test: add test that checks that we do not regress re/ non-standard co…

…lumn names

src/silo/preprocessing/preprocessor.test.cpp

@@ -83,6 +83,29 @@ const Scenario NDJSON_WITH_SQL_KEYWORD_AS_FIELD = {
    )
 };
 
+const Scenario NDJSON_WITH_NUMERIC_NAMES = {
+   .input_directory = "testBaseData/numericNames/",
+   .expected_sequence_count = 2,
+   .query = R"(
+      {
+         "action": {
+            "type": "Aggregated",
+            "groupByFields": ["2"],
+            "orderByFields": ["2"]
+         },
+         "filterExpression": {
+            "type": "True"
+         }
+      }
+   )",
+   .expected_query_result = nlohmann::json::parse(
+      R"([
+         {"count": 1, "2": null},
+         {"count": 1, "2": "google.com"}
+   ])"
+   )
+};
+
 const Scenario TSV_FILE_WITH_SQL_KEYWORD_AS_FIELD = {
    .input_directory = "testBaseData/tsvWithSqlKeywordField/",
    .expected_sequence_count = NDJSON_WITH_SQL_KEYWORD_AS_FIELD.expected_sequence_count,
@@ -99,7 +122,8 @@ INSTANTIATE_TEST_SUITE_P(
       FASTA_FILES_WITH_MISSING_SEGMENTS_AND_GENES,
       NDJSON_FILE_WITH_MISSING_SEGMENTS_AND_GENES,
       NDJSON_WITH_SQL_KEYWORD_AS_FIELD,
-      TSV_FILE_WITH_SQL_KEYWORD_AS_FIELD
+      TSV_FILE_WITH_SQL_KEYWORD_AS_FIELD,
+      NDJSON_WITH_NUMERIC_NAMES
    ),
    printTestName
 );

testBaseData/numericNames/database_config.yaml

@@ -0,0 +1,31 @@
+schema:
+  instanceName: Test
+  metadata:
+    - name: date
+      type: date
+    - name: dateSubmitted
+      type: date
+    - name: "2"
+      type: string
+    - name: age
+      type: int
+    - name: sex
+      type: string
+    - name: pangoLineage
+      type: pango_lineage
+    - name: qc
+      type: float
+    - name: accession
+      type: string
+    - name: version
+      type: int
+    - name: submissionId
+      type: string
+    - name: accessionVersion
+      type: string
+    - name: isRevocation
+      type: string
+    - name: versionStatus
+      type: string
+  primaryKey: accessionVersion
+  dateToSortBy: date

testBaseData/numericNames/input_file.ndjson

@@ -0,0 +1,2 @@
+{"metadata":{"qc":0.9,"age":42,"sex":null,"date":"2002-12-15","2":"google.com","pangoLineage":"XBB.1.5","dateSubmitted":null,"accession":"1","version":1,"submissionId":"custom0","accessionVersion":"1.1","isRevocation":"false","versionStatus":"REVOKED"},"unalignedNucleotideSequences":{"main":"NNACTGNN","3":null},"alignedNucleotideSequences":{"main":"ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCT","3":null},"nucleotideInsertions":{"main":["123:ACTG"],"3":[]},"alignedAminoAcidSequences":{"someLongGene":"ACDEFGHIKLMNPQRSTVWYBZX-*","someShortGene":"MADS"},"aminoAcidInsertions":{"someLongGene":["123:RNRNRN"],"someShortGene":["123:RN"]}}
+{"metadata":{"qc":null,"age":null,"sex":null,"date":null,"2":null,"pangoLineage":null,"dateSubmitted":null,"accession":"1","version":3,"submissionId":"custom0","accessionVersion":"1.3","isRevocation":"true","versionStatus":"REVISED"},"unalignedNucleotideSequences":{"main":null,"3":null},"alignedNucleotideSequences":{"main":null,"3":null},"nucleotideInsertions":{"main":[],"3":[]},"alignedAminoAcidSequences":{"someLongGene":null,"someShortGene":null},"aminoAcidInsertions":{"someLongGene":[],"someShortGene":[]}}

testBaseData/numericNames/preprocessing_config.yaml

@@ -0,0 +1,4 @@
+inputDirectory: "testBaseData/numericNames"
+ndjsonInputFilename: "input_file.ndjson"
+referenceGenomeFilename: "reference_genomes.json"
+preprocessingDatabaseLocation: "debug.duckdb"

testBaseData/numericNames/reference_genomes.json

@@ -0,0 +1,22 @@
+{
+  "nucleotideSequences": [
+    {
+      "name": "main",
+      "sequence": "ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCT"
+    },
+    {
+      "name": "3",
+      "sequence": "AAAAAAAAAAAAAAAA"
+    }
+  ],
+  "genes": [
+    {
+      "name": "someLongGene",
+      "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAA"
+    },
+    {
+      "name": "someShortGene",
+      "sequence": "MADS"
+    }
+  ]
+}