End of day commit. Working on the Background Task method to annotate a CDSTAR Archive

Signed-off-by: Marcel Parciak <marcel.parciak@gmail.com>

.gitignore

+# SPDX-FileCopyrightText: 2020 https://github.com/github/gitignore
+#
+# SPDX-License-Identifier: CC0-1.0
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -135,4 +139,4 @@ dmypy.json
 .pytype/
 
 # Cython debug symbols
-cython_debug/
+cython_debug/
\ No newline at end of file

.gitlab-ci.yml

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 stages:
   - test
   - publish
 
+variables:
+  CDSTAR_URI: "https://c109-199.cloud.gwdg.de/v3"
+  CDSTAR_USER: "medic1"
+  CDSTAR_PASS: "medIC!umG!9"
+  CDSTAR_VAULT: "medic"
+  COUCH_URI: "https://c109-199.cloud.gwdg.de:5984"
+  COUCH_USER: "annotation_agent_test"
+  COUCH_PASS: "aXu9vcAugzQFvZij0TQOfnnN"
+  COUCH_DB: "annotation_test"
+
 build_image:
   stage: test
   tags:
@@ -23,10 +37,13 @@ run_tests:
     - umg
 
   before_script:
-    - pip3 install --user pytest
+    - curl --connect-timeout 5 $CDSTAR_URI
+    - curl --connect-timeout 5 $COUCH_URI
+    - python3 -m pip install --upgrade pip
+    - python3 -m pip install -r requirements.txt
 
   script:
-    - pytest --junitxml=report.xml
+    - python3 -m pytest --junitxml=report.xml
 
   artifacts:
     reports:
@@ -114,4 +131,4 @@ publish_to_harbor:
     - docker build -t harbor.umg.eu/medic/$CI_PROJECT_NAME:latest .
     - docker tag harbor.umg.eu/medic/$CI_PROJECT_NAME:latest harbor.umg.eu/medic/$CI_PROJECT_NAME:$AGENTVERSION
     - docker push harbor.umg.eu/medic/$CI_PROJECT_NAME:latest
-    - docker push harbor.umg.eu/medic/$CI_PROJECT_NAME:$AGENTVERSION
+    - docker push harbor.umg.eu/medic/$CI_PROJECT_NAME:$AGENTVERSION
\ No newline at end of file

.reuse/dep5

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: annotator-agent
+Upstream-Contact: Department of Medical Informatics, University Medical Center Göttingen, Germany <marcel.parciak@med.uni-goettingen.de>
+Source: https://gitlab.gwdg.de/medinfpub/umg-medic/aw-agents/annotation-agent/
+
+# Sample paragraph, commented out:
+#
+# Files: src/*
+# Copyright: $YEAR $NAME <$CONTACT>
+# License: ...

.vscode/settings.json.license

+SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+
+SPDX-License-Identifier: CC0-1.0

Dockerfile

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 FROM docker.io/tiangolo/uvicorn-gunicorn-fastapi:python3.8
 
 ENV MODULE_NAME="annotator.main"

LICENSES/CC0-1.0.txt

+Creative Commons Legal Code
+
+CC0 1.0 Universal CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES
+NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE
+AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION
+ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE
+OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS
+LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION
+OR WORKS PROVIDED HEREUNDER.
+
+Statement of Purpose
+
+The laws of most jurisdictions throughout the world automatically confer exclusive
+Copyright and Related Rights (defined below) upon the creator and subsequent
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+Certain owners wish to permanently relinquish those rights to a Work for the
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+distribution for their Work in part through the use and efforts of others.
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+of additional consideration or compensation, the person associating CC0 with
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+1. Copyright and Related Rights. A Work made available under CC0 may be protected
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+including without limitation commercial, advertising or promotional purposes
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+was applied by Affirmer to the Work. Should any part of the License for any
+reason be judged legally invalid or ineffective under applicable law, such
+partial invalidity or ineffectiveness shall not invalidate the remainder of
+the License, and in such case Affirmer hereby affirms that he or she will
+not (i) exercise any of his or her remaining Copyright and Related Rights
+in the Work or (ii) assert any associated claims and causes of action with
+respect to the Work, in either case contrary to Affirmer's express Statement
+of Purpose.
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+   4. Limitations and Disclaimers.
+
+a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered,
+licensed or otherwise affected by this document.
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+of any kind concerning the Work, express, implied, statutory or otherwise,
+including without limitation warranties of title, merchantability, fitness
+for a particular purpose, non infringement, or the absence of latent or other
+defects, accuracy, or the present or absence of errors, whether or not discoverable,
+all to the greatest extent permissible under applicable law.
+
+c. Affirmer disclaims responsibility for clearing rights of other persons
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+responsibility for obtaining any necessary consents, permissions or other
+rights required for any use of the Work.
+
+d. Affirmer understands and acknowledges that Creative Commons is not a party
+to this document and has no duty or obligation with respect to this CC0 or
+use of the Work.

LICENSES/MIT.txt

+MIT License Copyright (c) <year> <copyright holders>
+
+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 (including the next
+paragraph) 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.

Pipfile

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 [[source]]
 name = "pypi"
 url = "https://pypi.org/simple"
@@ -7,6 +11,7 @@ verify_ssl = true
 fastapi = "*"
 uvicorn = "*"
 black = "*"
+pipenv-to-requirements = "*"
 
 [packages]
 cloudant = "*"
@@ -14,6 +19,7 @@ sqlalchemy = "*"
 alembic = "*"
 pytest = "*"
 pycdstar3 = {git = "https://gitlab.gwdg.de/cdstar/pycdstar3"}
+jinja2 = "*"
 
 [requires]
 python_version = "3.8"

Pipfile.lock.license

+SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+
+SPDX-License-Identifier: CC0-1.0

Readme.md

+<!--
+SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+
+SPDX-License-Identifier: GPL-3.0-or-later
+-->
+
 An agent barebone for Active Workflow agents. 
 
 # Active Workflow Barebone Agent

annotator/.gitignore

+# SPDX-FileCopyrightText: 2020 https://github.com/github/gitignore
+#
+# SPDX-License-Identifier: CC0-1.0
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -135,4 +139,4 @@ dmypy.json
 .pytype/
 
 # Cython debug symbols
-cython_debug/
+cython_debug/
\ No newline at end of file

annotator/__init__.py

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import logging
 
 access_log = logging.getLogger("gunicorn.access")
-error_log = logging.getLogger("gunicorn.error")
+error_log = logging.getLogger("gunicorn.error")
\ No newline at end of file

annotator/__version__.py

-VERSION = (0, 1, 0)
+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
 
-__version__ = ".".join(map(str, VERSION))
+VERSION = (0, 2, 0)
+
+__version__ = ".".join(map(str, VERSION))
\ No newline at end of file

annotator/config.py

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 from pydantic import BaseSettings
 import os
 
@@ -7,14 +11,16 @@ from annotator import __version__
 class BasicSettings(BaseSettings):
     application_name: str = "CouchDB Annotation Agent"
     application_version: str = __version__.__version__
+    tmp_directory: str = "/tmp"
     cdstar_uri: str = "http://localhost:8082/v3"
     cdstar_user: str = "medic1"
     cdstar_pass: str = "medIC!umG!9"
-    cdstar_vault: str = "medic"
+    vault_id: str = "medic"
     couch_uri: str = "http://localhost:5984"
     couch_user: str = "medic"
     couch_pass: str = "medic2020"
     couch_db: str = "medic"
+    static_directory: str = "annotator/static"
 
 
 def get_version():
@@ -25,4 +31,4 @@ agent_description = ""
 with open(
     os.path.join(os.path.abspath(os.path.dirname(__file__)), os.pardir, "Readme.md")
 ) as readme:
-    agent_description = readme.read()
+    agent_description = readme.read()
\ No newline at end of file

annotator/errors.py

-class ActiveWorkflowException(Exception):
+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+class ActiveWorkflowError(Exception):
     def __init__(self, name: str, message: str):
         self.name = name
         self.message = message
+
+
+class ConfigurationError(Exception):
+    def __init__(self, message: str):
+        self.name = "Agent Configuation Error"
+        self.message = message
\ No newline at end of file

annotator/main.py

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+from annotator.errors import ActiveWorkflowError, ConfigurationError
 import datetime
+import os
+from typing import Any, Dict, Optional, Union
 
 from annotator import access_log, error_log
-from annotator import stores
+from annotator import config
+from annotator import errors
 from annotator import models_activeworkflow as awmodels
-from annotator.config import BasicSettings
-from annotator.errors import ActiveWorkflowException
+from annotator import stores
+from annotator import utils
 
 from fastapi import BackgroundTasks, FastAPI, Request
 import fastapi
@@ -20,7 +28,7 @@ endpoint_name = "annotator"
 def appinfo():
     """ Prints the configuration of this instance.
     """
-    return BasicSettings().dict()
+    return config.BasicSettings().dict()
 
 
 @app.post(
@@ -44,12 +52,9 @@ def aw_endpoint(payload: awmodels.RequestCommon, background_tasks: BackgroundTas
         )
 
     elif payload.method is not None and payload.method == "check":
-        return check(
-            payload=awmodels.RequestCheck.parse_obj(payload.dict()),
-            background_tasks=background_tasks,
-        )
+        return check(payload=awmodels.RequestCheck.parse_obj(payload.dict()),)
 
-    raise ActiveWorkflowException(
+    raise errors.ActiveWorkflowError(
         name="Method Error",
         message=f"You did not supply a valid method. Valid methods are: register, receive, check",
     )
@@ -82,6 +87,7 @@ def register(payload: awmodels.RequestRegister):
     f"/{endpoint_name}/receive",
     response_model=awmodels.ResponseReceive,
     response_model_exclude_none=True,
+    status_code=fastapi.status.HTTP_202_ACCEPTED,
 )
 def receive(payload: awmodels.RequestReceive, background_tasks: BackgroundTasks):
     """ Receives a message that will annotate a CDSTAR archive.
@@ -92,17 +98,109 @@ def receive(payload: awmodels.RequestReceive, background_tasks: BackgroundTasks)
     )
 
     response = awmodels.ResponseReceive()
+    response.result.memory.archives += payload.params.memory.archives
 
     archive_id = payload.params.message.payload.archive_id
-    if not stores.is_valid_archive(archive_id):
-        raise ActiveWorkflowException(
-            "Invalid value for `archive_id`",
-            "The `archive_id` you supplied is not available in CDSTAR.",
+    vault_id = get_setting_from_payload(payload, "vault_id")
+    if not vault_id:
+        # real error please
+        raise errors.ConfigurationError(
+            "There is an configuration error regarding the chosen CDSTAR vault. Please check the configuration of the agent."
+        )
+    couch_db = get_setting_from_payload(payload, "couch_db")
+    if not couch_db:
+        # real error please
+        raise errors.ConfigurationError(
+            "There is an configuration error regarding the chosen CouchDB database. Please check the configuraton of the agent."
+        )
+
+    if not stores.is_valid_archive(vault_id, archive_id):
+        response.result.errors.append(
+            f"Archive {archive_id} is not available in CDSTAR vault {vault_id}."
+        )
+        return response
+
+    if utils.annotation_in_progress(vault_id, archive_id):
+        response.result.logs.append(
+            f"Archive {archive_id} is currently being processed."
+        )
+        return response
+
+    annotations_archive = payload.params.options.annotations_archive
+    for k, v in payload.params.message.payload.annotations_archive.items():
+        annotations_archive[k] = v
+
+    annotations_file = payload.params.options.annotations_file
+    for k, v in payload.params.message.payload.annotations_file.items():
+        annotations_file[k] = v
+
+    metafile = utils.create_file_for_archive(vault_id, archive_id)
+    if not metafile:
+        raise errors.ConfigurationError(
+            "There is something wrong with the configured temporary directory to save the annotation state. Please check the configuration of the agent."
+        )
+
+    if payload.params.message.payload.couch_db:
+        couch_db = payload.params.message.payload.couch_db
+
+    background_tasks.add_task(
+        run_annotation,
+        archive_id=archive_id,
+        vault_id=vault_id,
+        annotations_archive=annotations_archive,
+        annotations_file=annotations_file,
+        couch_db=couch_db,
+        metafile=metafile,
+    )
+
+    response.result.logs.append(f"Starting annotation of CDSTAR archive {archive_id}")
+    response.result.memory.archives.append((vault_id, archive_id))
+
+    return response
+
+
+def run_annotation(
+    archive_id: str,
+    vault_id: str,
+    annotations_archive: Dict[str, Any],
+    annotations_file: Dict[str, Any],
+    couch_db: str,
+    metafile: str,
+) -> None:
+    archive, filelist = stores.get_cdstar_metadata(vault_id, archive_id)
+    if not archive:
+        errmsg = f"Not able to retrieve archive {archive_id} in BackgroundTask. How is that possible?"
+        error_log.error(errmsg)
+        os.unlink(metafile)
+        return
+
+    jsonld_archive = utils.merge_jsonld(archive.to_jsonld(), annotations_archive)
+    jsonld_files = [
+        utils.merge_jsonld(f.to_jsonld(), annotations_file) for f in filelist
+    ]
+
+    if "hasPart" not in jsonld_archive or type(jsonld_archive["hasPart"]) is not list:
+        jsonld_archive["hasPart"] = []
+
+    for meta_file in jsonld_files:
+        jsonld_archive["hasPart"].append(utils.get_jsonld_reference(meta_file))
+        meta_file["isPartOf"] = utils.get_jsonld_reference(jsonld_archive)
+
+    if not stores.upload_archive(jsonld_archive, couch_db):
+        errmsg = (
+            f"Could not upload archive annotations for archive {archive_id} to CouchDB."
         )
+        error_log.error(errmsg)
+        os.unlink(metafile)
+        return
 
-    # TODO: in sync or async?...
-    # historically, couchdb was rather slow (lib fault?)
-    # if sync: what do I need check for?
+    if not stores.upload_files(jsonld_files, couch_db):
+        errmsg = f"Could not upload file annotations for files of archive {archive_id} to CouchDB."
+        error_log.error(errmsg)
+        utils.write_state_to_metafile(utils.AnnotationState.incomplete, metafile)
+        return
+
+    utils.write_state_to_metafile(utils.AnnotationState.completed, metafile)
 
 
 @app.post(
@@ -111,23 +209,83 @@ def receive(payload: awmodels.RequestReceive, background_tasks: BackgroundTasks)
     response_model_exclude_none=True,
     status_code=fastapi.status.HTTP_200_OK,
 )
-def check(payload: awmodels.RequestCheck, background_tasks: BackgroundTasks):
+def check(payload: awmodels.RequestCheck):
     """ Checks on a running TOS Job or retrieves the output of a completed Job.
     """
 
     access_log.info(f"{datetime.datetime.now().isoformat()} - Check: {payload.dict()}")
 
-    # TODO: implement check here!
-    pass
+    resp = awmodels.ResponseCheck()
+
+    for vault_id, archive_id in payload.params.memory.archives:
+        metafile = utils.get_path_for_archive(vault_id, archive_id)
+        state = utils.get_state_from_metafile(metafile)
+        if not state:
+            error_log.warning(
+                f"An archive with id {archive_id} has not been found. Erasing from memory."
+            )
+
+        elif state["state"] == utils.AnnotationState.started:
+            resp.result.memory.archives.append((vault_id, archive_id))
+            resp.result.logs.append(
+                f"Archive annotation ({archive_id}) in progress since {state['started_at']}."
+            )
+
+        elif state["state"] == utils.AnnotationState.completed:
+            msg = awmodels.MessageOutput(
+                archive_id=archive_id, couch_uri=f"", stats=state
+            )
+            resp.result.messages.append(msg)
+            utils.remove_metafile(metafile)
+
+        elif state["state"] == utils.AnnotationState.incomplete:
+            resp.result.errors.append(
+                f"There was an error annotating archive {archive_id}. Please check the logs of the agent."
+            )
+            utils.remove_metafile(metafile)
+
+        else:
+            error_log.warning(
+                f"Orphan annotation archive id ({archive_id}) found and removed."
+            )
+
+    return resp
+
 
+def get_setting_from_payload(
+    payload: Union[awmodels.RequestReceive, awmodels.RequestCheck], key: str
+) -> Optional[str]:
+    msg_payload = payload.params.message.payload.dict()
+    if key in msg_payload.keys() and msg_payload[key]:
+        return msg_payload[key]
+    opt_payload = payload.params.options.dict()
+    if key in opt_payload.keys() and opt_payload[key]:
+        return opt_payload[key]
+    cfg = config.BasicSettings().dict()
+    if key in cfg.keys() and cfg[key]:
+        return cfg[key]
+    return None
 
-@app.exception_handler(ActiveWorkflowException)
-async def aw_exception_handler(request: Request, exc: ActiveWorkflowException):
+
+@app.exception_handler(errors.ConfigurationError)
+async def config_exception_handler(request: Request, exc: errors.ConfigurationError):
     error_log.error(f"{exc.name}: {exc.message}")
     resp = awmodels.ResponseCheck()
     resp.result.errors.append(f"{exc.name}: {exc.message}")
 
     return fastapi.responses.JSONResponse(
-        status_code=fastapi.status.HTTP_400_BAD_REQUEST,
+        status_code=fastapi.status.HTTP_500_INTERNAL_SERVER_ERROR,
         content=resp.dict(exclude_none=True),
     )
+
+
+@app.exception_handler(errors.ActiveWorkflowError)
+async def aw_exception_handler(request: Request, exc: errors.ConfigurationError):
+    error_log.error(f"{exc.name}: {exc.message}")
+    resp = awmodels.ResponseCheck()
+    resp.result.errors.append(f"{exc.name}: {exc.message}")
+
+    return fastapi.responses.JSONResponse(
+        status_code=fastapi.status.HTTP_400_BAD_REQUEST,
+        content=resp.dict(exclude_none=True),
+    )
\ No newline at end of file

annotator/models_activeworkflow.py

+# SPDX-FileCopyrightText: 2020 UMG MeDIC <marcel.parciak@med.uni-goettingen.de>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 import abc
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional, Tuple
 
 from pydantic import BaseModel, Field, validator
 
 from annotator import config
-from annotator.models_metadata import MetadataBase
+