Bugfix/kbdev 1133 incorrect matching

data_3.json

@@ -0,0 +1,161 @@
+{
+    "TSC2:c.3365G>C": {
+        "comment": "KBDEV-1024",
+        "matches": {
+            "displayName": [
+                ""
+            ],
+            "type": [
+                ""
+            ]
+        },
+        "does_not_matches":{
+            "displayName": [
+                ""
+            ],
+            "type": [
+                ""
+            ]
+        }
+    },
+    "TSC2:c.4700G>A": {
+        "comment": "",
+        "matches": {
+            "displayName": [
+                "ENST00000219476:c.4700G>A",
+                "ENST00000219476:r.4810G>A",
+                "TSC2 mutation",
+                "TSC2:p.G1567D",
+                "chr16:g.2086230G>A"
+            ],
+            "type": [
+                "missense mutation",
+                "mutation",
+                "substitution"
+            ]
+        },
+        "does_not_matches":{
+            "displayName": [
+                "TSC2 nonsense"
+            ],
+            "type": [
+                "nonsense"
+            ]
+        }
+    },
+    "KRAS:p.G12D": {
+        "comment": "",
+        "matches": {
+            "displayName": [
+                "ENST00000256078:r.225_226delinsAC",
+                "ENST00000311936.7:c.35G>A",
+                "KRAS mutation",
+                "KRAS:c.35G>A",
+                "KRAS:p.(G12_G13)mut",
+                "KRAS:p.?12mut",
+                "KRAS:p.G12",
+                "KRAS:p.G12D",
+                "KRAS:p.G12X",
+                "KRAS:p.G12mut"
+            ],
+            "type": [
+                "indel",
+                "missense",
+                "missense mutation",
+                "mutation",
+                "substitution"
+            ]
+        },
+        "does_not_matches":{
+            "displayName": [
+                "chr12:g.25245349_25245351delinsGCT",
+                "cosm516",
+                "ensp00000452512:p.G12V"
+            ],
+            "type": [
+                "nonsense"
+            ]
+        }
+    },
+    "TP53:p.M237I": {
+        "comment": "GERO-299",
+        "matches": {
+            "displayName": [
+                "ENST00000269305:r.901G>T",
+                "TP53 missense",
+                "TP53 mutation",
+                "TP53:p.M237I",
+                "TP53:p.M237X",
+                "chr17:g.7577570C>T"
+            ],
+            "type": [
+                "missense",
+                "missense mutation",
+                "mutation",
+                "substitution"
+            ]
+        },
+        "does_not_matches":{
+            "displayName": [
+                "TP53 nonsense"
+            ],
+            "type": [
+                "nonsense"
+            ]
+        }
+    }
+}
+
+########################
+## KBDEV-1038
+########################
+# "FGFR4:p.N535K",
+# "EGFR:p.D942N",
+########################
+## KBDEV-1052
+########################
+# "EGFR:c.28246G>A",
+# "chr7:g.55198839G>A",
+# "EGFR:p.D942N",
+# '(PCM1,JAK2):fusion(r.6280,r.1821)',  # dummy test for Infers edges
+########################
+## KBDEV-1054
+########################
+# "ERBB2:p.R814C",
+########################
+## KBDEV-1056
+########################
+"ENST00000340107:c.1212dupC",
+"ENST00000340107:c.1212dupACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT",
+"ENST00000340107:c.1212_1213insC",
+"ENST00000340107:c.1212C>A",
+"chr1:g.33344590_33344592del",
+"FGFR3:g.5000_5001del",
+"FGFR3:g.5000_5100del",
+"ENST00000340107:c.9002_9050delinsTTT",
+"ENST00000340107:c.9002_9051delinsTTT",
+########################
+## GERO-299
+########################
+# "chr17:g.7674252C>T",
+# "ENST00000269305:c.711G>A",
+# "TP53:p.M237I",
+########################
+## KBDEV-1024
+########################
+# "TSC2:c.3365G>C",
+# "NM_000548.5:c.3365G>A",
+# "NM_000548.5:p.Arg1122His",
+# "TSC2: p.R112H",
+########################
+## KBDEV-1044
+########################
+# "TSC2:c.4700G>A",
+########################
+## OTHER Ex.
+########################
+# "ENST00000219476:c.4700_4701delinsAT",
+# "NM_000548.5:c.3365G>A",
+# "TSC2:p.R112H",
+# "TSC2:p.G1567D",
+# "KRAS:p.G12D",

displayStatement.js

@@ -0,0 +1,24 @@
+const { schema, sentenceTemplates } = require('@bcgsc-pori/graphkb-schema');
+
+const previewFunction = (obj) => schema.getPreview(obj);
+
+// const statement = {
+//     displayName: 'displayName',
+//     '@class': 'Statement',
+//     '@rid': '22:0',
+//     displayNameTemplate: 'Given {conditions} {relevance} applies to {subject} ({evidence})',
+//     relevance: { displayName: 'Mood Swings', '@rid': '1' },
+//     conditions: [{ displayName: 'Low blood sugar', '@class': 'Disease', '@rid': '2'  }],
+//     subject: { displayName: 'hungertitis', '@rid': '3', '@class': 'Disease'  },
+//     evidence: [{ displayName: 'A reputable source', '@rid': '4'  }],
+// };
+
+console.log('################################')
+console.log(process.argv[2])
+const statement = JSON.parse(process.argv[2])
+
+const { content } = sentenceTemplates.generateStatementSentence(previewFunction, statement);
+// Given Low blood sugar Mood Swings applies to hungertitis (A reputable source)
+
+statementLabel = schema.getPreview(content);
+console.log(statementLabel)

genes.txt

@@ -0,0 +1,56 @@
+AKT1
+APC
+ATM
+AXIN2
+BAP1
+BLM
+BMPR1A
+BRCA1
+BRCA2
+BRIP1
+CBL
+CDH1
+CDK4
+CDKN2A
+CHEK2
+DICER1
+EGFR
+EPCAM
+ETV6
+EZH2
+FH
+FLCN
+GATA2
+HRAS
+KIT
+MEN1
+MET
+MLH1
+MSH2
+MSH6
+MUTYH
+NBN
+NF1
+PALB2
+PDGFRA
+PMS2
+PTCH1
+PTEN
+PTPN11
+RAD51C
+RAD51D
+RB1
+RET
+RUNX1
+SDHA
+SDHB
+SDHC
+SDHD
+SMAD4
+SMARCA4
+STK11
+TP53
+TSC1
+TSC2
+VHL
+WT1

graphkb/constants.py

@@ -175,44 +175,47 @@ def __getitem__(self, key):
     "nonsense": ">",
 }
 
-# For match.type_screening() [KBDEV-1056]
-DEFAULT_NON_STRUCTURAL_VARIANT_TYPE = 'mutation'
+# For match.structural_type_screening() [KBDEV-1056, KBDEV-1133]
+STRUCTURAL_VARIANT_ALIASES = [
+    "rearrangement",
+    "structural variant",
+]
 STRUCTURAL_VARIANT_SIZE_THRESHOLD = 48  # bp
 STRUCTURAL_VARIANT_TYPES = [
-    "structural variant",
-    "insertion",
-    "in-frame insertion",
+    "amplification",
+    "copy gain",
+    "copy loss",
+    "copy number gain",
+    "copy number loss",
+    "copy number variant",
+    "copy number variation",
+    "copy variant",
+    "deep deletion",
     "deletion",
     "deletion polymorphism",
-    "in-frame deletion",
-    "translocation",
-    "inverted translocation",
-    "inversion",
-    "indel",
-    "fusion",
-    "out-of-frame fusion",
-    "oncogenic fusion",
-    "in-frame fusion",
     "disruptive fusion",
+    "domain duplication",
     "duplication",
+    "focal amplification",
+    "fusion",
+    "gene deletion",
+    "indel",
+    "insertion",
     "internal duplication",
-    "tandem duplication",
     "internal tandem duplication",
+    "inversion",
+    "inverted translocation",
+    "in-frame deletion",
+    "in-frame fusion",
+    "in-frame insertion",
     "itd",
-    "domain duplication",
     "kinase domain duplication",
-    "copy variant",
-    "copy number variation",
-    "copy number variant",
-    "copy loss",
-    "copy number loss",
-    "shallow deletion",
-    "deep deletion",
-    "gene deletion",
-    "copy gain",
-    "copy number gain",
     "low level copy gain",
-    "amplification",
-    "focal amplification",
+    "oncogenic fusion",
+    "out-of-frame fusion",
     "rearrangement",
+    "shallow deletion",
+    "structural variant",
+    "tandem duplication",
+    "translocation",
 ]