Publishing complete - Githubissues

Colin J. Carlson, PhD • Georgetown University Assistant Research Professor, Center for Global Health Science & Security Director, Verena: an NSF Biology Integration Institute • viralemergence.org Contact: Website http://carlsonlab.bio • Scholar https://scholar.google.com/citations?user=2ZwUC84AAAAJ&hl=en&authuser=2 • Github https://github.com/cjcarlson • Twitter https://twitter.com/wormmaps

On Mon, Apr 24, 2023 at 4:12 PM Ryan Zimmerman @.***> wrote:

You can view, comment on, or merge this pull request online at:

https://github.com/talus-analytics-bus/pharos-api/pull/64 Commit Summary

007f615 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/007f61586eb31b826b074119a48312d3d6d03964 Adding Extra.forbid to the save_register route

30a6e66 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/30a6e66f7a089d6d5a1bb74fb90037087958aad0 Adding pydantic dependency

f11ce80 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/f11ce80476cccd34c876c6a414eafe6646aa4657 Removing old models.py file

9439619 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/9439619a32ddb214a239a73f4a312af914266cd6 Finally fixing the relationships between the models

aeb27b3 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/aeb27b30094468faa993b52a2a2bea480c1f3dbf Fully commenting out database tests; this needs to be implemented with postgres

6f37266 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/6f372665aadbe4bb5f91f154a3ff2808b3bd9925 Making the access_permissions function responsible for setting up the database tables so the publish function doesn't run it

290158b https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/290158b540c7ea3b58a6efd048bd2d1bbba68549 First pass working publish function

95fea0d https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/95fea0db1f673c4cc2d99fe9968dddc86281dde7 Adding simple "unpublish" function which deletes all PublishedRecords associated with the project from the database

63cb2c7 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/63cb2c71f525055b88ff2e41dbff80e0f7e542ef Adding get_engine() function to centralize database connection logic

23ded1d https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/23ded1d0daec4ae53545ef5c8e82bde31527f8c3 Adding unpublishProjectFunction to the template

044c2f5 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/044c2f5af3abed5e4386490a25069d5ef3c73191 Adding back fixed permissions function and custom resource for both database plugins setup and tables setup

56a5ecf https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/56a5ecfa92d9c033732dc263e4f9628949b80ab8 Adding project_id, dataset_id, record_id, and fixing WKT formatting on the point

be6d806 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/be6d80680d10d25d5e36f2572a52e9857d1f3eb9 Making pathogen no longer requred

5c94459 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/5c944597291bb1d6a31b27fe1944c6661c824527 Making these conversions return None in the case of ValueError, the ValueError happens when the value is an empty string because the validator considers those equivalent to none

c90e854 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/c90e854cfd283f45c014b3a916480a899308fc77 Making pathogen optional in the database

01d74b5 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/01d74b5e6c136c3879322b8fb60db0f82b7f8787 Rename models2 to just models.py

c20d05d https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/c20d05d4fe295cd1bc1c3cacba745dcb18f1c44a Update imports

8b58277 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/8b58277af08600ceb863138e723ad81aec1cdba0 Changing organism_id back to animal_id

3359501 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/3359501c3ddf77437b8714ea73192584eca9b697 Adding create tables call even when the secret exists; this will do nothing if the tables already exist.

7af35e8 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/7af35e83a386c62f750cda8ebda79f06f2d86691 This doesn't work because CustomResources don't re-run on subsequent deployments

c38235f https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/c38235fdebd9da461cfa206b35d4a5b0e3755944 Catching the last case of Organism ID

571ea3e https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/571ea3ea5448c8a610e842978744a6464baedb78 Increase timeout and memory size

4509fec https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/4509fecb4d08d39769a85d15539b57c2d6f54e40 Reimplementing publish_register to skip validation entirely and only construct classes which will be used

ef23890 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/ef23890209bb280e50a9f13a6fe74872a11223d8 Adding lots of comments because this process ended up being non-obvious

8a08198 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/8a081984bb8500c32d25e298aab11b3cfc6d4652 Clean up imports

4a7f0c9 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/4a7f0c9c54b6113cb69b713eef57e26120d1080f Adding "publishing" states to datasets and projects

c0b9398 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/c0b93987231d73597510b7906641d6d518ae825c Making "unpublish_project" act as a "roll back" function by rolling back metadata objects state and deleting all records from db

5b06235 https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/5b06235ddb63cc797b5de5713e4407005f11da55 Refactoring the actual publishing of registers into a separate function, which means it can run for up to 15 minutes straight

7cb4d8d https://github.com/talus-analytics-bus/pharos-api/pull/64/commits/7cb4d8dfb429c3609e077749a1c7002e0add2eb0 Cleaning up imports and print statements

File Changes

(21 files https://github.com/talus-analytics-bus/pharos-api/pull/64/files)

M src/lambda/access_permissions/app.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-e2d30b357aafd6cd59c07f7e1c7a0a0576248168211ae6e3da8862f22a6a0507 (7)

M src/lambda/access_permissions/requirements.txt https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-a96fde0fcce5a8b82697263f0148e8656268bf84e2e038a0fd183f62ceade123 (9)

M src/lambda/publish_project/app.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-361ab8c323988cb957fd2d7d4be8f5cb265c1ee3dcd9393e2691fc99cb486424 (254)

M src/lambda/publish_project/requirements.txt https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-47cca878329f17a14689e556f4fe96721645d4b489142ec744244da3aeeedf87 (8)

A src/lambda/publish_registers/AmazonRootCA1.pem https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-1cb6c639f98fcd40b3721165aa38a280aac9d2ecfe3b4ee1b995a3b0d97bd073 (20)

A src/lambda/publish_registers/init.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-b964019294c0858d8d93bb0bbfafb5578a92d41f799078ed1f71e67ac14a59ee (0)

A src/lambda/publish_registers/app.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-1fc8b1b2dac17d8f0b8188389aedb991c38bd7ddc0a7f1c92634d97375b25d4d (114)

A src/lambda/publish_registers/requirements.txt https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-ddc14dc14bdc27e127d23bc07e53c7665e6d72ce42febbb4051ebf05fcdb729c (5)

M src/lambda/save_register/app.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-fc5cb392358fe589a013a705edf5ee70213072fd852aa0dfef93c233ef63191a (5)

A src/lambda/unpublish_project/AmazonRootCA1.pem https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-9c36c73d2dcfa5a65232c2b4eea872d6cd0bc2e220af5c5a2b4ae81d9414e970 (20)

A src/lambda/unpublish_project/init.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-ee3ffee75693d9b74c50abca7b3fc49b103cbfdf0199793cad140f10a8d4bed9 (0)

A src/lambda/unpublish_project/app.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-2307e73a6cac6805fbfc76036550eeb5644a2448096858c07b3197711c245f97 (106)

A src/lambda/unpublish_project/requirements.txt https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-0621535ebe4ddce37457e0f526389aa9e9e12a25f318d15728143432419fa3ea (5)

M src/libraries/python/column_alias.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-e60e4131170111144beb62133b85592b29dedd0e1b4899ae1c4ffb64b9a0e3f8 (10)

A src/libraries/python/engine.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-830a487ba6914b3e404270f65ab5b29807a355c76dc226dc5fffad677cc1b409 (31)

M src/libraries/python/models.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-dca7fbd45f76659f35eec331fcfdfbd0fd842b240e133df8c598dbdd162cad1d (302)

D src/libraries/python/models2.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-59a047878a848b8a4ea13a7f9c663a5893dc7e452a662a5c5ea5ea050c18a306 (175)

M src/libraries/python/publish_register.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-82a8cf5ad857d629b4d71ab68c1c022d456a6705b9b2c3b0b86a050f7000c760 (62)

M src/libraries/python/register.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-0b5f665c317eb1d53887bd0c743b115a4796636569ae132e27655dda66196eec (8)

M template.yaml https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-1363ef5ce8886100842332c97163aad7934237e1fe49b5d40422b45fdc30f38e (221)

M tests/unit_testing/test_database.py https://github.com/talus-analytics-bus/pharos-api/pull/64/files#diff-3599de8859bf0800eff233e89a920ed7fd4bd7bc5b02ce4068aa327069287b2a (284)

Patch Links:

https://github.com/talus-analytics-bus/pharos-api/pull/64.patch

https://github.com/talus-analytics-bus/pharos-api/pull/64.diff

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viralemergence / pharos-api

Publishing complete #64