jinja2
+Requires-Dist: gitpython
+Requires-Dist: kaleido<1.0.0
+Requires-Dist: dash
+Requires-Dist: mkdocs
+Dynamic: license-file

fred_metadata-0.0.15/README.md

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+# FRED
+
+https://loosolab.pages.gwdg.de/software/metadata-organizer/
+
+
+# How to install
+
+1. Clone the repository 
+```
+git clone git@gitlab.gwdg.de:loosolab/software/metadata-organizer.git
+```
+2. Move to the new repository directory
+```
+cd metadata-organizer
+```
+3. Create a pip environment
+```
+python3 -m venv .venv
+```
+4. Activate the environment
+```
+source .venv/bin/activate
+```
+5. Install the package
+```
+pip install .
+```

fred_metadata-0.0.15/fred/config/config.yaml

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+structure: fred # fred, mampok or path to yaml file
+whitelist_repository: https://gitlab.gwdg.de/loosolab/software/metadata_whitelists.git
+private_access:
+  name: # github: username for access token; gitlab: oauth2 for project access token
+  token: # personal (github) or project (gitlab) access token
+branch: v1.2.*
+whitelist_path: fred
+update_whitelists: True
+output_path: .
+filename: '_metadata' # example_metadata.yaml
+email: bcu.support@mpi-bn.mpg.de

fred_metadata-0.0.15/fred/config/mamplan_config.yaml

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+structure: mampok
+whitelist_repository: https://gitlab.gwdg.de/loosolab/software/metadata_whitelists.git
+private_access:
+  name: # github: username for access token; gitlab: oauth2 for project access token
+  token: # personal (github) or project (gitlab) access token
+branch: v1.2.*
+whitelist_path: fred
+update_whitelists: True
+output_path: .
+filename: 'mamplan' # example_metadata.yaml

fred_metadata-0.0.15/fred/metaTools.py

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+import argparse
+import copy
+import pathlib
+import sys
+import os
+import time
+
+sys.path.append(os.path.dirname(__file__))
+from src.generate import Generate
+from src import find_metafiles
+from src import validate_yaml
+from src import file_reading
+from src import utils
+from src import git_whitelists
+from src.heatmap import create_heatmap
+
+
+
+class FRED:
+
+    def __init__(self, config):
+        self.whitelist_repo, self.whitelist_branch, self.whitelist_path, \
+        self.username, self.password, structure, self.update_whitelists, \
+        self.output_path, self.filename, self.email = utils.parse_config(config)
+        if self.whitelist_path == 'fred':
+            self.whitelist_path = os.path.join(os.path.dirname(__file__), 'FRED_whitelists')
+        else:
+            self.whitelist_path = os.path.join(self.whitelist_path, 'FRED_whitelists')
+        self.fetch_whitelists()
+        self.structure = utils.read_in_yaml(structure)
+
+    def fetch_whitelists(self):
+        git_whitelists.get_whitelists(self.whitelist_path, self.whitelist_repo, self.whitelist_branch, self.update_whitelists)
+
+    def find(self, search_path, search, output, output_filename, skip_validation):
+        result = find_metafiles.find_projects(self.structure, search_path,
+                                              search, True, skip_validation)
+        if output == 'print':
+            if len(result) > 0:
+
+                # print summary of matching files
+                print(find_metafiles.print_summary(result, output))
+
+            else:
+
+                # print information that there are no matching files
+                print('No matches found')
+        elif output == 'json':
+            if not output_filename:
+                output_filename = 'search_result'
+            json_filename = f'{output_filename}.json'
+            utils.save_as_json({'data': find_metafiles.print_summary(result, output)}, json_filename)
+            print(
+                f'The report was saved to the file \'{json_filename}\'.')
+
+    def generate(self, path, project_id, mandatory_only):
+        gen = Generate(path, project_id, mandatory_only, self.filename, self.structure, self.email)
+        gen.generate()
+
+    def validate(self, logical_validation, path, output, output_filename, save_empty=False):
+        validation_reports = {'all_files': 1,
+                              'corrupt_files': {'count': 0, 'report': []},
+                              'error_count': 0, 'warning_count': 0}
+        if os.path.isdir(path):
+            metafiles, validation_reports = file_reading.iterate_dir_metafiles(
+                self.structure, [path], filename=self.filename,
+                logical_validation=logical_validation, yaml=copy.deepcopy(self.structure),
+                whitelist_path=self.whitelist_path)
+        else:
+            metafile = utils.read_in_yaml(path)
+            file_reports = {'file': metafile, 'error': None, 'warning': None}
+            valid, missing_mandatory_keys, invalid_keys, \
+            invalid_entries, invalid_values, logical_warn = validate_yaml.validate_file(
+                metafile, self.structure, self.filename,
+                logical_validation=logical_validation, yaml=copy.deepcopy(self.structure),
+                whitelist_path=self.whitelist_path)
+            metafile['path'] = path
+            if not valid:
+                validation_reports['corrupt_files']['count'] = 1
+                validation_reports['error_count'] += (
+                            len(missing_mandatory_keys) + len(
+                        invalid_keys) + len(invalid_entries) + len(
+                        invalid_values))
+                file_reports['error'] = (
+                missing_mandatory_keys, invalid_keys, invalid_entries,
+                invalid_values)
+            if len(logical_warn) > 0:
+                validation_reports['corrupt_files']['count'] = 1
+                validation_reports['warning_count'] += len(logical_warn)
+                file_reports['warning'] = logical_warn
+            validation_reports['corrupt_files']['report'].append(file_reports)
+
+        print(f'{validation_reports["all_files"]} files were validated.')
+        print(
+            f'Found {validation_reports["error_count"]} errors and {validation_reports["warning_count"]} warnings in {validation_reports["corrupt_files"]["count"]} of those files.')
+
+        if validation_reports['corrupt_files']['count'] > 0 or save_empty is True:
+
+            res = None
+            if output is not None:
+                if output == 'print':
+                    res = ['print report']
+                elif output == 'txt':
+                    res = ['save report to txt file']
+                elif output == 'json':
+                    res = ['save report to json file']
+                elif output == 'yaml':
+                    res = ['save report to yaml file']
+            else:
+                options = ['print report', 'save report to txt file',
+                           'save report to json file',
+                           'save report to yaml file']
+                print(
+                    f'Do you want to see a report? Choose from the following options (1,...,{len(options)} or n)')
+                ask = Generate('', '', False, self.filename, self.structure, self.email)
+                ask.print_option_list(options, '')
+                res = ask.parse_input_list(options, True)
+
+            try:
+                output_report = {
+                    'report': copy.deepcopy(validation_reports)['corrupt_files']['report']}
+            except KeyError:
+                output_report = {'report': []}
+            for elem in output_report['report']:
+                id = list(utils.find_keys(elem['file'], 'id'))
+                if len(id) > 0:
+                    elem['id'] = id[0]
+                else:
+                    elem['id'] = 'missing'
+                elem['path'] = elem['file']['path']
+                errors = list(elem['error']) if 'error' in elem and elem[
+                    'error'] is not None else []
+                elem['error'] = {}
+                elem.pop('file')
+                for i in range(len(errors)):
+
+                    if len(errors[i]) > 0:
+                        if i == 0:
+                            elem['error']['missing_mandatory_keys'] = errors[i]
+                        elif i == 1:
+                            elem['error']['invalid_keys'] = errors[i]
+                        elif i == 2:
+                            whitelist_values = []
+                            for v in errors[i]:
+                                key = ':'.join(v.split(':')[:-1])
+                                entry = v.split(':')[-1]
+                                whitelist_values.append(
+                                    entry + ' in ' + key + '\n')
+                            elem['error']['invalid_entries'] = whitelist_values
+                        elif i == 3:
+                            value = []
+                            for v in errors[i]:
+                                value.append(f'{v[0]}: {v[1]} -> {v[2]}')
+                            elem['error']['invalid_values'] = value
+
+                if 'warning' in elem:
+                    if elem['warning'] is not None:
+                        for i in range(len(elem['warning'])):
+                            elem['warning'][
+                                i] = f'{elem["warning"][i][0]}: {elem["warning"][i][1]}'
+                    else:
+                        elem.pop('warning')
+
+            if res is not None:
+                if output_filename is None:
+                    timestamp = time.time()
+                    output_filename = f'validation_report_{str(timestamp).split(".")[0]}'
+
+                rep = ''
+                for report in validation_reports['corrupt_files']['report']:
+                    rep += f'{"".center(80, "_")}\n\n'
+                    rep += validate_yaml.print_full_report(report['file'],
+                                                           report['error'],
+                                                           report['warning'])
+                rep += f'{"".center(80, "_")}\n\n'
+
+                if 'save report to txt file' in res:
+                    txt_filename = f'{output_filename}.txt'
+                    txt_f = open(txt_filename, 'w')
+                    txt_f.write(rep)
+                    print(
+                        f'The report was saved to the file \'{txt_filename}\'.')
+                    txt_f.close()
+
+                if 'save report to json file' in res:
+                    json_filename = f'{output_filename}.json'
+                    utils.save_as_json(output_report, json_filename)
+                    print(
+                        f'The report was saved to the file \'{json_filename}\'.')
+
+                if 'save report to yaml file' in res:
+                    yaml_filename = f'{output_filename}.yaml'
+                    utils.save_as_yaml(output_report, yaml_filename)
+                    print(
+                        f'The report was saved to the file \'{yaml_filename}\'.')
+
+                if 'print report' in res:
+                    print(rep)
+
+        return validation_reports["error_count"], validation_reports["warning_count"]
+
+    #def edit(self, path, mandatory_only):
+    #    try:
+    #        size = os.get_terminal_size()
+    #        size = size.columns
+    #    except OSError:
+    #        size = 80
+
+    #    edit_file.edit_file(path, self.filename, mandatory_only, size)
+
+    def add_value(self, path, position, value, edit_existing):
+        files, errors = file_reading.iterate_dir_metafiles(self.structure,
+                                                           [path],
+                                                           self.filename, False,
+                                                           return_false=True,
+                                                           whitelist_path=
+                                                           self.whitelist_path)
+        position = position.split(':')
+        # TODO: type
+        for file in files:
+            file = utils.add_value_at_pos(self.structure, file, position, value,
+                                          edit_existing)
+            save_path = file['path']
+            file.pop('path')
+            print(f'edited file {save_path}')
+            utils.save_as_yaml(file, save_path)
+
+def find(args):
+    """
+    calls script find_metafiles to find matching files and print results
+    :param args:
+        path: a path of a folder that should be searched for metadata files
+        search: a string specifying search parameters linked via 'and', 'or'
+                and 'not'
+    """
+    finding = FRED(args.config)
+    finding.find(args.path, args.search, args.output, args.filename,
+                 args.skip_validation)
+
+
+def generate(args):
+    """
+    calls script generate_metafile to start dialog
+    :param args:
+    """
+    generating = FRED(args.config)
+    generating.generate(args.path, args.id, args.mandatory_only)
+
+
+def validate(args):
+    validating = FRED(args.config)
+    errors, warnings = validating.validate(not args.skip_logic, args.path, args.output, args.filename)
+
+
+def plot(args):
+    fred_object = FRED(args.config)
+    input_file = utils.read_in_yaml(args.path)
+    plots = create_heatmap.get_heatmap(input_file, fred_object.structure, mode=args.mode, labels=args.labels, background=args.background, sample_labels=args.sample_labels, condition_labels=args.condition_labels, transpose=args.transpose, drop_defaults=args.drop_defaults)
+    output_filename = args.filename if args.filename is not None else 'fig1'
+    if len(plots) > 0:
+        try:
+            plot = plots[args.setting-1][1]
+        except IndexError:
+            print(f'Setting exp{args.setting} does not exist. Defaulting to exp1.')
+            plot = plots[0][1]
+        
+        if plot is not None:
+            if args.output == 'png':
+                plot.write_image(f'{output_filename}.{args.output}', format='png')
+                print(f'Plot was saved to {output_filename}.{args.output}')
+            elif args.output == 'html':
+                with open(f'{output_filename}.{args.output}', 'w') as file:
+                    file.write(plot.to_html(full_html=False, include_plotlyjs='cdn'))
+                print(f'Plot was saved to {output_filename}.{args.output}')
+            else:
+                plot.show()
+        else:
+            print('Plot could not be created due to missing samples or conditions.')
+    else:
+        print('No settings found.')
+
+#def edit(args):
+#    editing = FRED(args.config)
+#    editing.edit(args.path, args.mandatory_only)
+
+def add_value(args):
+    adding = FRED(args.config)
+    adding.add_value(args.path, args.position, args.value, args.edit_existing)
+
+def main():
+
+    parser = argparse.ArgumentParser(prog='metaTools.py')
+    subparsers = parser.add_subparsers(title='commands')
+
+    find_function = subparsers.add_parser('find',
+                                          help='This command is used to find '
+                                               'projects by searching the '
+                                               'metadata files.')
+
+    find_group = find_function.add_argument_group('mandatory arguments')
+    find_group.add_argument('-p', '--path', type=pathlib.Path, required=True,
+                               help='The path to be searched')
+    find_group.add_argument('-s', '--search', type=str, required=True,
+                               help='The search parameters')
+    find_group.add_argument('-c', '--config', type=pathlib.Path,
+                              help='Config file', default=os.path.join(os.path.dirname(__file__), 'config', 'config.yaml'))
+    find_group.add_argument('-o', '--output', default='print', choices=['json', 'print'])
+    find_group.add_argument('-f', '--filename', default=None)
+    find_group.add_argument('-sv', '--skip_validation', default=False,
+                            action='store_true')
+    find_function.set_defaults(func=find)
+
+    create_function = subparsers.add_parser('generate',
+                                            help='This command is used to '
+                                                 'create a metadata file.')
+    create_group = create_function.add_argument_group('mandatory arguments')
+    create_group.add_argument('-p', '--path', type=pathlib.Path,
+                                 required=True,
+                                 help='The path to save the yaml')
+    create_group.add_argument('-c', '--config', type=pathlib.Path,
+                              help='Config file', default=os.path.join(os.path.dirname(__file__), 'config', 'config.yaml'))
+    create_group.add_argument('-id', '--id', type=str,
+                                 required=True,
+                                 help='The ID of the experiment')
+    create_function.add_argument('-mo', '--mandatory_only', default=False,
+                                 action='store_true',
+                                 help='If True, only mandatory keys will '
+                                      'be filled out')
+    create_function.add_argument('-m', '--mode', default='metadata', choices=['metadata', 'mamplan'])
+    create_function.set_defaults(func=generate)
+
+    validate_function = subparsers.add_parser('validate',
+                                              help='')
+    validate_group = validate_function.add_argument_group('mandatory arguments')
+    validate_group.add_argument('-p', '--path', type=pathlib.Path, required=True)
+    validate_function.add_argument('-l', '--skip_logic', default=False,
+                                   action='store_true')
+    validate_function.add_argument('-m', '--mode', default='metadata', choices=['metadata', 'mamplan'])
+    validate_function.add_argument('-o', '--output', default=None, choices=['json', 'txt', 'print', 'yaml'])
+    validate_function.add_argument('-f', '--filename', default=None)
+    validate_function.add_argument('-c', '--config', type=pathlib.Path,
+                              help='Config file', default=os.path.join(os.path.dirname(__file__), 'config', 'config.yaml'))
+    validate_function.set_defaults(func=validate)
+
+    #edit_function = subparsers.add_parser('edit', help='')
+    #edit_group = edit_function.add_argument_group('mandatory_arguments')
+    #edit_group.add_argument('-p', '--path', type=pathlib.Path, required=True)
+    #edit_function.add_argument('-mo', '--mandatory_only', default=False,
+    #                             action='store_true',
+    #                             help='If True, only mandatory keys will '
+    #                                  'be filled out')
+    #edit_function.add_argument('-c', '--config', type=pathlib.Path,
+    #                          help='Config file', default='config.yaml')
+    #edit_function.add_argument('-m', '--mode', default='metadata', choices=['metadata', 'mamplan'])
+    #edit_function.set_defaults(func=edit)
+
+    add_value_function = subparsers.add_parser('add_value', help='')
+    add_value_function.add_argument('-m', '--mode', default='metadata', choices=['metadata', 'mamplan'])
+    add_value_function.add_argument('-pos', '--position', required=True)
+    add_value_function.add_argument('-v', '--value', required=True)
+    add_value_function.add_argument('-t', '--type', default='str', choices=['str', 'int', 'float', 'bool'])
+    add_value_function.add_argument('-p', '--path', type=pathlib.Path, required=True)
+    add_value_function.add_argument('-e', '--edit_existing', default=False, action='store_true')
+    add_value_function.add_argument('-c', '--config', type=pathlib.Path,
+                              help='Config file', default=os.path.join(os.path.dirname(__file__), 'config', 'config.yaml'))
+    add_value_function.set_defaults(func=add_value)
+
+    plot_function = subparsers.add_parser('plot', help='')
+    plot_function.add_argument('-p', '--path', type=pathlib.Path, required=True)
+    plot_function.add_argument('-c', '--config', type=pathlib.Path,
+                              help='Config file', default=os.path.join(os.path.dirname(__file__), 'config', 'config.yaml'))
+    plot_function.add_argument('-m', '--mode', default='samples', choices=['samples', 'conditions'])
+    plot_function.add_argument('-s', '--setting', type=int, default=1)
+    plot_function.add_argument('-l', '--labels', default='factors', choices=['factors', 'all', 'none'])
+    plot_function.add_argument('-o', '--output', default='show', choices=['show', 'png', 'html', 'dash'])
+    plot_function.add_argument('-f', '--filename', type=pathlib.Path)
+    plot_function.add_argument('-b', '--background', default=False, action='store_true', 
+                               help='If stated, the background will be displayed in white. Per default it is transparent.')
+    plot_function.add_argument('-cl', '--condition_labels', default=False, action='store_true', 
+                               help='If stated, the label of the condition will be displayed as a name. Per default an index is stated. ')
+    plot_function.add_argument('-sl', '--sample_labels', default=False, action='store_true', 
+                               help='If stated, the label of the sample will be displayed as a name. Per default an index is stated. ')
+    plot_function.add_argument('-t', '--transpose', default=False, action='store_true', 
+                               )
+    plot_function.add_argument('-d', '--drop_defaults', default=False, action='store_true', 
+                               )
+    plot_function.set_defaults(func=plot)
+
+    args = parser.parse_args()
+
+    try:
+        args.func(args)
+    except AttributeError:
+        parser.print_help()
+
+
+if __name__ == "__main__":
+
+    main()