hpcflow 0.1.9__py3-none-any.whl → 0.2.0a271__py3-none-any.whl

hpcflow/archive/archive.py

@@ -1,308 +0,0 @@
-"""`hpcflow.archive.archive.py`
-
-This module contains a database model class for the archiving capabilities.
-
-"""
-
-import shutil
-import enum
-import time
-from datetime import datetime
-from pathlib import Path
-from pprint import pprint
-from shutil import ignore_patterns
-from time import sleep
-
-from sqlalchemy import (Table, Column, Integer, DateTime, ForeignKey, String,
-                        UniqueConstraint, Enum, Boolean)
-from sqlalchemy.orm import relationship, Session
-from sqlalchemy.exc import IntegrityError, OperationalError
-
-from hpcflow.config import Config as CONFIG
-from hpcflow.archive.cloud.cloud import CloudProvider
-from hpcflow.archive.cloud.errors import CloudProviderError, CloudCredentialsError
-from hpcflow.archive.errors import ArchiveError
-from hpcflow.base_db import Base
-from hpcflow.copytree import copytree_multi
-
-
-archive_is_active = Table(
-    'archive_is_active',
-    Base.metadata,
-    Column(
-        'archive_id',
-        Integer,
-        ForeignKey('archive.id'),
-        primary_key=True
-    ),
-    Column(
-        'directory_value_id',
-        Integer,
-        ForeignKey('var_value.id'),
-        primary_key=True
-    ),
-)
-
-
-class RootDirectoryName(enum.Enum):
-
-    parent = 'parent'
-    datetime = 'datetime'
-    null = ''
-
-
-class TaskArchiveStatus(enum.Enum):
-
-    pending = 'pending'
-    active = 'active'
-    complete = 'complete'
-
-
-class Archive(Base):
-    """Class to represent an archive location."""
-
-    __tablename__ = 'archive'
-    __table_args__ = (
-        UniqueConstraint('path', 'host', 'cloud_provider',
-                         name='archive_location'),
-    )
-
-    id_ = Column('id', Integer, primary_key=True)
-    name = Column(String(255))
-    _path = Column('path', String(255))
-    host = Column(String(255))
-    cloud_provider = Column(Enum(CloudProvider))
-    root_directory_name = Column(Enum(RootDirectoryName))
-    root_directory_increment = Column(Boolean)
-
-    command_groups = relationship('CommandGroup', back_populates='archive')
-    directories_archiving = relationship('VarValue', secondary=archive_is_active)
-    workflow = relationship('Workflow', back_populates='root_archive', uselist=False)
-
-    def __init__(self, name, path, host='', cloud_provider='', root_directory_name='',
-                 root_directory_increment=True):
-
-        self.name = name
-        self._path = path
-        self.host = host
-        self.cloud_provider = CloudProvider(cloud_provider)
-        self.root_directory_name = RootDirectoryName(root_directory_name)
-        self.root_directory_increment = root_directory_increment
-
-        if not self.check_exists(self.path):
-            raise ValueError('Archive path "{}" does not exist.'.format(self.path))
-
-    @property
-    def path(self):
-        return Path(self._path)
-
-    def get_directories(self):
-        """Get sub directories currently on the archive path.
-
-        Returns
-        -------
-        list of str
-            Sub-directory names.
-
-        """
-
-        if not self.host:
-            if self.cloud_provider != CloudProvider.null:
-                directories = self.cloud_provider.get_directories(self.path)
-            else:
-                directories = [i.name for i in self.path.glob('*') if i.is_dir()]
-        else:
-            raise NotImplementedError()
-
-        return directories
-
-    def check_exists(self, directory):
-        'Check if a given directory exists on the Archive.'
-
-        if not self.host:
-            if self.cloud_provider != CloudProvider.null:
-                exists = self.cloud_provider.check_exists(directory)
-            else:
-                exists = directory.is_dir()
-        else:
-            raise NotImplementedError()
-
-        return exists
-
-    def get_archive_dir(self, workflow):
-        'This should be called once per unique workflow Archive.'
-
-        if self.root_directory_name != RootDirectoryName.null:
-
-            if self.root_directory_name == RootDirectoryName.parent:
-                archive_dir = workflow.directory.stem
-            elif self.root_directory_name == RootDirectoryName.datetime:
-                archive_dir = time.strftime('%Y-%m-%d-%H%M')
-
-            sub_dirs = self.get_directories()
-            if archive_dir in sub_dirs:
-                if self.root_directory_increment:
-                    count = 0
-                    max_count = 10
-                    while archive_dir in sub_dirs:
-                        count += 1
-                        if count > max_count:
-                            msg = ('Maximum iteration reached ({}) in searching for '
-                                   'available archive directory.'.format(max_count))
-                            raise RuntimeError(msg)
-                        archive_dir = archive_dir + '_1'
-                else:
-                    msg = ('Archive directory "{}" already exists.')
-                    raise ValueError(msg.format(archive_dir))
-
-        else:
-            archive_dir = ''
-
-        return archive_dir
-
-    def execute(self, exclude, archive_dir):
-        """Execute the archive process with no lock. Used for root archive.
-
-        Parameters
-        ----------
-        exclude : list of str
-
-        """
-
-        self._copy(self.workflow.directory, self.path.joinpath(archive_dir), exclude)
-
-    def execute_with_lock(self, task):
-        """Execute the archive process of a given working directory.
-
-        Parameters
-        ----------
-        directory_value : VarValue
-        exclude : list of str
-
-        """
-
-        print('Archive.execute_with_lock: task.is_archive_required: {}'.format(
-            task.is_archive_required()))
-
-        session = Session.object_session(self)
-
-        cg_sub = task.command_group_submission_iteration.command_group_submission
-        directory_value = task.get_working_directory()
-        exclude = cg_sub.command_group.archive_excludes
-        archive_dir = cg_sub.command_group.archive_directory
-
-        root_dir = self.command_groups[0].workflow.directory
-        src_dir = root_dir.joinpath(directory_value.value)
-        dst_dir = self.path.joinpath(archive_dir, directory_value.value)
-
-        sleep_time = 5
-        context = 'Archive.execute_with_lock'
-        block_msg = ('{{}} {}: Archiving blocked. Sleeping for {} '
-                     'seconds'.format(context, sleep_time))
-        unblock_msg = ('{{}} {}: Archiving available. Archiving from source directory: '
-                       '"{}" to destination directory: "{}".'.format(
-                           context, src_dir, dst_dir))
-        apply_block_msg = ('{{}} {}: Applying archive lock to directory: {}.'.format(
-            context, directory_value))
-        remove_block_msg = ('{{}} {}: Removing archive lock from directory: {}'.format(
-            context, directory_value))
-        arch_done_msg = ('{{}} {}: Archive of the working directory {} performed by '
-                         'another task.'.format(context, directory_value))
-
-        if task.is_archive_required():
-
-            blocked = True
-            while blocked:
-
-                session.refresh(self)
-                if not task.is_archive_required():
-                    print(arch_done_msg.format(datetime.now()), flush=True)
-                    task.archive_status = TaskArchiveStatus('complete')
-                    session.commit()
-                    return
-
-                if directory_value in self.directories_archiving:
-                    print(block_msg.format(datetime.now()), flush=True)
-                    sleep(sleep_time)
-                else:
-                    try:
-                        self.directories_archiving.append(directory_value)
-                        session.commit()
-                        print(apply_block_msg.format(datetime.now()), flush=True)
-                        blocked = False
-
-                    except IntegrityError:
-                        # Another process has already set `directories_archiving`
-                        session.rollback()
-                        print(block_msg.format(datetime.now()), flush=True)
-                        sleep(sleep_time)
-
-                    except OperationalError:
-                        # Database is likely locked.
-                        session.rollback()
-                        print(block_msg.format(datetime.now()), flush=True)
-                        sleep(sleep_time)
-
-                    if not blocked:
-
-                        start_time = datetime.now()
-                        print(unblock_msg.format(start_time), flush=True)
-                        task.archive_status = TaskArchiveStatus('active')
-                        task.archive_start_time = start_time
-                        session.commit()
-
-                        self._copy(src_dir, dst_dir, exclude)
-
-                        end_time = datetime.now()
-                        task.archive_status = TaskArchiveStatus('complete')
-                        task.archive_end_time = end_time
-                        self.directories_archiving.remove(directory_value)
-                        session.commit()
-
-                        print(remove_block_msg.format(end_time), flush=True)
-
-        else:
-            print(arch_done_msg.format(datetime.now()), flush=True)
-            task.archive_status = TaskArchiveStatus('complete')
-            session.commit()
-
-    def _copy(self, src_dir, dst_dir, exclude):
-        """Do the actual copying.
-
-        Need to ensure this function catches all exceptions, so the block is
-        released if copying fails.
-
-        TODO: does copytree overwrite all files or just copy
-        non-existing files?
-
-        TODO: later (safely) copy the database to archive as well?
-
-        """
-
-        ignore = [CONFIG.get('hpcflow_directory')] + (exclude or [])
-        start = datetime.now()
-
-        try:
-
-            if self.cloud_provider != CloudProvider.null:
-                try:
-                    self.cloud_provider.archive_directory(src_dir, dst_dir, ignore)
-                except (CloudProviderError, CloudCredentialsError, ArchiveError) as err:
-                    raise ArchiveError(err)
-            else:
-                if ignore:
-                    ignore_func = ignore_patterns(*ignore)
-                else:
-                    ignore_func = None
-                try:
-                    copytree_multi(str(src_dir), str(dst_dir), ignore=ignore_func)
-                except shutil.Error as err:
-                    raise ArchiveError(err)
-
-        except ArchiveError as err:
-            print('Archive copying error: {}'.format(err))
-
-        end = datetime.now()
-        copy_seconds = (end - start).total_seconds()
-        print('Archive to "{}" took {} seconds'.format(
-            self.name, copy_seconds), flush=True)

hpcflow/archive/cloud/cloud.py

@@ -1,47 +0,0 @@
-"""`hpcflow.archive.cloud.cloud.py
-
-TODO: if we have multiple cloud providers, perhaps it would be better to
-implement the `upload_directory` function generally, and then just rely on 
-the provider-specific `upload_file` functions.
-
-"""
-
-import enum
-import posixpath
-import os
-
-from hpcflow.archive.cloud.providers import dropbox
-
-
-class CloudProvider(enum.Enum):
-
-    dropbox = 'dropbox'
-    onedrive = 'onedrive'
-    null = ''
-
-    def check_access(self):
-        if self.name == 'dropbox':
-            dropbox.check_access()
-
-    def archive_directory(self, local_path, remote_path, exclude):
-        if self.name == 'dropbox':
-            dropbox.archive_directory(
-                dropbox.get_dropbox(), local_path, remote_path, exclude)
-
-    def get_directories(self, path):
-        'Get sub directories within a path'
-
-        if self.name == 'dropbox':
-            dbx = dropbox.get_dropbox()
-            return dropbox.get_folders(dbx, path)
-
-    def check_exists(self, directory):
-        'Check a given directory exists on the cloud storage.'
-        if self.name == 'dropbox':
-            directory = dropbox.normalise_path(directory)
-            dbx = dropbox.get_dropbox()
-            return dropbox.is_folder(dbx, directory)
-
-    def get_token(self):
-        if self.name == 'dropbox':
-            return dropbox.get_token()

hpcflow/archive/cloud/errors.py

@@ -1,9 +0,0 @@
-"""`hpcflow.archive.cloud.errors.py"""
-
-
-class CloudProviderError(Exception):
-    pass
-
-
-class CloudCredentialsError(Exception):
-    pass