TSPS-174 renaming non cosmetic things from tsps to teaspoons #93

jsotobroad · 2024-06-17T16:30:56Z

Description

We decided to rename out internal short name from tsps to teaspoons. This is making the changes in our repo first so we know what downstream things we should look into changing and try to merge the changes in logical order

working workflow with the consolidated db changesets - https://bvdp-saturn-dev.appspot.com/#workspaces/teaspoons-imputation-dev/teaspoons_imputation_dev_control_workspace_20240726/job_history/89bce976-a937-4829-bbe7-ad7d4e5dece8

Jira Ticket

https://broadworkbench.atlassian.net/browse/TSPS-174

jsotobroad · 2024-06-17T16:31:18Z

.github/workflows/build-and-test.yml

@@ -138,8 +138,8 @@ jobs:
          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
        with:
          status: failure
-          channel: "#terra-tsps-alerts"
-          username: "TSPS push to main branch"
+          channel: "#terra-teaspoons-alerts"


how hard is it to change slack channel names?

when should we make this change? right before merging this PR?

jsotobroad · 2024-06-17T16:31:55Z

README.md

@@ -82,7 +82,7 @@ SonarQube and want to debug the problem locally, you need to get the sonar token
 before running the gradle task.

 ```shell
-export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/tsps)
+export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/teaspoons)


do we want to change our vault path?

good question for @choover-broad

jsotobroad · 2024-06-17T16:32:15Z

README.md


 For more information about deployment to dev, check out DevOps' [excellent documentation](https://docs.google.com/document/d/1lkUkN2KOpHKWufaqw_RIE7EN3vN4G2xMnYBU83gi8VA/).

 ### Tracing

 We use [OpenTelemetry](https://opentelemetry.io/) for tracing, so that every request has a tracing span that can 
-be viewed in [Google Cloud Trace](https://cloud.google.com/trace). (This is not yet fully set up here - to be done in TSPS-107). 
+be viewed in [Google Cloud Trace](https://cloud.google.com/trace). (This is not yet fully set up here - to be done in Teaspoons-107). 


can we change the shortname of our jira board/tickets easily and what do we rename it to if it is?

jsotobroad · 2024-06-17T16:34:01Z

service/src/main/resources/application.yml

@@ -9,7 +9,7 @@ env:
      pass: ${DATABASE_USER_PASSWORD:dbpwd}
      user: ${DATABASE_USER:dbuser}
    stairway:
-      name: ${STAIRWAY_DATABASE_NAME:tsps_stairway_db}
+      name: ${STAIRWAY_DATABASE_NAME:teaspoons_stairway_db}


def need to make sure these database values are changed upstream

yeah i wonder what the process will be for updating BEEs

mmorgantaylor · 2024-06-17T17:00:22Z

.github/workflows/build-and-test.yml

@@ -138,8 +138,8 @@ jobs:
          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
        with:
          status: failure
-          channel: "#terra-tsps-alerts"
-          username: "TSPS push to main branch"
+          channel: "#terra-teaspoons-alerts"


mmorgantaylor · 2024-06-17T17:39:08Z

README.md

@@ -82,7 +82,7 @@ SonarQube and want to debug the problem locally, you need to get the sonar token
 before running the gradle task.

 ```shell
-export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/tsps)
+export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/teaspoons)


good question for @choover-broad

mmorgantaylor · 2024-06-17T17:39:41Z

README.md


 For more information about deployment to dev, check out DevOps' [excellent documentation](https://docs.google.com/document/d/1lkUkN2KOpHKWufaqw_RIE7EN3vN4G2xMnYBU83gi8VA/).

 ### Tracing

 We use [OpenTelemetry](https://opentelemetry.io/) for tracing, so that every request has a tracing span that can 
-be viewed in [Google Cloud Trace](https://cloud.google.com/trace). (This is not yet fully set up here - to be done in TSPS-107). 
+be viewed in [Google Cloud Trace](https://cloud.google.com/trace). (This is not yet fully set up here - to be done in TEASPOONS-107). 


did we decide on a new Jira handle yet?

i dont think we have. I thougth i put a comment about that somewhere but i dont see it =/

mmorgantaylor · 2024-06-17T17:40:50Z

service/src/main/java/bio/terra/pipelines/App.java

@@ -26,7 +26,7 @@
      "bio.terra.common.retry.transaction",
      // Stairway initialization and status
      "bio.terra.common.stairway",
-      // Scan all TSPS service packages
+      // Scan all Teaspoons service packages


should we change the whole "pipelines" package to "teaspoons"? (referenced in the next line)

i actually like pipelines. Similar to like workspace manager, their package name is workspace

mmorgantaylor · 2024-06-17T17:41:42Z

service/src/main/java/bio/terra/pipelines/dependencies/cbas/CbasService.java

@@ -43,11 +43,11 @@ public MethodListResponse getAllMethods(String cbasBaseUri, String accessToken)
   * .methodDescription("method description") //
   * .methodSource(PostMethodRequest.MethodSourceEnum.GITHUB) // .methodUrl(pipeline.getWdlUrl()) //
   * .methodVersion("1.0"); // logger.info( // "this is creating a new method in cbas: {}", //
-   * cbasService.createMethod( // cbasUri, samService.getTspsServiceAccountToken(),
+   * cbasService.createMethod( // cbasUri, samService.getTeasponnsServiceAccountToken(),


typo (though I kinda love "teasponns" 😂 )

its so hard to spell it sometimes!!!

mmorgantaylor · 2024-06-17T17:42:24Z

service/src/main/java/bio/terra/pipelines/dependencies/sam/SamService.java

    try {
      GoogleCredentials creds =
          GoogleCredentials.getApplicationDefault().createScoped(SAM_OAUTH_SCOPES);
      creds.refreshIfExpired();
      return creds.getAccessToken().getTokenValue();
    } catch (IOException e) {
      throw new InternalServerErrorException(
-          "Internal server error retrieving TSPS credentials", e);
+          "Internal server error retrieving Teaspoons credentials", e);


does this message get returned to the user? do we want a different user-facing name?

oh thats a good point, should we say Terra Scientific Pipeline Services instead?

mmorgantaylor · 2024-06-17T17:46:30Z

service/src/main/java/bio/terra/pipelines/dependencies/stairway/JobService.java

@@ -155,7 +155,8 @@ public <T> JobResultOrException<T> retrieveJobResult(

      switch (flightState.getFlightStatus()) {
        case FATAL:
-          logAlert("TSPS Stairway flight {} encountered dismal failure", flightState.getFlightId());
+          logAlert(
+              "Teaspoons Stairway flight {} encountered dismal failure", flightState.getFlightId());


we probably don't need to include "teaspoons" in these log messages at all...

mmorgantaylor · 2024-06-17T17:49:21Z

service/src/main/resources/application.yml

@@ -9,7 +9,7 @@ env:
      pass: ${DATABASE_USER_PASSWORD:dbpwd}
      user: ${DATABASE_USER:dbuser}
    stairway:
-      name: ${STAIRWAY_DATABASE_NAME:tsps_stairway_db}
+      name: ${STAIRWAY_DATABASE_NAME:teaspoons_stairway_db}


yeah i wonder what the process will be for updating BEEs

sonarcloud · 2024-06-26T20:14:33Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

jsotobroad · 2024-11-07T00:13:37Z

service/src/main/resources/db/changesets/20241106-base-data-insertion.yaml

+                  value: imputation
+              - column:
+                  name: wdl_url
+                  value: https://github.com/broadinstitute/warp/blob/TSPS-183_mma_beagle_imputation_hg38/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.wdl


wasnt sure if this was correct but i think this is the latest value we have

i think that's right too (it matches what we currently have)

mmorgantaylor

looking great, a couple comments/questions. is the next step to walk through this with Chelsea?

mmorgantaylor · 2024-11-12T19:08:17Z

.github/workflows/run-e2e-tests.yaml

@@ -89,7 +89,7 @@ jobs:
    permissions:
      contents: read
      id-token: write
-    uses: broadinstitute/dsp-reusable-workflows/.github/workflows/run_tsps_e2e_tests.yaml@main
+    uses: broadinstitute/dsp-reusable-workflows/.github/workflows/run_teaspoons_e2e_tests.yaml@main


we'll need to open a PR in dsp-reusable-workflows to update the names of all the relevant files - they all say "tsps" currently, e.g. https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/.github/workflows/run_tsps_e2e_tests.yaml

mmorgantaylor · 2024-11-12T19:09:00Z

.github/workflows/build-and-test.yml

@@ -138,8 +138,8 @@ jobs:
          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
        with:
          status: failure
-          channel: "#terra-tsps-alerts"
-          username: "TSPS push to main branch"
+          channel: "#terra-teaspoons-alerts"


when should we make this change? right before merging this PR?

mmorgantaylor · 2024-11-12T19:09:57Z

README.md

@@ -106,7 +106,7 @@ does all the setup for you. Clone that repo and make sure you're either on Broad
 to the VPN. Then run the following command:

 ```shell
-./db/psql-connect.sh dev tsps
+./db/psql-connect.sh dev teaspoons


does this work already? any changes we need to make in that script?

it does not, we'd have to make all the related tsps -> teaspoon changes affter this pr gets merged

mmorgantaylor · 2024-11-12T19:10:58Z

README.md

@@ -129,7 +129,7 @@ See [this DSP blog post](https://broadworkbench.atlassian.net/wiki/x/AoGlrg) for
 ### Running the end-to-end tests

 The end-to-end test is specified in `.github/workflows/run-e2e-tests.yaml`. It calls [the test script defined 
-in the dsp-reusable-workflows repo](https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/e2e-test/tsps_e2e_test.py).
+in the dsp-reusable-workflows repo](https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/e2e-test/teaspoons_e2e_test.py).


current path is https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/e2e-test/tsps_gcp_e2e_test.py; we should change it in that repo and here to https://github.com/broadinstitute/dsp-reusable-workflows/blob/main/e2e-test/teaspoons_gcp_e2e_test.py

mmorgantaylor · 2024-11-12T19:11:58Z

service/src/main/resources/db/changelog.xml

-  <include file="changesets/20241030_add_pipeline_quotas.yaml" relativeToChangelogFile="true"/>
-  <include file="changesets/20241103_add_user_quotas.yaml" relativeToChangelogFile="true"/>
-  <include file="changesets/20241106_array_imputation_rename.yaml" relativeToChangelogFile="true"/>
+  <include file="changesets/20241106-base-tables.yaml" relativeToChangelogFile="true"/>


mmorgantaylor · 2024-11-12T19:14:25Z

service/src/main/resources/db/changesets/20241106-base-data-insertion.yaml

+                  value: imputation
+              - column:
+                  name: wdl_url
+                  value: https://github.com/broadinstitute/warp/blob/TSPS-183_mma_beagle_imputation_hg38/pipelines/broad/arrays/imputation_beagle/ImputationBeagle.wdl


i think that's right too (it matches what we currently have)

mmorgantaylor · 2024-11-12T19:17:04Z

...ice/src/test/java/bio/terra/pipelines/common/utils/StairwaySetPipelineRunStatusHookTest.java

@@ -7,6 +7,7 @@

 import bio.terra.pipelines.db.entities.PipelineRun;
 import bio.terra.pipelines.db.repositories.PipelineRunsRepository;
+import bio.terra.pipelines.db.repositories.PipelinesRepository;


was this just missing by accident before?

huh i have no idea why that was added, i removed it and tests still seem to be passing. I prob messed up something while i was refactoring stuff 🤷

jsotobroad · 2024-11-13T00:21:50Z

looking great, a couple comments/questions. is the next step to walk through this with Chelsea?

yea I think the next step would be to chat with chelsea for the vault stuff and then co-ordinate the new CI with this codebase with a clean DB. For the slack and e2e test renaming stuff i figure we can knock that out as we merge this pr in

mmorgantaylor · 2024-11-13T16:10:47Z

service/src/main/resources/application.yml

@@ -25,7 +25,7 @@ env:
    authorityEndpoint: ${OIDC_AUTHORITY_ENDPOINT:https://terradevb2c.b2clogin.com/terradevb2c.onmicrosoft.com/oauth2/v2.0/authorize?p=b2c_1a_signup_signin_dev}
    tokenEndpoint: ${OIDC_TOKEN_ENDPOINT:https://terradevb2c.b2clogin.com/terradevb2c.onmicrosoft.com/oauth2/v2.0/token?p=b2c_1a_signup_signin_dev}
  ingress:
-    domainName: ${TSPS_INGRESS_DOMAIN_NAME:localhost:8080}
+    domainName: ${TEAPSOONS_INGRESS_DOMAIN_NAME:localhost:8080}


is this env var all set up (probably a question for @choover-broad)

… changes

sonarcloud · 2024-11-21T17:53:15Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
80.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

jsotobroad requested a review from mmorgantaylor June 17, 2024 16:30

jsotobroad commented Jun 17, 2024

View reviewed changes

mmorgantaylor reviewed Jun 17, 2024

View reviewed changes

jsotobroad force-pushed the js_TSPS-174 branch 4 times, most recently from f675487 to e1813d1 Compare June 26, 2024 20:09

jsotobroad changed the title ~~TSPS-174 first pass at renaming things from tsps to teaspoons~~ TSPS-174 renaming non cosmetic things from tsps to teaspoons Jun 26, 2024

jsotobroad force-pushed the js_TSPS-174 branch 2 times, most recently from 9bdcf67 to 44fcd84 Compare November 7, 2024 00:12

jsotobroad commented Nov 7, 2024

View reviewed changes

mmorgantaylor reviewed Nov 12, 2024

View reviewed changes

mmorgantaylor reviewed Nov 13, 2024

View reviewed changes

Jose Soto added 6 commits November 21, 2024 12:41

first pass at renaming things from tsps to teaspoons for non cosmetic…

b2684a8

… changes

consilidate changesets before releasing teaspoons

b18df5e

get consolidate changesets working with tests and against dev

2c942f2

pr feedback

5b47985

TEAPSOONS!!!

465a5da

reorder migrations to do data insertion after indexes are created

e1db2a7

jsotobroad force-pushed the js_TSPS-174 branch from 553e505 to e1db2a7 Compare November 21, 2024 17:44

jsotobroad merged commit c406d89 into main Nov 22, 2024
14 checks passed

jsotobroad deleted the js_TSPS-174 branch November 22, 2024 18:18

TSPS-174 renaming non cosmetic things from tsps to teaspoons #93

TSPS-174 renaming non cosmetic things from tsps to teaspoons #93

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jsotobroad commented Jun 17, 2024 • edited Loading

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sonarcloud bot commented Jun 26, 2024

Quality Gate passed

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jsotobroad commented Nov 13, 2024

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sonarcloud bot commented Nov 21, 2024

Quality Gate passed

jsotobroad commented Jun 17, 2024 •

edited

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