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15223: generate empty in convert (#16137)
* 15223: generate empty report for garbled convert data * fixup! 15223: generate empty report for garbled convert data * fixup! 15223: generate empty report for garbled convert data * fixup! 15223: generate empty report for garbled convert data * fixup! 15223: generate empty report for garbled convert data * fixup! 15223: generate empty report for garbled convert data
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| Original file line number | Diff line number | Diff line change |
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@@ -127,6 +127,24 @@ OBX|4|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69||N^No^HL70136| | |
| OBX|5|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69||N^No^HL70136||||||F|||202102090000-0600|||||||||||||||QST | ||
| SPM|1|0cba76f5-35e0-4a28-803a-2f31308aae9b||258500001^Nasopharyngeal swab^SCT||||71836000^Nasopharyngeal structure (body structure)^SCT^^^^2020-09-01|||||||||202102090000-0600|202102090000-0600""" | ||
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| // This report is trying to contain two items, but the HL7 is garbled, the first is missing an MSH segment and the second | ||
| // has a typo in its MSH segment | ||
| @Suppress("ktlint:standard:max-line-length") | ||
| const val garbledHL7Record = | ||
| """FT|Centers for Disease Control and Prevention|0.1-SNAPSHOT|PRIME ReportStream|0.1-SNAPSHOT||20210210 | ||
| PID|1||2a14112c-ece1-4f82-915c-7b3a8d152eda^^^Avante at Ormond Beach^PI||Buckridge^Kareem^Millie^^^^L||19580810|F||2106-3^White^HL70005^^^^2.5.1|688 Leighann Inlet^^South Rodneychester^TX^67071^^^^48077||7275555555:1:^PRN^^[email protected]^1^211^2240784|||||||||U^Unknown^HL70189||||||||N | ||
| ORC|RE|73a6e9bd-aaec-418e-813a-0ad33366ca85^6^7^8&F^9|73a6e9bd-aaec-418e-813a-0ad33366ca85|||||||||1629082607^Eddin^Husam^^^^^^CMS&2.16.840.1.113883.3.249&ISO^^^^NPI||^WPN^^^1^386^6825220|20210209||||||Avante at Ormond Beach|170 North King Road^^Ormond Beach^FL^32174^^^^12127|^WPN^^[email protected]^1^407^7397506|^^^^32174 | ||
| OBR|1|73a6e9bd-aaec-418e-813a-0ad33366ca85|0cba76f5-35e0-4a28-803a-2f31308aae9b|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN|||202102090000-0600|202102090000-0600||||||||1629082607^Eddin^Husam^^^^^^CMS&2.16.840.1.113883.3.249&ISO^^^^NPI|^WPN^^^1^386^6825220|||||202102090000-0600|||F | ||
| OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN||260415000^Not detected^SCT|||N^Normal (applies to non-numeric results)^HL70078|||F|||202102090000-0600|||CareStart COVID-19 Antigen test_Access Bio, Inc._EUA^^99ELR||202102090000-0600||||Avante at Ormond Beach^^^^^CLIA&2.16.840.1.113883.4.7&ISO^^^^10D0876999^CLIA|170 North King Road^^Ormond Beach^FL^32174^^^^12127 | ||
| OBX|2|CWE|95418-0^Whether patient is employed in a healthcare setting^LN^^^^2.69||Y^Yes^HL70136||||||F|||202102090000-0600|||||||||||||||QST | ||
| OBX|3|CWE|95417-2^First test for condition of interest^LN^^^^2.69||Y^Yes^HL70136||||||F|||202102090000-0600|||||||||||||||QST | ||
| OBX|4|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69||N^No^HL70136||||||F|||202102090000-0600|||||||||||||||QST | ||
| OBX|5|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69||N^No^HL70136||||||F|||202102090000-0600|||||||||||||||QST | ||
| SPM|1|0cba76f5-35e0-4a28-803a-2f31308aae9b||258500001^Nasopharyngeal swab^SCT||||71836000^Nasopharyngeal structure (body structure)^SCT^^^^2020-09-01|||||||||202102090000-0600|202102090000-0600 | ||
| SH|^~\&#!|CDC PRIME - Atlanta, Georgia (Dekalb)^2.16.840.1.114222.4.1.237821^ISO|Avante at Ormond Beach^10D0876999^CLIA|PRIME_DOH|Prime ReportStream|20210210170737||ORU^R01^ORU_R01|371784|P|2.5.1|||NE|NE|USA||||PHLabReportNoAck^ELR_Receiver^2.16.840.1.113883.9.99^ISO | ||
| SFT|Centers for Disease Control and Prevention|0.1-SNAPSHOT|PRIME ReportStream|0.1-SNAPSHOT||20210210 | ||
| PID|1||2a14112c-ece1-4f82-915c-7b3a8d152eda^^^Avante at Ormond Beach^PI||Buckridge^Kareem^Millie^^^^L||19580810|F||2106-3^White^HL70005^^^^2.5.1|688 Leighann Inlet^^South Rodneychester^TX^67071^^^^48077||7275555555:1:^PRN^^[email protected]^1^211^2240784|||||||||U^Unknown^HL70189||||||||N""" | ||
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| @Suppress("ktlint:standard:max-line-length") | ||
| const val validRadxMarsHL7Message = | ||
| """MSH|^~\&|MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|CAREEVOLUTION^00Z0000024^CLIA|AIMS.INTEGRATION.PRD^2.16.840.1.114222.4.3.15.1^ISO|AIMS.PLATFORM^2.16.840.1.114222.4.1.217446^ISO|20240403205305+0000||ORU^R01^ORU_R01|20240403205305_dba7572cc6334f1ea0744c5f235c823e|P|2.5.1|||NE|NE|||||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISO | ||
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@@ -257,12 +275,13 @@ object UniversalPipelineTestUtils { | |
| ) | ||
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| /** | ||
| * fetch child reports associated with a [parent] report and ensure we find an [expected] number of children | ||
| * fetch child reports associated with a [parent] report and ensure we find an [expectedItems] number of children | ||
| */ | ||
| fun fetchChildReports( | ||
| parent: Report, | ||
| txn: DataAccessTransaction, | ||
| expected: Int? = null, | ||
| expectedItems: Int? = null, | ||
| expectedReports: Int = 1, | ||
| ): List<ReportFile> { | ||
| val itemLineages = DSL | ||
| .using(txn) | ||
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@@ -271,15 +290,15 @@ object UniversalPipelineTestUtils { | |
| .where(ItemLineage.ITEM_LINEAGE.PARENT_REPORT_ID.eq(parent.id)) | ||
| .fetchInto(gov.cdc.prime.router.azure.db.tables.pojos.ItemLineage::class.java) | ||
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| if (expected != null) { | ||
| assertThat(itemLineages).hasSize(expected) | ||
| assertThat(itemLineages.map { it.childIndex }).isEqualTo(MutableList(expected) { 1 }) | ||
| if (expectedItems != null) { | ||
| assertThat(itemLineages).hasSize(expectedItems) | ||
| assertThat(itemLineages.map { it.childIndex }).isEqualTo(MutableList(expectedItems) { 1 }) | ||
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| // itemCount is on the report created by the test. It will not be null. | ||
| if (parent.itemCount > 1) { | ||
| assertThat(itemLineages.map { it.parentIndex }).isEqualTo((1..expected).toList()) | ||
| assertThat(itemLineages.map { it.parentIndex }).isEqualTo((1..expectedItems).toList()) | ||
| } else { | ||
| assertThat(itemLineages.map { it.parentIndex }).isEqualTo(MutableList(expected) { 1 }) | ||
| assertThat(itemLineages.map { it.parentIndex }).isEqualTo(MutableList(expectedItems) { 1 }) | ||
| } | ||
| } | ||
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@@ -290,9 +309,7 @@ object UniversalPipelineTestUtils { | |
| .where(ReportLineage.REPORT_LINEAGE.PARENT_REPORT_ID.eq(parent.id)) | ||
| .fetchInto(gov.cdc.prime.router.azure.db.tables.pojos.ReportLineage::class.java) | ||
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| if (expected != null) { | ||
| assertThat(reportLineages).hasSize(expected) | ||
| } | ||
| assertThat(reportLineages).hasSize(expectedReports) | ||
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| val childReportIds = reportLineages.map { | ||
| it.childReportId | ||
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@@ -307,11 +324,13 @@ object UniversalPipelineTestUtils { | |
| ) | ||
| ) | ||
| .fetchInto(ReportFile::class.java) | ||
| if (expected != null) { | ||
| assertThat(reportFiles).hasSize(expected) | ||
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| assertThat(reportFiles).hasSize(expectedReports) | ||
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| if (expectedItems != 0) { | ||
| assertThat(itemLineages).transform { lineages -> lineages.map { it.childReportId }.sorted() } | ||
| .isEqualTo(reportFiles.map { it.reportId }.sorted()) | ||
| } | ||
| assertThat(itemLineages).transform { lineages -> lineages.map { it.childReportId }.sorted() } | ||
| .isEqualTo(reportFiles.map { it.reportId }.sorted()) | ||
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| return reportFiles | ||
| } | ||
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