How to use relative_filename method in autotest

Best Python code snippet using autotest_python

action_executor.py

Source:action_executor.py

1import os2import platform3import typing4import shutil5from photomanager.db.models import ImageMeta6from sqlalchemy import and_7from sqlalchemy.orm import Session8from photomanager.lib.errors import MultiFileError9from photomanager.lib.pmconst import PATH_SEP10from photomanager.db.config import Config, FieldBackupDir11from photomanager.utils.pathutils import is_abspath12class ActionExecutor(object):13    def __init__(self, base_folder: str, db_session: Session, action_item: typing.Dict[str, typing.List]):14        self.base_folder = base_folder15        self.db_session = db_session16        self.action_item = action_item17        self.config = Config(db_session)18    def do(self):19        raise NotImplementedError20class ActionRemoveFile(ActionExecutor):21    def do(self):22        if self.action_item["action"] != "remove_file":23            raise ValueError24        for relative_file in self.action_item["files"]:25            self.do_remove_file(relative_file)26    def do_remove_file(self, relative_filename):27        self._do_backup_file(relative_filename)28        self._do_remove_file_from_disk(relative_filename)29        self._do_remove_file_from_db(relative_filename)30    def _do_backup_file(self, relative_filename):31        full_name = self._get_fullname(relative_filename)32        if not os.path.exists(full_name):33            return34        backup_dir = self.config.get_value(FieldBackupDir)35        if not is_abspath(backup_dir):36            backup_dir = self.base_folder + PATH_SEP + backup_dir37        # remove driver letter38        if platform.system() == "Windows" and not self.base_folder[1] == ":":39            relative_filename = relative_filename[2:]40        # remove first path separator41        if relative_filename[0] == PATH_SEP:42            relative_filename = relative_filename[1:]43        backup_filename = f"{backup_dir}{PATH_SEP}{relative_filename}"44        backup_file_path, _ = os.path.split(backup_filename)45        os.makedirs(backup_file_path, exist_ok=True)46        if os.path.exists(backup_filename):47            ori_backup_name = backup_filename48            for i in range(10000):49                if not os.path.exists(f"{ori_backup_name}.{i}"):50                    backup_filename = f"{ori_backup_name}.{i}"51                    break52        shutil.copyfile(full_name, backup_filename)53    def _get_fullname(self, relative_filename: str):54        full_base_folder = self.base_folder55        if platform.system() == "Linux" and not self.base_folder.startswith(PATH_SEP):  # relative path:56            full_base_folder = os.getcwd() + PATH_SEP + self.base_folder57        elif platform.system() == "Windows" and not self.base_folder[1] == ":":58            full_base_folder = os.getcwd() + PATH_SEP + self.base_folder59        return f"{full_base_folder}/{relative_filename}"60    def _do_remove_file_from_disk(self, relative_filename: str):61        fullname = self._get_fullname(relative_filename)62        if os.path.exists(fullname):63            os.remove(fullname)64    def _do_remove_file_from_db(self, relative_filename):65        relative_dir = os.path.dirname(relative_filename)66        basename = os.path.basename(relative_filename)67        image_metas = self.db_session.query(ImageMeta).filter(68            and_(ImageMeta.folder == relative_dir, ImageMeta.filename == basename)).all()69        if len(image_metas) > 1:70            raise MultiFileError()71        image_meta = image_metas[0]72        self.db_session.delete(image_meta)73class ActionExecutorList(object):74    def __init__(self, base_folder: str, db_session, actions: list):75        """76        :param base_folder:77        :param db_session: a sqlalchemy session78        :param action_contents: a action list79        example:80          [{"action": "remove_file", "files": ["file2:, "files4"]}81        allow action:82          {"action": "remove_file", "files": ["file2:, "files4"]}83          {"action": "move_file", "from": "file1", "to": "file2"}84        """85        self.base_folder = base_folder86        self.db_session = db_session87        self.actions = actions88    def do(self):89        for action_item in self.actions:90            executor = self._create_executor(action_item)91            executor.do()92    def _create_executor(self, action_item) -> ActionExecutor:93        if action_item["action"] == "remove_file":94            return ActionRemoveFile(self.base_folder, self.db_session, action_item)95        else:...

api.py

Source:api.py

1from flask import request, Blueprint, jsonify, redirect, url_for2from flask_login import login_required, current_user3from cromwell_frontend.db_models import WorkflowDefinition, db4from cromwell_frontend.exceptions import NotFoundException, AuthException5from cromwell_frontend.login_manager import authenticate_user, get_jwt6from cromwell_frontend.util import handle_exception7from cromwell_frontend.workflow import Workflow8api = Blueprint('api', __name__, url_prefix='/api')9@api.route('/unauthorized')10def unauthorized():11    return jsonify({'message': 'Not authenticated.'}), 40112@api.route('/authenticate', methods=['POST'])13def jwt_authenticate():14    try:15        credentials = request.get_json(force=True)16        authenticate_user(request)17        token = get_jwt(credentials['username'], credentials['password'])18        return jsonify({'token': str(token)}), 20019    except Exception as e:20        return jsonify({'message': f'authentication failed: {e}'}), 40321@api.route('/workflow_definitions', methods=['GET', 'POST'])22@login_required23def list_workflow_definitions():24    try:25        if request.method == 'POST':26            data = request.get_json(force=True)27            workflow_definition = WorkflowDefinition(relative_filename=data['relative_filename'],28                                                     name=data['name'],29                                                     description=data['description'],30                                                     owner=current_user)31            db.session.add(workflow_definition)32            db.session.commit()33            return redirect(url_for('api.get_workflow_definition',34                                    relative_filename=workflow_definition.relative_filename))35        else:36            return jsonify([definition.to_dict for definition in WorkflowDefinition.query.all()])37    except Exception as e:38        return handle_exception(e)39@api.route('/workflow_definitions/<relative_filename>', methods=['GET', 'POST', 'DELETE'])40@login_required41def get_workflow_definition(relative_filename):42    try:43        workflow_definition = WorkflowDefinition.query.filter_by(relative_filename=relative_filename).first()44        if workflow_definition is None:45            raise NotFoundException(f'No workflow with relative filename {relative_filename} exists!')46        if request.method == 'POST':47            data = request.get_json(force=True)48            workflow_definition.update(data, current_user)49            db.session.commit()50        if request.method == 'DELETE':51            if current_user is workflow_definition.owner or current_user.admin:52                db.session.delete(workflow_definition)53                db.session.commit()54                return jsonify({'message': f'Workflow definition {workflow_definition.relative_filename} deleted'})55            else:56                raise AuthException(f'User {current_user.username} cannot delete {workflow_definition.relative_filename}')57        return jsonify(workflow_definition.to_dict())58    except Exception as e:59        return handle_exception(e)60@api.route('/workflow_chart/<workflow_id>', methods=['GET'])61@login_required62def get_workflow_chart_data(workflow_id):63    try:64        workflow = Workflow(workflow_id)65        return jsonify(workflow.get_chart_metadata())66    except Exception as e:67        return handle_exception(e)68@api.route('/workflows/<workflow_id>/release_hold', methods=['POST'])69@login_required70def release_workflow_hold(workflow_id):71    try:72        workflow = Workflow(workflow_id)73        if current_user == workflow.owner or current_user.admin:74            return jsonify(workflow.resume())75        else:76            raise AuthException(f'User {current_user.id} cannot release hold on {workflow_id}')77    except Exception as e:78        return handle_exception(e)79@api.route('/workflows/<workflow_id>/cancel', methods=['POST'])80@login_required81def cancel_workflow(workflow_id):82    try:83        workflow = Workflow(workflow_id)84        if current_user == workflow.owner or current_user.admin:85            return jsonify(workflow.cancel())86        else:87            raise AuthException(f'User {current_user.id} cannot release hold on {workflow_id}')88    except Exception as e:...

workflow_definitions.py

Source:workflow_definitions.py

1import os2from flask import Blueprint, render_template, request, url_for, redirect3from flask_login import login_required4from cromwell_frontend import config5from cromwell_frontend.db_models import WorkflowDefinition, db6from cromwell_frontend.page_data import WorkflowDefinitionEntry, WorkflowDefinitionList7from cromwell_frontend.util import handle_exception_browser8from cromwell_frontend.exceptions import NotFoundException9workflow_definitions = Blueprint('workflow_definitions', __name__, url_prefix='/workflow_definitions')10@workflow_definitions.route('/')11@login_required12def list_workflow_definitions():13    return render_template('workflow_definition_list.html', page_data=WorkflowDefinitionList('Workflow Definitions'))14@workflow_definitions.route('/create', methods=['GET', 'POST'])15@login_required16def create_workflow_definition():17    try:18        if request.method == 'POST':19            workflow_definition = WorkflowDefinition(20                name=request.form.get('name'),21                description=request.form.get('description'),22                relative_filename=request.form.get('relative_path'),23                file_contents=request.form.get('definition'))24            db.session.add(workflow_definition)25            db.session.commit()26            return redirect(url_for('workflow_definitions.view_workflow_definition',27                                    relative_path=workflow_definition.relative_filename))28        else:29            count = WorkflowDefinition.query.count()30            filename = f'workflow{count}.wdl'31            while config.WORKFLOW_DEFINITION_DIR.joinpath(filename).exists():32                count += 133                filename = f'workflow{count}.wdl'34            workflow_definition = WorkflowDefinition(relative_filename=str(filename), name=str(filename))35            return render_template('workflow_definition_entry.html', page_data=WorkflowDefinitionEntry('Create workflow definition', workflow_definition))36    except Exception as e:37        return handle_exception_browser(e)38@workflow_definitions.route('/<relative_path>', methods=['GET', 'POST', 'DELETE'])39@login_required40def view_workflow_definition(relative_path):41    try:42        workflow_definition = WorkflowDefinition.query.filter_by(relative_filename=relative_path).first()43        if workflow_definition is None:44            raise NotFoundException(f'No workflow with path {relative_path} exists!')45        if request.method == 'POST':46            name = request.form.get('name')47            description = request.form.get('description')48            relative_filename = request.form.get('relative_path')49            file_contents = request.form.get('definition')50            if workflow_definition is None:51                workflow_definition = WorkflowDefinition(52                    relative_filename=relative_filename,53                    name=name,54                    description=description55                )56                workflow_definition.file_contents = file_contents57                db.session.add(workflow_definition)58            else:59                workflow_definition.name = name60                workflow_definition.description = description61                workflow_definition.relative_filename = relative_filename62                workflow_definition.file_contents = file_contents63            db.session.commit()64        elif request.method == 'DELETE':65            db.session.delete(workflow_definition)66            db.session.commit()67        else:68            if workflow_definition is None:69                count = WorkflowDefinition.query.count()70                filename = f'workflow{count}.wdl'71                while os.path.exists(os.path.join(config.WORKFLOW_DEFINITION_DIR, filename)):72                    count += 173                    filename = f'workflow{count}.wdl'74                workflow_definition = WorkflowDefinition(relative_filename=filename)75        return render_template('workflow_definition_entry.html',76                               page_data=WorkflowDefinitionEntry(workflow_definition.name, workflow_definition))77    except Exception as e:...

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