diff --git a/schema/versions/44d5bbbf2615_workspaces_init.py b/schema/versions/44d5bbbf2615_workspaces_init.py
index 0b3922aa3d64c1ac96c2eae9e82eef3c62c7cbea..c73021e8c7fc9868820760f30be3bd4f7e5f6228 100644
--- a/schema/versions/44d5bbbf2615_workspaces_init.py
+++ b/schema/versions/44d5bbbf2615_workspaces_init.py
@@ -21,7 +21,7 @@ def upgrade():
op.create_table('workflow_templates',
sa.Column('filename', sa.String, primary_key=True, comment='the filename of the template'),
- sa.Column('content', sa.String, nullable=False, comment='the content of the template'),
+ sa.Column('content', sa.LargeBinary, nullable=False, comment='the content of the template'),
sa.Column('workflow_name', sa.String, sa.ForeignKey('workflows.workflow_name'), primary_key=True,
comment='the name of the workflow this template belongs to'),
comment='Templates associated with workflows')
@@ -37,7 +37,7 @@ def upgrade():
sa.Column('workflow_request_id', sa.Integer, sa.ForeignKey('workflow_requests.workflow_request_id'),
comment='the id of the workflow request.'),
sa.Column('filename', sa.String, comment='the name of this file', nullable=False),
- sa.Column('content', sa.String, comment='the contents of the file', nullable=False),
+ sa.Column('content', sa.LargeBinary, comment='the contents of the file', nullable=False),
comment='A man-to-many mapping table tracking which files were used for workflow requests.')
op.create_unique_constraint('workflow_request_filenames_uniq', 'workflow_request_files',
@@ -45,7 +45,7 @@ def upgrade():
# populate with some initial data
op.execute("INSERT INTO workflows (workflow_name) VALUES ('null')")
- op.execute("INSERT INTO workflow_templates (workflow_name, filename, content) VALUES ('null', 'null.sh', 'null {{arguments}}')")
+ op.execute("INSERT INTO workflow_templates (workflow_name, filename, content) VALUES ('null', 'null.sh', E'null {{arguments}}')")
def downgrade():
diff --git a/services/workflow/src/workflow/server.py b/services/workflow/src/workflow/server.py
index 72c1ea70c4c6fba3190960e3aece1f49a78e094d..457015ac0190a5b8175fe8737d6b02e681f86169 100644
--- a/services/workflow/src/workflow/server.py
+++ b/services/workflow/src/workflow/server.py
@@ -6,7 +6,7 @@ from pyramid_beaker import session_factory_from_settings
from pyramid.renderers import JSONP
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
-from workspaces.services import WorkflowInfo, WorkflowService
+from workspaces.services import WorkflowInfo, WorkflowService, get_session_factory, get_engine
"""
Work done:
@@ -154,27 +154,6 @@ class WorkflowFilesRestService:
# ---------------------------------------------------------
-def get_engine():
- """
- Generate the SQL Alchemy engine for us, using Capo.
- :return:
- """
- capo = CapoConfig().settings('metadataDatabase')
- url = capo.jdbcUrl.replace('jdbc:', '').replace('://', f'://{capo.jdbcUsername}:{capo.jdbcPassword}@')
- return create_engine(url)
-
-
-def get_session_factory(engine):
- """
- Generate the SQL Alchemy session factory for us, using the supplied engine
- :param engine:
- :return:
- """
- factory = sessionmaker()
- factory.configure(bind=engine)
- return factory
-
-
def get_tm_session(session_factory, transaction_manager):
"""
Enable Zope's transaction manager on our session
diff --git a/shared/workspaces/src/workspaces/schema.py b/shared/workspaces/src/workspaces/schema.py
index 41e2f8199f2af22ea30cfe104fbf5833dc3e0843..b018f6e9cc849c4b96e6b3c7e6be9abe20c1d01d 100644
--- a/shared/workspaces/src/workspaces/schema.py
+++ b/shared/workspaces/src/workspaces/schema.py
@@ -7,7 +7,9 @@ from pathlib import Path
from typing import Dict, List
import sqlalchemy as sa
-from sqlalchemy.orm import relationship
+from pycapo import CapoConfig
+from sqlalchemy import create_engine
+from sqlalchemy.orm import relationship, sessionmaker
from sqlalchemy.ext.declarative import declarative_base
@@ -16,15 +18,22 @@ class AbstractFile:
Abstract file is exactly that, an abstract concept of what a file is, to be
returned from various non-filesystem places.
"""
- def __init__(self, filename, content):
+ filename: str
+ content: bytes
+
+ def __init__(self, filename: str, content: bytes):
self.filename, self.content = filename, content
def write_to(self, directory: Path):
- raise NotImplementedError('Actually save the file into the directory passed')
+ (directory / self.filename).write_bytes(self.content)
def __json__(self, request):
return {'filename': self.filename, 'content': self.content}
+ @classmethod
+ def from_path(cls, path: Path) -> 'AbstractFile':
+ return cls(path.name, path.read_bytes())
+
Base = declarative_base()
@@ -42,6 +51,9 @@ class Workflow(Base):
def __json__(self, request):
return {'workflow_name': self.workflow_name, 'templates': self.templates}
+ def __repr__(self):
+ return f'<Workflow workflow_name={self.workflow_name}>'
+
def render_templates(self, argument: Dict, files: List[Path]) -> List[AbstractFile]:
"""
Render the templates associated with this workflow
@@ -49,7 +61,7 @@ class Workflow(Base):
:param files: the files to be processed
:return: a list of rendered templates
"""
- raise NotImplementedError(f'{self.__class__.__name__}.{inspect.stack()[0][3]}')
+ raise NotImplementedError
class WorkflowTemplate(Base):
@@ -58,7 +70,7 @@ class WorkflowTemplate(Base):
"""
__tablename__ = 'workflow_templates'
filename = sa.Column('filename', sa.String, primary_key=True)
- content = sa.Column('content', sa.String, nullable=False)
+ content = sa.Column('content', sa.LargeBinary, nullable=False)
workflow_name = sa.Column('workflow_name', sa.String, sa.ForeignKey('workflows.workflow_name'), primary_key=True)
def render(self, argument: Dict) -> AbstractFile:
@@ -68,10 +80,17 @@ class WorkflowTemplate(Base):
def template_file(self) -> AbstractFile:
return AbstractFile(self.filename, self.content)
+ @template_file.setter
+ def template_file(self, file: AbstractFile):
+ self.filename, self.content = file.filename, file.content
+
def __json__(self, request):
# Defer to the actual template file's contents for JSON conversion
return self.template_file.__json__(request)
+ def __repr__(self):
+ return f'<WorkflowTemplate filename={self.filename} for workflow={self.workflow_name}>'
+
class WorkflowRequest(Base):
"""
@@ -89,11 +108,40 @@ class WorkflowRequestFile(Base):
A Workflow Request File is a file supplied by the user and attached to the request they have submitted.
"""
__tablename__ = 'workflow_request_files'
- workflow_request_id = sa.Column('workflow_request_id', sa.Integer, sa.ForeignKey('workflow_requests.workflow_request_id'),
+ workflow_request_id = sa.Column('workflow_request_id', sa.Integer,
+ sa.ForeignKey('workflow_requests.workflow_request_id'),
primary_key=True)
filename = sa.Column('filename', sa.String, primary_key=True)
- content = sa.Column('content', sa.String, nullable=False)
+ content = sa.Column('content', sa.LargeBinary, nullable=False)
@property
def file(self) -> AbstractFile:
return AbstractFile(self.filename, self.content)
+
+ @file.setter
+ def set_file(self, file: AbstractFile):
+ self.filename, self.content = file.filename, file.content
+
+ def __repr__(self):
+ return f'<WorkflowRequestFile filename={self.filename}>'
+
+
+def get_engine():
+ """
+ Generate the SQL Alchemy engine for us, using Capo.
+ :return:
+ """
+ capo = CapoConfig().settings('metadataDatabase')
+ url = capo.jdbcUrl.replace('jdbc:', '').replace('://', f'://{capo.jdbcUsername}:{capo.jdbcPassword}@')
+ return create_engine(url)
+
+
+def get_session_factory(engine):
+ """
+ Generate the SQL Alchemy session factory for us, using the supplied engine
+ :param engine:
+ :return:
+ """
+ factory = sessionmaker()
+ factory.configure(bind=engine)
+ return factory