ctp-client 1.0.1__tar.gz

ctp_client-1.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.docker/ctpm-temp/**
+# C extensions
+*.so
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+# Distribution / packaging
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+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
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+# pyenv
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+#   intended to run in multiple environments; otherwise, check them in:
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+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
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+/ctpy/version.py

ctp_client-1.0.1/LICENSE

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+Copyright 2017 Biomedical Imaging Group Rotterdam, Departments of
+Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

ctp_client-1.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: ctp-client
+Version: 1.0.1
+Summary: ctp-client is a Python client for [Clinical Trials Processor](https://mircwiki.rsna.org/index.php?title=MIRC_CTP).
+Project-URL: CI/CD, https://gitlab.com/radiology/infrastructure/data-curation-tools/ctp-client/-/pipelines
+Project-URL: Changelog, https://ctp-client.readthedocs.io/en/latest/changelog.html
+Project-URL: Documentation, https://ctp-client.readthedocs.io
+Project-URL: Download, https://gitlab.com/radiology/infrastructure/data-curation-tools/ctp-client/-/archive/master/ctp-client-master.zip
+Project-URL: Homepage, https://gitlab.com/radiology/infrastructure/data-curation-tools/ctp-client.git
+Project-URL: Issues, https://gitlab.com/radiology/infrastructure/data-curation-tools/ctp-client/-/issues
+Author-email: BIGR Imaging Infrastructure Group <imaging.infrastructure@erasmusmc.nl>
+License: Apache 2.0
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Information Technology
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: System :: Logging
+Classifier: Topic :: Utilities
+Requires-Python: >=3.9
+Requires-Dist: beautifulsoup4==4.12.3
+Requires-Dist: click-log==0.4.0
+Requires-Dist: click-loglevel==0.5.1
+Requires-Dist: click==8.1.3
+Requires-Dist: pydantic==2.10.3
+Requires-Dist: pyyaml==6.0.2
+Requires-Dist: requests>=2.22.0
+Requires-Dist: tabulate==0.9.0
+Description-Content-Type: text/markdown
+
+# CTPy
+
+CTPy is a Python client for [Clinical Trials Processor](https://mircwiki.rsna.org/index.php?title=MIRC_CTP).

ctp_client-1.0.1/README.md

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+# CTPy
+
+CTPy is a Python client for [Clinical Trials Processor](https://mircwiki.rsna.org/index.php?title=MIRC_CTP).

ctp_client-1.0.1/ctpy/__init__.py

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+# Copyright 2017 Biomedical Imaging Group Rotterdam, Departments of
+# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+from typing import Optional
+
+from .import version
+from .client import CTPYclient
+
+__version__ = version.version
+
+
+def connect(host: str,
+            port: int,
+            username: str,
+            password: str,
+            rate_limit: Optional[int] = None) -> CTPYclient:
+    """
+    Createa a connection to a CTP server
+
+    :param host: host to connect to
+    :param port: port to connect to
+    :param username: username to login as
+    :param password: password for user
+    :param rate_limit: optionally limit the time between requests, this is specified
+                       as the maximum requests per second
+
+    :return: CTP client object
+    """
+    ctpy_client = CTPYclient(host, port, username, password, rate_limit)
+    return ctpy_client

ctp_client-1.0.1/ctpy/cli/__init__.py

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+# Copyright 2017 Biomedical Imaging Group Rotterdam, Departments of
+# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+from .cli import cli

ctp_client-1.0.1/ctpy/cli/cli.py

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+# Copyright 2017 Biomedical Imaging Group Rotterdam, Departments of
+# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import socket
+import logging
+from pathlib import Path
+
+import click
+import tabulate
+from click_loglevel import LogLevel
+import yaml
+from yaml.loader import SafeLoader
+
+from ctpy import CTPYclient
+from ctpy import exceptions
+from ctpy.helpers import poll_object_tracker_for_studyuid, summarize_object_tracker_content
+
+@click.group()
+@click.version_option()
+@click.pass_context
+def cli(ctx):
+    ctx.ensure_object(dict)
+
+@cli.command()
+@click.option('--lookup-table-filename', type=Path, required=True)
+@click.option('--ctp-host', required=True)
+@click.option('--ctp-port', type=int, default=1180, required=True)
+@click.option('--dicom-anonymizer-id', required=True)
+@click.option('--username', required=True)
+@click.option('--password', required=True, prompt=True, hide_input=True)
+@click.option('--log-level', type=LogLevel(), default=logging.INFO)
+@click.pass_context
+def post_lookup_table(_, lookup_table_filename, ctp_host, ctp_port,
+                        dicom_anonymizer_id, username, password, log_level):
+    logging.basicConfig(
+        format=f"%(asctime)s - {socket.gethostname()} - [%(levelname)-8s] %(message)s",
+        level=log_level,
+    )
+    ctpy_client = CTPYclient(ctp_host, ctp_port, username, password, rate_limit=0.2)
+    with open(lookup_table_filename, encoding='utf-8') as lookup_table_file:
+        lut = yaml.load(lookup_table_file, Loader=SafeLoader)
+        for key, value in lut.items():
+            try:
+                ctpy_client.add_to_lookup(dicom_anonymizer_id, key, value)
+            except exceptions.CTPYFailedAddingLUT:
+                pass
+            break
+
+@cli.command()
+@click.option('--ctp-host', required=True)
+@click.option('--ctp-port', type=int, default=1180, required=True)
+@click.option('--pipeline-id', type=int, default=0, required=True)
+@click.option('--object-tracker-id', type=int, default=1, required=True)
+@click.option('--username', required=True, default="king")
+@click.option('--password', required=True, default="password", prompt=True, hide_input=True)
+@click.option('--patient-id', required=True)
+@click.option('--study-uid', 'study_uid_filter')
+@click.option('--delay', type=int, default=5)
+@click.option('--timeout', type=int, default=900)
+@click.option('--log-level', type=LogLevel(), default=logging.INFO)
+@click.pass_context
+def check_object_tracker(_, ctp_host, ctp_port, pipeline_id, object_tracker_id,
+                         username, password, patient_id, study_uid_filter, delay,
+                         timeout, log_level):
+    logging.basicConfig(
+        format=f"%(asctime)s - {socket.gethostname()} - [%(levelname)-8s] %(message)s",
+        level=log_level,
+    )
+    ctpy_client = CTPYclient(ctp_host, ctp_port, username, password, rate_limit=0.2)
+    object_tracker_data = poll_object_tracker_for_studyuid(ctpy_client,
+                                                           pipeline_id,
+                                                           object_tracker_id,
+                                                           patient_id,
+                                                           study_uid_filter,
+                                                           delay,
+                                                           timeout)
+    logging.debug('patient_data: %s', object_tracker_data)
+    if object_tracker_data and patient_id in object_tracker_data:
+        for study_uid, series_info in object_tracker_data[patient_id].items():
+            for series_uid, instances in series_info.items():
+                logging.info('%s|%s|%s', study_uid, series_uid, instances)
+
+@cli.command()
+@click.option('--ctp-host', required=True)
+@click.option('--ctp-port', type=int, default=1180, required=True)
+@click.option('--pipeline-id', type=int, default=0, required=True)
+@click.option('--idmap-id', type=int, default=1, required=True)
+@click.option('--username', required=True, default="king")
+@click.option('--password', required=True, default="password", prompt=True, hide_input=True)
+@click.option('--keytype', required=True)
+@click.option('--key', required=True)
+@click.option('--log-level', type=LogLevel(), default=logging.INFO)
+@click.pass_context
+def query_idmap(_, ctp_host, ctp_port, pipeline_id, idmap_id, keytype, key,
+                username, password, log_level):
+    logging.basicConfig(
+        format=f"%(asctime)s - {socket.gethostname()} - [%(levelname)-8s] %(message)s",
+        level=log_level,
+    )
+    ctpy_client = CTPYclient(ctp_host, ctp_port, username, password, rate_limit=0.2)
+    study_uid = ctpy_client.idmap_search(pipeline_id, idmap_id, key, keytype)
+    if study_uid:
+        logging.info(study_uid)
+
+
+@cli.command()
+@click.option('--ctp-host', required=True)
+@click.option('--ctp-port', type=int, default=1180, required=True)
+@click.option('--username', required=False)
+@click.option('--password', required=False)
+def get_summary(ctp_host, ctp_port, username, password):
+    logging.basicConfig(
+        format=f"%(asctime)s - {socket.gethostname()} - [%(levelname)-8s] %(message)s",
+        level='INFO',
+    )
+    ctpy_client = CTPYclient(ctp_host, ctp_port, username, password, rate_limit=0.2)
+    summary = ctpy_client.get_ctp_summary()
+    logging.info(f"\n{tabulate.tabulate([s.to_table_row() for s in summary], headers=['pipeline', 'import', 'export', 'quarantines'])}")
+
+
+@cli.command()
+@click.option('--ctp-host', required=True)
+@click.option('--ctp-port', type=int, default=1180, required=True)
+@click.option('--username', required=True)
+@click.option('--password', required=True)
+@click.option('--pipeline-name', required=True)
+def get_tracker_summary(ctp_host, ctp_port, username, password, pipeline_name):
+    logging.basicConfig(
+        format=f"%(asctime)s - {socket.gethostname()} - [%(levelname)-8s] %(message)s",
+        level='INFO',
+    )
+    
+    ctpy_client = CTPYclient(ctp_host, ctp_port, username, password, rate_limit=0.2)
+    pipeline = ctpy_client.server.pipelines.get(pipeline_name)
+    if pipeline is None:
+        raise exceptions.CTPYPipelineNotFound(f"Pipeline {pipeline_name} not found!")
+    
+    trackers_summary = list()
+    object_trackers = ctpy_client.find_object_tracker_stages(pipeline)
+    for tracker_id, object_tracker in object_trackers:
+        object_tracker_contents = ctpy_client.get_object_tracker_patient_info(pipeline_id=pipeline.pipeline_id, stage_id=tracker_id)
+                
+        trackers_summary.append([object_tracker.name, *summarize_object_tracker_content(object_tracker_contents)])
+    logging.info(f"\n{tabulate.tabulate(trackers_summary, headers=['name', 'subjects', 'experiments', 'scans', 'instances'])}")