fix: Cataloging large number asynchronously by batch + download is stuck when there are large number of files #194
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… for large granules
wphyojpl
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ngachung
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Aug 16, 2023
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Sep 7, 2023
…uck when there are large number of files (#194) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * feat: default poll checking to 0 times + conflict bug in dapa client * feat: add facade endpoint + real endpoint for cnm * fix: update version * fix: need to call PUT. not POST * fix: update test case * chore: add large data catalog testcase * fix: use Manager().Q instead of normal Q to fix it for download stuck for large granules * chore: adding support files for test * fix: calling catalog api in batch * chore: update changelog * chore: add missing test file * fix: mismatch version
wphyojpl
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Sep 18, 2023
* testing github actions * fix: tweak for github action * fix: still testing github actions * fix: remove name from steps * fix: tweaking python3 command * fix: remove pip to see if requirements.txt error goes away * feat: add release + upload procedure * fix: remove double quotes * fix: fixing `" error * fix: still fixing getting software_version line * fix: still fixing software_version * fix: breaking the script to debug * fix: more debugging stmt * fix: still tweaking around * fix: more tweaking * fix: still tweaking * feat: add terraform module for lambdas * feat: update ci/cd to include terraform * chore: bump version * fix: add terraform zip as asset * fix: upload multiple assets * fix: still trying to upload multiple assets * feat: bypass A&A in cumulus * fix: update hardcoded prefix to prefix come from config + add missing ENV in terraform * feat: add collection_id to the query * chore: existing api gateway yaml for dapa * feat: add collectionId as path parameter * feat: add new lambda for collections * fix: update terraform module * fix: collection lambda error * chore: bump version * fix: update lambda executing role * fix: collection listing lambda bug * feat: add code for granules download + docker for it * feat: update swagger doc for api gateway * fix: zip terraform in current directory. not in a folder * fix: add missing terraform output * feat: add bearer token to docker call * chore: readme on how to get cognito token * feat: add l1a metadata extraction code * feat: add level1 generate cmr to terraform * chore: update version * fix: terraform invalid character error * fix: terraform unsupported argument * fix: terraform unsupported argument * fix: use granuleId value from cma * chore: github workflow to trigger only on main branch * feat: add docker build github action * Create dockerbuild.yml * fix: hardcoding username for now * fix: testing with dockerhub + fixed name * fix: trying docker build * fix: still figuring out docker * fix: add missing Dockerfile * fix: using absolute path * fix: updating context * feat: use version from setup.py * feat: add file configuration as links in collection to STAC * feat: add granuleId and others to summaries * feat: allow bucket+key / url_path. add bucket+key if url_path is present * fix: add additional metadata in cmr xml output to match other file to avoid NULL error in workflow * chore: bump version * feat: dapa endpoint to ingest to cnm * feat: add sns msg * fix: use main branch to deploy docker (which is not working) * Proposed CONTRIBUTING.md file / template * fix: get collection id only. not versin + add sample test input json * fix: github workflow needs to run only on main branch * feat: docker script to upload granules via cnm + cnm ingest lambda bugfix * feat: update terraform to include a new lambda * breaking: update docker entry script * fix: missing path in upload script * fix: checking if querystring is NULL * fix: added lambda_processing_role_arn as a variable to resolve terraform dependency issues * fix: version bump * release/1.5.14 (#56) * feat: docker script to upload granules via cnm + cnm ingest lambda bugfix * feat: update terraform to include a new lambda * breaking: update docker entry script * fix: missing path in upload script * fix: checking if querystring is NULL * fix: added lambda_processing_role_arn as a variable to resolve terraform dependency issues * fix: version bump Co-authored-by: Wai Phyo <wai.phyo@jpl.nasa.gov> * change: get github-actions to publish docker image to ghcr.io (#57) * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker github action * fix: docker build github action * fix: docker build github action * fix: docker build github action * fix: docker build github action * fix: docker build github action * chore: run github action in main branch * ADD: adding extra keys based on extra-config in input event (#59) * feat: adding extra keys based on extra-config in input event * chore: reformat code * fix: dataVersion = collection_version for cnm SNS msg * fix: validate if datetime is null * ADD: user username & password to get token from cognito (#61) * feat: user username & password to get token from cognito * chore: update changelog to match with version * chore: change release order * fix: l1A granule id is `<collection-id>___<collection-version>:<granule-id>` not to duplicate re-runs * chore: update error description * feat: add size, prev, next url for granules * feat: add stats for collection + size. fix: check if queryString is NULL * fix: encap code in try-catch to avoid `internal server error` * Updated README.md template (#69) * fix: add err msg when next & prev url does not generate + update makefile for local * feat: STAC style pagination (#70) * fix: add err msg when next & prev url does not generate + update makefile for local * feat: update to STAC specific schema ref from CMR * feat: make pagination class * breaking: pystac validation test + upload / download docker unit test + update collection STAC schema update (#71) * breaking: testing with pystac + make changes accordingly * chore: convert manual test to unittest case * fix: update test case * fix: update upload granule to match new pystac collection schema * chore: stashing collection transformer to use pystac (in-progress) * chore: remove unused file * chore: update gitignore file * fix: update test cases * chore: Open api yaml for documentation (#72) * chore: add open_api doc * fix: update open api yaml errors * chore: add test yaml * chore: add test yaml * chore: add test yaml * chore: add test yaml * feat: add other venue urls * chore: add unit test for param store cognito login (#74) * chore: move the unit test (#75) * Update setup.py * fix: GitHub.action.update (#76) * fix: disable building upon pull request * chore: bump version * /version 1.7.0 release * fix: level.1.a.missing.filename (#80) * fix: loop all files before returning metadata file * chore: bump version * fix: not honoring offset and limit in Collection query (#82) * fix: not assigning limit and offset from api endpoint * chore: bump version * feat: Collection Creation endpoint with DAPA format (#79) * chore: move the unit test * feat: add create collection for cumulus * feat: adding stac to cumulus for json * feat: finished transforming from stac to cumulus * fix: try creating collection with min requirement * feat: add class to create dapa collection obj * fix: add class to create dapa collection object for unity * feat: add class to create STAC collection * feat: update to python3.9 + new lambda for collection creation * chore: python3.9 for github action * fix: ci/cd on develop branch with additional release postfix * fix: testing different output number * fix: testing different output number * fix: testing different output number * fix: testing different output number * fix: testing different output number * fix: testing different output number * fix: testing different output number * fix: testing different output number * fix: testing different output number * chore: add testcase.. in progress * fix: wrong handler for new lambda * fix: require libraries at the worng location * fix: add mock url if url_path is misisng * feat: add rule when creating a collection * fix: wrong quotes in terraform * fix: use thread to run the actual collection creation in background thread * fix: revert background process. does not work as expected in lambda * fix: addig facade for collection creation * fix: api gateway wants string for body. not dict * fix: no need to hash the dict * feat: add single collection details * feat: add single collection detail logic * fix: update testcase + yaml for api gateway * feat: delete collection if rule creation fails * chore: update version * fix: check pathParameters is None (#89) * chore: bump version + update changelog (#90) * fix: Completed.granules.only + validate start + end time for STAC (#93) * feat: add completed status on granules * fix: check start & end datetime before pushing add them to stac + defaulted it to unix 0 * Added DAPA lambdas invoke arn values to parameter store * Updated to store function name instead. * Updated to store function name instead. * fix: accept provider from ENV or optionally from user call * chore: update test case * fix: add provider in rules * chore: update changelog * Updated CHANGELOG.md * fix: status=completed is only for granules, not for collections * feat: return upload result (#103) * feat: return upload result * chore: update version * feat: added Updated time in collection & item STAC dictionaries (#104) * feat: add updated key in granules and collections * chore: use pystac collection object to create a collection * chore: use pystac to transform to item * chore: update changelog * chore: update version * fix: update dockerfile base image to 3.9 (#112) * fix: update dockerfile base image to 3.9 * fix: local manual test with latest image * fix: new stage-in stage-out * fix: remove old download scripts * fix: docker scripts for split download + search * chore: update version + change log * feat: add upload step + test * feat: add catalog stage * chore: remove old class * chore: update sample docker-compose files * fix: print method output in docker + tweak docker compose files * chore: update changelog * feat: add CMR granules search which returns STAC * breaking: configurable file postfixes for PDS metadata extraction (#124) * feat: configurable file postfixes for PDS metadata extraction * fix: some bugfix + update manual deployment update * breaking: rename lvl0 and lvl1 to s4pa and cas * fix: rename output variables * chore: update contributing * feat: reduce pystac length by keeping only data asset (#126) * feat: reduce pystac length by keeping only data asset * chore: update version * feat: granules query pagination (#131) * feat: reduce pystac length by keeping only data asset * chore: update version * feat: pagination for cumulus granules search * feat: add pagination for CMR + bugfix in Cumulus pagination * chore: update version * fix: add filter stac items to assets only * fix: add missing ENV in sample yaml * feat: add EDL token class * feat: adding DAAC download in docker stage in (in-progress) * feat: add option to parse downloading stac from file (#134) * feat: add option to parse downloading stac from file * fix: version increment error + update change log * fix: uncomment temporal in CMR granules search (#136) * fix: uncomment temporal * chore: update changelog * fix: some typo in download daac * chore: add some TODOs * fix: update client id * fix: update client id * chore: update changelog * feat: Checkout stage with STAC catalog json (#138) * feat: reduce pystac length by keeping only data asset * chore: update version * feat: pagination for cumulus granules search * feat: add pagination for CMR + bugfix in Cumulus pagination * chore: update version * fix: add filter stac items to assets only * feat: upload by stac catalog * chore: update version * feat: daac download from stac json file * chore: update version * fix: downloaded stac to return local absolute path * chore: update PR link * feat: add metadata extraction from stac + refactor * chore: refactor * chore: refactor * fix: error during refactor * chore: still refactoring * fix: update code for stac lambda * feat: add terraform * chore: update version * feat: optional output to file * fix: add unit test + create folder if needed * fix: tweak it a bit to avoid writing it twice in case some steps are calling one another * chore: update readme * fix: use cas structure to generate metadata for stac (#148) * fix: use cas to generate metadata for stac * chore: update Makefile * chore: update version * fix: need to run for every file so that every file is updated even after correct file is found * fix: allow catalog stage input from file * chore: update changelog * fix: remove local var. using parent var * fix: production datetime not in +00:00 format * chore: update version + readme * feat: add public http download class * breaking: search return entire feature-collection * breaking: daac downloader accepts only features collection * chore: update daac testcase * feat: refactor download classes to use inheritance * fix: http downloader had a typo bug * chore: update readme * chore: update readme * feat: new upload handler for relative paths + user granule-id from the granule-stac-json * feat: output to be an item-collection * feat: update catalog to accept item collection * chore: update version * breaking: removing old upload styles + default it to new style if missing * chore: delete old classes * chore: update version since it is breaking change now * fix: convert all outputs into json str * chore: update version * chore: update PR number * feat: added filter keyword in granules endpoint + repeatedly checking with time boundary for cataloging result (#156) * feat: first cut of checking cataloging granules * fix: add missing file * fix: unit test + bugfix * feat: update response json in catalog * chore: update version * chore: update documentation * chore: remove invalid MD in changelog * fix: update due to feature-collection update from other PR * feat: parallelize download (#169) * feat: starting parallel job manager * fix: get parallel process working for download * feat: update testcases * chore: update version * chore: update readme * feat: add configurable parallel count * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * fix: download error (#182) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * fix: retry on Temporary failure in name resolution * chore: update version * fix: add new test case for error * Updated CHANGELOG.md to include Unity Release 23.2 release notes. * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * fix: Update stage out task to read STAC items from STAC catalog (#188) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * fix: user item, not child in rel * chore: update PR link * feat: Using Fastapi for all API endpoints (#190) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * fix: add root link in collection stac * feat: updating terraform * fix: actual creation has some error * fix: json to invoke magnum lambda is updated * chore: update log statement * fix: attempting bugfix * fix: some weird error. updating function name to confirm it * fix: teraform error due to partial update only * fix: dummy commit * fix: allow slash and no slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * feat: add uds endpoint tests * feat: am-uds-dapa comes from config with defaulted to that string * fix: S3 upload structure (add collection folder) (#193) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * feat: add collection folder in s3 upload * fix: update note * fix: update wrong PR number * fix: update missed file during merge * fix: remove old test case * fix: Cataloging large number asynchronously by batch + download is stuck when there are large number of files (#194) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * feat: default poll checking to 0 times + conflict bug in dapa client * feat: add facade endpoint + real endpoint for cnm * fix: update version * fix: need to call PUT. not POST * fix: update test case * chore: add large data catalog testcase * fix: use Manager().Q instead of normal Q to fix it for download stuck for large granules * chore: adding support files for test * fix: calling catalog api in batch * chore: update changelog * chore: add missing test file * fix: mismatch version * chore: remove old code * chore: move dapa client to stage in-out coz it is only used in that module * chore: update version --------- Co-authored-by: Nga Chung <17833879+ngachung@users.noreply.github.com> Co-authored-by: nchung <nga.t.chung@jpl.nasa.gov> Co-authored-by: Rishi Verma <riverma@apache.org>
wphyojpl
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Sep 28, 2023
* fix: print method output in docker + tweak docker compose files * chore: update changelog * feat: add CMR granules search which returns STAC * breaking: configurable file postfixes for PDS metadata extraction (#124) * feat: configurable file postfixes for PDS metadata extraction * fix: some bugfix + update manual deployment update * breaking: rename lvl0 and lvl1 to s4pa and cas * fix: rename output variables * chore: update contributing * feat: reduce pystac length by keeping only data asset (#126) * feat: reduce pystac length by keeping only data asset * chore: update version * feat: granules query pagination (#131) * feat: reduce pystac length by keeping only data asset * chore: update version * feat: pagination for cumulus granules search * feat: add pagination for CMR + bugfix in Cumulus pagination * chore: update version * fix: add filter stac items to assets only * fix: add missing ENV in sample yaml * feat: add EDL token class * feat: adding DAAC download in docker stage in (in-progress) * feat: add option to parse downloading stac from file (#134) * feat: add option to parse downloading stac from file * fix: version increment error + update change log * fix: uncomment temporal in CMR granules search (#136) * fix: uncomment temporal * chore: update changelog * fix: some typo in download daac * chore: add some TODOs * fix: update client id * fix: update client id * chore: update changelog * feat: Checkout stage with STAC catalog json (#138) * feat: reduce pystac length by keeping only data asset * chore: update version * feat: pagination for cumulus granules search * feat: add pagination for CMR + bugfix in Cumulus pagination * chore: update version * fix: add filter stac items to assets only * feat: upload by stac catalog * chore: update version * feat: daac download from stac json file * chore: update version * fix: downloaded stac to return local absolute path * chore: update PR link * feat: add metadata extraction from stac + refactor * chore: refactor * chore: refactor * fix: error during refactor * chore: still refactoring * fix: update code for stac lambda * feat: add terraform * chore: update version * feat: optional output to file * fix: add unit test + create folder if needed * fix: tweak it a bit to avoid writing it twice in case some steps are calling one another * chore: update readme * fix: use cas structure to generate metadata for stac (#148) * fix: use cas to generate metadata for stac * chore: update Makefile * chore: update version * fix: need to run for every file so that every file is updated even after correct file is found * fix: update requests version for git error * fix: update requests version for git error * fix: reshuffle to fix version mismatch * fix: reshuffle to fix version mismatch * fixing urllib3 version * fixing urllib3 version * fix: allow catalog stage input from file * chore: update changelog * fix: remove local var. using parent var * fix: production datetime not in +00:00 format * chore: update version + readme * fix: add tags to opensearch * fix: add tags to opensearch * fix: add tags in tf * fix: add tags in tf * feat: add public http download class * breaking: search return entire feature-collection * breaking: daac downloader accepts only features collection * chore: update daac testcase * feat: refactor download classes to use inheritance * fix: http downloader had a typo bug * chore: update readme * chore: update readme * feat: new upload handler for relative paths + user granule-id from the granule-stac-json * feat: output to be an item-collection * feat: update catalog to accept item collection * chore: update version * breaking: removing old upload styles + default it to new style if missing * chore: delete old classes * chore: update version since it is breaking change now * fix: convert all outputs into json str * chore: update version * chore: update PR number * feat: added filter keyword in granules endpoint + repeatedly checking with time boundary for cataloging result (#156) * feat: first cut of checking cataloging granules * fix: add missing file * fix: unit test + bugfix * feat: update response json in catalog * chore: update version * chore: update documentation * chore: remove invalid MD in changelog * fix: update due to feature-collection update from other PR * feat: parallelize download (#169) * feat: starting parallel job manager * fix: get parallel process working for download * feat: update testcases * chore: update version * chore: update readme * feat: add configurable parallel count * fix: retry 5 times + wait 45 sec for DAAC * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: make re-try configurable * fix: download error (#182) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * fix: retry on Temporary failure in name resolution * chore: update version * fix: add new test case for error * Updated CHANGELOG.md to include Unity Release 23.2 release notes. * feat: adding fastapi (in-progress) * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * fix: get collection creation working (in-progress) * fix: Update stage out task to read STAC items from STAC catalog (#188) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * fix: user item, not child in rel * chore: update PR link * fix: add root link in collection stac * fix: add root link in collection stac * feat: updating terraform * feat: updating terraform * fix: actual creation has some error * fix: actual creation has some error * fix: json to invoke magnum lambda is updated * fix: json to invoke magnum lambda is updated * chore: update log statement * chore: update log statement * fix: attempting bugfix * fix: attempting bugfix * fix: some weird error. updating function name to confirm it * fix: some weird error. updating function name to confirm it * fix: teraform error due to partial update only * fix: teraform error due to partial update only * fix: dummy commit * fix: dummy commit * fix: allow slash and no slash * fix: allow slash and no slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * feat: add uds endpoint tests * feat: add uds endpoint tests * feat: am-uds-dapa comes from config with defaulted to that string * feat: am-uds-dapa comes from config with defaulted to that string * feat: adding fastapi * feat: adding fastapi * feat: endpoint to setup es * feat: endpoint to setup es * feat: Using Fastapi for all API endpoints (#190) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * fix: add root link in collection stac * feat: updating terraform * fix: actual creation has some error * fix: json to invoke magnum lambda is updated * chore: update log statement * fix: attempting bugfix * fix: some weird error. updating function name to confirm it * fix: teraform error due to partial update only * fix: dummy commit * fix: allow slash and no slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * fix: trying slash and no-slash * feat: add uds endpoint tests * feat: am-uds-dapa comes from config with defaulted to that string * fix: make venjue specific ssm params * fix: make venjue specific ssm params * fix: need to dump model to become json * fix: need to dump model to become json * fix: json validator error * fix: json validator error * fix: json validator error * fix: json validator error * feat: adding auth to endpoints * feat: adding auth to endpoints * fix: typo * fix: typo * fix: add some logs * fix: add some logs * fix: add some logs * fix: add some logs * fix: add some logs * fix: add some logs * fix: update new collection to custom collection table * fix: update new collection to custom collection table * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: need token now for internal call * fix: no need to ignore case * fix: no need to ignore case * fix: S3 upload structure (add collection folder) (#193) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * feat: add collection folder in s3 upload * fix: update note * fix: update wrong PR number * fix: update missed file during merge * fix: remove old test case * fix: Cataloging large number asynchronously by batch + download is stuck when there are large number of files (#194) * fix: retry 5 times + wait 45 sec for DAAC * feat: make re-try configurable * feat: adding fastapi (in-progress) * fix: get collection creation working (in-progress) * feat: default poll checking to 0 times + conflict bug in dapa client * feat: add facade endpoint + real endpoint for cnm * fix: update version * fix: need to call PUT. not POST * fix: update test case * chore: add large data catalog testcase * fix: use Manager().Q instead of normal Q to fix it for download stuck for large granules * chore: adding support files for test * fix: calling catalog api in batch * chore: update changelog * chore: add missing test file * fix: mismatch version * feat: starting endpoint to create granules collections * fix: add missing import statement * chore: update version * chore: dummy commit * fix: dummy commit * fix: make name valid for ES index * fix: make name valid for ES index * fix: make name valid for ES index * fix: make name valid for ES index * fix: make alias name lowercase * feat: add destroy endpoint * feat: add destroy endpoint * fix: wrong method in destroy * fix: use read alias to get all indices * feat: add get and delete single index endpoint * chore: remove urn:nasa:unity from test case. we will not store them as part of the name * feat: also store custom metadata during extraction * feat: update tf module to support custom metadata * fix: update test + fix some bugs * feat: item transformer to expect custom_metadata * feat: query granule to include custom metadata (not tested) * fix: deleting accidental commits * fix: allow report_to_ems from config + event_time for record entry * fix: delete accidental commits * fix: checking why custom metadata not being ingested * fix: granule id + collection id for uniqueness * fix: wrong dsl to get granules custom metadata * fix: debugging granules retrieval bug * fix: ingest granule_id starting with collection id * fix: granule_id already starts with collection * fix: hide granule_id in custom_metadata result * chore: add end to end test for custom metadata * feat: adding endpoint to get custom metadata fields * feat: hiding default fields and other settings * fix: format error * fix: format error * fix: why collections not returning * fix: still fixing why collections not showing up * fix: debugging code has error * fix: remove debugging query * chore: update changelog --------- Co-authored-by: Nga Chung <17833879+ngachung@users.noreply.github.com> Co-authored-by: Nga Chung <nga.t.chung@jpl.nasa.gov>
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Closes #195
Closes #196