| Name | jpl.labcas.utils JSON |
| Version |
0.0.2
JSON |
| download |
| home_page | None |
| Summary | Utilities for the Laboratory Catalog and Archive Service of the Early Detection Research Network |
| upload_time | 2025-10-15 18:12:17 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.12 |
| license | Apache License
==============
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_<<http://www.apache.org/licenses/>>_
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|
| keywords |
archive
cancer
catalog
data
edrn
jpl
labcas
nasa
nci
nih
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# LabCAS Utilities
This is a hodge-podge collection of various utilities for managing, reporting on, and maintaining instances of the [Laboratory Catalog and Archive System](https://github.com/jpl-labcas) (LabCAS).
## 📀 Installation
Using Python 3.9 or newer, create a virtual environment and install it:
python3 -m venv venv
venv/bin/pip install jpl.labacs.utils
## 🔧 The Utilities
The numerous utilities are quickly summarized below:
- `assign-uuids` — finds Solr documents without a UUID and assign one
- `backup-labcas` — issues backup commands for the Solr cores for LabCAS, "collections", "datasets", and "files"
- `common-prefixes` — allegedly finds common prefixes in FileLocation fields in Solr (but doesn't?)
- `date-report` — writes a CSV to stdout of protocols with dates and dates of corresponding collections in LabCAS
- `dcm-header-usage` — shows usage of DICOM headers in Lung_Team_Project_2 and Prostate_MRI collections based on a Google spreadsheet for input
- `delete-collection` — deletes a collection (including all of its datasets and files) from LabCAS Solr
- `delete-datasets` — deletes datasets from LabCAS Solr while producing a CSV of the corresponding files that will need to be deleted from disk
- `delete-field` — deletes a field from documents in Solr
- `field-usage` — tells what fields are in use by collections, datasets, and files in Solr and marks those that appear in collection and dataset `.cfg` files
- `fix-event-ids` — repairs event IDs in Solr after publication of a dataset (or collection) that uses event IDs based on a [LabCAS publish](https://github.com/jpl-labcas/publish) `alias.json` file
- `fix-patient-ids` — overwrites `PatiendID` field in DICOM files with event IDs from Solr
- `fix-principals` — sets the `OwnerPrincipal` fields of the "collections", "datasets", and "files" cores in Solr based on information in [metadata `.cfg` files](https://github.com/EDRN/EDRN-metadata)
- `mangle-headers` — mangles DICOM headers according to Radka's specifications
- `mass-spec-fix` — fixed misspelled "mass spectrometry" in Solr cores
- `missing-bbd-dcis` — finds missing anonymized BBD and DCIS not specified in a given `.csv` file
- `missing-event-ids` — given event IDs, report which are missing in LabCAS Solr
- `populate-bbd-dcis` — populate the BBD or DCIS files in Solr with filenames in a BBD or DCIS `.csv` file
- `replace-field` — replace a list field in Solr with a new single value
- `replace-fields` — replace a list field in Solr with multiple values
- `report` — generate various reports, including events, privacy, event correlation, availability, or patient IDs
- `report-fields` — generate a report on requested fields
- `report-file-size` — report total size of all files in LabCAS using Solr metadata
- `restructure-bbd-dcis` — make symlinks into the `Validation` and `Discovery` folders for BBD and DCIS data on disk
- `s3-report` — generate a report about files, sub-folders, and average number of files in sub-folders in S3
- `split-brsi` — split the contents of a gzip'd tar file into training and validation folders based on a spreadsheet input
- `sub-field` — substitute the value of a field in multiple documents
Many of these utilities are one-offs, which is typical for LabCAS.
## 🔁 Looping
Some of these utilities loop over large collections of data, paginating through results and making updates. You may have to run the utilities multiple times until they report updating no more documents.
## 🛤️ Solr and Tunneling
Many of these utilities operate on Solr that's assumed to be at `https://localhost:8984/solr/` with a self-signed certificate. You can override these with a `--solr` option.
Feel free to tunnel these connection over `ssh` to a preferential Solr, or run it directly on a host like `edrn-labcas`, `mcl-labcas`, `labcas-dev`, and so forth.
## 🖥️ Development
To install from source:
git clone https://github.com/jpl-labcas/jpl.labcas.utils.git
cd jpl.labcas.utils
pre-commit install
python3 -m venv .venv
source .venv/bin/activate # or activate.csh if you're a csh/tcsh user
pip install --editable .
To release to PyPI:
python3 -m build .
twine upload dist/*
## 👩🎨 Creators
The principal developer is:
- [Sean Kelly](https://github.com/nutjob4life)
To contact the team as a whole, [email the Informatics Center](mailto:ic-portal@jpl.nasa.gov).
## 📃 License
The project is licensed under the [Apache version 2](LICENSE.md) license.
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"description": "# LabCAS Utilities\n\nThis is a hodge-podge collection of various utilities for managing, reporting on, and maintaining instances of the [Laboratory Catalog and Archive System](https://github.com/jpl-labcas) (LabCAS).\n\n\n## \ud83d\udcc0 Installation\n\nUsing Python 3.9 or newer, create a virtual environment and install it:\n\n python3 -m venv venv\n venv/bin/pip install jpl.labacs.utils\n\n\n## \ud83d\udd27 The Utilities\n\nThe numerous utilities are quickly summarized below:\n\n- `assign-uuids` \u2014 finds Solr documents without a UUID and assign one\n- `backup-labcas` \u2014 issues backup commands for the Solr cores for LabCAS, \"collections\", \"datasets\", and \"files\"\n- `common-prefixes` \u2014 allegedly finds common prefixes in FileLocation fields in Solr (but doesn't?)\n- `date-report` \u2014 writes a CSV to stdout of protocols with dates and dates of corresponding collections in LabCAS\n- `dcm-header-usage` \u2014 shows usage of DICOM headers in Lung_Team_Project_2 and Prostate_MRI collections based on a Google spreadsheet for input\n- `delete-collection` \u2014 deletes a collection (including all of its datasets and files) from LabCAS Solr\n- `delete-datasets` \u2014 deletes datasets from LabCAS Solr while producing a CSV of the corresponding files that will need to be deleted from disk\n- `delete-field` \u2014 deletes a field from documents in Solr\n- `field-usage` \u2014 tells what fields are in use by collections, datasets, and files in Solr and marks those that appear in collection and dataset `.cfg` files\n- `fix-event-ids` \u2014 repairs event IDs in Solr after publication of a dataset (or collection) that uses event IDs based on a [LabCAS publish](https://github.com/jpl-labcas/publish) `alias.json` file\n- `fix-patient-ids` \u2014 overwrites `PatiendID` field in DICOM files with event IDs from Solr\n- `fix-principals` \u2014 sets the `OwnerPrincipal` fields of the \"collections\", \"datasets\", and \"files\" cores in Solr based on information in [metadata `.cfg` files](https://github.com/EDRN/EDRN-metadata)\n- `mangle-headers` \u2014 mangles DICOM headers according to Radka's specifications\n- `mass-spec-fix` \u2014 fixed misspelled \"mass spectrometry\" in Solr cores\n- `missing-bbd-dcis` \u2014 finds missing anonymized BBD and DCIS not specified in a given `.csv` file\n- `missing-event-ids` \u2014 given event IDs, report which are missing in LabCAS Solr\n- `populate-bbd-dcis` \u2014 populate the BBD or DCIS files in Solr with filenames in a BBD or DCIS `.csv` file\n- `replace-field` \u2014 replace a list field in Solr with a new single value\n- `replace-fields` \u2014 replace a list field in Solr with multiple values\n- `report` \u2014 generate various reports, including events, privacy, event correlation, availability, or patient IDs\n- `report-fields` \u2014 generate a report on requested fields\n- `report-file-size` \u2014 report total size of all files in LabCAS using Solr metadata\n- `restructure-bbd-dcis` \u2014 make symlinks into the `Validation` and `Discovery` folders for BBD and DCIS data on disk\n- `s3-report` \u2014 generate a report about files, sub-folders, and average number of files in sub-folders in S3\n- `split-brsi` \u2014 split the contents of a gzip'd tar file into training and validation folders based on a spreadsheet input\n- `sub-field` \u2014 substitute the value of a field in multiple documents\n\nMany of these utilities are one-offs, which is typical for LabCAS.\n\n\n## \ud83d\udd01 Looping\n\nSome of these utilities loop over large collections of data, paginating through results and making updates. You may have to run the utilities multiple times until they report updating no more documents.\n\n\n## \ud83d\udee4\ufe0f Solr and Tunneling\n\nMany of these utilities operate on Solr that's assumed to be at `https://localhost:8984/solr/` with a self-signed certificate. You can override these with a `--solr` option.\n\nFeel free to tunnel these connection over `ssh` to a preferential Solr, or run it directly on a host like `edrn-labcas`, `mcl-labcas`, `labcas-dev`, and so forth.\n\n\n## \ud83d\udda5\ufe0f Development\n\nTo install from source:\n\n git clone https://github.com/jpl-labcas/jpl.labcas.utils.git\n cd jpl.labcas.utils\n pre-commit install\n python3 -m venv .venv\n source .venv/bin/activate # or activate.csh if you're a csh/tcsh user\n pip install --editable .\n\nTo release to PyPI:\n\n python3 -m build .\n twine upload dist/*\n\n\n## \ud83d\udc69\u200d\ud83c\udfa8\u00a0Creators\n\nThe principal developer is:\n\n- [Sean Kelly](https://github.com/nutjob4life)\n\nTo contact the team as a whole, [email the Informatics Center](mailto:ic-portal@jpl.nasa.gov).\n\n## \ud83d\udcc3\u00a0License\n\nThe project is licensed under the [Apache version 2](LICENSE.md) license.\n",
"bugtrack_url": null,
"license": "Apache License\n ==============\n \n _Version 2.0, January 2004_ \n _<<http://www.apache.org/licenses/>>_\n \n ### Terms and Conditions for use, reproduction, and distribution\n \n #### 1. Definitions\n \n \u201cLicense\u201d shall mean the terms and conditions for use, reproduction, and\n distribution as defined by Sections 1 through 9 of this document.\n \n \u201cLicensor\u201d shall mean the copyright owner or entity authorized by the copyright\n owner that is granting the License.\n \n \u201cLegal Entity\u201d shall mean the union of the acting entity and all other entities\n that control, are controlled by, or are under common control with that entity.\n For the purposes of this definition, \u201ccontrol\u201d means **(i)** the power, direct or\n indirect, to cause the direction or management of such entity, whether by\n contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of the\n outstanding shares, or **(iii)** beneficial ownership of such entity.\n \n \u201cYou\u201d (or \u201cYour\u201d) shall mean an individual or Legal Entity exercising\n permissions granted by this License.\n \n \u201cSource\u201d form shall mean the preferred form for making modifications, including\n but not limited to software source code, documentation source, and configuration\n files.\n \n \u201cObject\u201d form shall mean any form resulting from mechanical transformation or\n translation of a Source form, including but not limited to compiled object code,\n generated documentation, and conversions to other media types.\n \n \u201cWork\u201d shall mean the work of authorship, whether in Source or Object form, made\n available under the License, as indicated by a copyright notice that is included\n in or attached to the work (an example is provided in the Appendix below).\n \n \u201cDerivative Works\u201d shall mean any work, whether in Source or Object form, that\n is based on (or derived from) the Work and for which the editorial revisions,\n annotations, elaborations, or other modifications represent, as a whole, an\n original work of authorship. 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Grant of Patent License\n \n Subject to the terms and conditions of this License, each Contributor hereby\n grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free,\n irrevocable (except as stated in this section) patent license to make, have\n made, use, offer to sell, sell, import, and otherwise transfer the Work, where\n such license applies only to those patent claims licensable by such Contributor\n that are necessarily infringed by their Contribution(s) alone or by combination\n of their Contribution(s) with the Work to which such Contribution(s) was\n submitted. If You institute patent litigation against any entity (including a\n cross-claim or counterclaim in a lawsuit) alleging that the Work or a\n Contribution incorporated within the Work constitutes direct or contributory\n patent infringement, then any patent licenses granted to You under this License\n for that Work shall terminate as of the date such litigation is filed.\n \n #### 4. 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Submission of Contributions\n \n Unless You explicitly state otherwise, any Contribution intentionally submitted\n for inclusion in the Work by You to the Licensor shall be under the terms and\n conditions of this License, without any additional terms or conditions.\n Notwithstanding the above, nothing herein shall supersede or modify the terms of\n any separate license agreement you may have executed with Licensor regarding\n such Contributions.\n \n #### 6. Trademarks\n \n This License does not grant permission to use the trade names, trademarks,\n service marks, or product names of the Licensor, except as required for\n reasonable and customary use in describing the origin of the Work and\n reproducing the content of the NOTICE file.\n \n #### 7. 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