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Add Receive step to UP

Open brick-green opened this issue 1 year ago • 4 comments

This PR adds a new step to the universal pipeline called Receive. The purpose is to accept messages from the submissions microservice then update the postgresql database and the azure storage account table. Upon successful processing, the message will be added to the convert step queue.

Test Steps:

  1. run unit tests
  2. run integration tests
  3. run smoke tests

Submit Test message:

  1. run ./gradlew bootRun and ./gradlew quickRun
  2. submit message to submission api:
  curl --location 'http://localhost:8880/api/v1/reports' \
--header 'Content-Type: application/hl7-v2' \
--header 'client_id: ignore.ignore-full-elr' \
--header 'x-azure-clientip: 1' \
--data-raw 'MSH|^~\&#|STARLIMS.CDC.Stag^2.16.840.1.114222.4.3.3.2.1.2^ISO|CDC Atlanta^11D0668319^CLIA|MEDSS-ELR ^2.16.840.1.114222.4.3.3.6.2.1^ISO|MNDOH^2.16.840.1.114222.4.1.3661^ISO|20230501102531-0400||ORU^R01^ORU_R01|3003786103_4988249_33033|T|2.5.1|||NE|NE|USA||||PHLabReport-NoAck^PHIN^2.16.840.1.113883.9.11^ISO
SFT|CDC^^^^^CDC&2.16.840.1.114222.4&ISO^XX^^^CDC CLIA|ELIMS V11|STARLIMS|Binary ID unknown
PID|1||PID03953346^^^STARLIMS.CDC.Stag&2.16.840.1.114222.4.3.3.2.1.2&ISO^PI~10171284^^^SPHL-000034&2.16.840.1.114222.4.1.3661&ISO^PI||~^^^^^^U||0000||||^^^^^USA^H
NTE|1|L|SPHL Submitter: MN PHL Division, Minnesota Department of Health, Submitter ID: SPHL-000034, Address: 601 Robert St. N.  St. Paul, Minnesota 55164-0899 United States, Email: [email protected], Submitter Patient ID: 10171284, Submitter Alt Patient ID: , Submitter Specimen ID: 230011927, Submitter Alt Specimen ID:|RE^Remark^HL70364^^^^2.5.1^^^^^^^2.16.840.1.113883.12.364
ORC|RE|230011927^SPHL-000034^2.16.840.1.114222.4.1.3661^ISO|40_3003786103_4988249_1087^STARLIMS.CDC.Stag^2.16.840.1.114222.4.3.3.2.1.2^ISO|||||||||SPHL-000034^MN PHL Division, Minnesota Department of Health^^^^^^^STARLIMS.CDC.Stag&2.16.840.1.114222.4.3.3.2.1.2&ISO^^^^XX||^NET^Internet^[email protected]|||||||MN PHL Division, Minnesota Department of Health^D^^^^STARLIMS.CDC.Stag&2.16.840.1.114222.4.3.3.2.1.2&ISO^XX^^^SPHL-000034|601 Robert St. N.^^St. Paul^MN^55164-0899^USA^M|^WPN^Internet^[email protected]|601 Robert St. N.^^St. Paul^MN^55164-0899^USA^M
OBR|1|230011927^SPHL-000034^2.16.840.1.114222.4.1.3661^ISO|40_3003786103_4988249_1087^STARLIMS.CDC.Stag^2.16.840.1.114222.4.3.3.2.1.2^ISO|PLT1228^Mold and Yeast XXX MS.MALDI-TOF^PLT^1087^MALDI-TOF-CLIA^L^2.69^v unknown^^CDC-10179^Fungal Identification^L^^2.16.840.1.113883.6.1|||20230322|||||||||SPHL-000034^MN PHL Division, Minnesota Department of Health^^^^^^^STARLIMS.CDC.Stag&2.16.840.1.114222.4.3.3.2.1.2&ISO^^^^XX|^NET^Internet^[email protected]|||||202304271044-0400|||F
OBX|1|CWE|PLT1228^Mold and Yeast XXX MS.MALDI-TOF^PLT^3562^MALDI-TOF-CLIA^L^2.69^v_unknown^MALDI-TOF-CLIA|N8KHKA9H-1|712760003^Candida metapsilosis (organism)^SCT^^^^09012018^^Candida metapsilosis||||||F|||20230322|11D0668319^Centers for Disease Control and Prevention^CLIA^40^Fungus Reference Laboratory^L|[email protected]^Gade^Lalitha|||20230427092900||||Centers for Disease Control and Prevention^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^11D0668319|1600 Clifton Rd^^Atlanta^GA^30329^USA^B
SPM|1|230011927&SPHL-000034&2.16.840.1.114222.4.1.3661&ISO^3003786103&STARLIMS.CDC.Stag&2.16.840.1.114222.4.3.3.2.1.2&ISO||119365002^Specimen from wound^SCT^WND^Wound^L^0912017^Adobe_Code^Wound||||56459004^Foot^SCT^FOT^Foot^L^09012017^Adobe_Code^Foot||||||Isolate,|||20230322|20230421124150
'
  1. Open local azure storage explorer to confirm that a new record for for the report ID has been inserted with Accepted value
  2. Query local database to confirm the convert step action was logged

Checklist

Testing

  • [X] Tested locally?
  • [X] Ran ./prime test or ./gradlew testSmoke against local Docker ReportStream container?

Linked Issues

  • Linked #14603

brick-green avatar Aug 15 '24 17:08 brick-green

Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

OpenSSF Scorecard

PackageVersionScoreDetails

Scanned Manifest Files

github-actions[bot] avatar Aug 15 '24 17:08 github-actions[bot]

Test Results

1 229 tests  +12   1 225 :white_check_mark: +12   7m 42s :stopwatch: + 1m 15s   161 suites + 3       4 :zzz: ± 0    161 files   + 3       0 :x: ± 0 

Results for commit d10f3fc7. ± Comparison against base commit c660ea7b.

:recycle: This comment has been updated with latest results.

github-actions[bot] avatar Aug 15 '24 17:08 github-actions[bot]

Integration Test Results

 53 files   53 suites   27m 48s :stopwatch: 408 tests 399 :white_check_mark: 9 :zzz: 0 :x: 411 runs  402 :white_check_mark: 9 :zzz: 0 :x:

Results for commit d10f3fc7.

:recycle: This comment has been updated with latest results.

github-actions[bot] avatar Aug 15 '24 17:08 github-actions[bot]

Quality Gate Failed Quality Gate failed

Failed conditions
C Reliability Rating on New Code (required ≥ A)

See analysis details on SonarCloud

Catch issues before they fail your Quality Gate with our IDE extension SonarLint

sonarqubecloud[bot] avatar Sep 09 '24 19:09 sonarqubecloud[bot]