rxome-generator 0.1.0

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Files changed (18) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +484 -0
  3. package/demos/demo_data_full.json +149 -0
  4. package/demos/demo_data_full_compressed.json +76 -0
  5. package/demos/demo_from_gui.json +64 -0
  6. package/demos/rxome.decrypt.json +1 -0
  7. package/demos/rxome.encrypt.json +1 -0
  8. package/demos/testmessage_cipher +19 -0
  9. package/index.js +3 -0
  10. package/lib/phenopackets.json +1948 -0
  11. package/lib/rxome-api-demo.js +56 -0
  12. package/lib/rxome-api.js +119 -0
  13. package/lib/rxome-api.test.js +22 -0
  14. package/lib/rxome-generator.js +349 -0
  15. package/lib/rxome-generator.test.js +379 -0
  16. package/package.json +50 -0
  17. package/rxcode +401 -0
  18. package/rxcode.test.js +104 -0
package/demos/demo_data_full_compressed.json ADDED
@@ -0,0 +1,76 @@
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+ {
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+ "id": "QR-Code ID",
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+ "comment": "useful remarks De do do do de da da da",
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+ "subject": {
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+ "id": "proband A",
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+ "dateOfBirth": "1994-01-01T00:00:00Z",
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+ "sex": "FEMALE"
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+ },
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+ "interpretations": [
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+ {
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+ "id": "interpretation.id",
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+ "progressStatus": "SOLVED",
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+ "diagnosis": {
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+ "disease": { "id": "OMIM:263750" },
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+ "genomicInterpretations": [
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+ {
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+ "variantInterpretation": {
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+ "acmgPathogenicityClassification": "PATHOGENIC",
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+ "variationDescriptor": {
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+ "geneContext": { "valueId": "HGNC:9884", "symbol": "RB1" },
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+ "expressions": [
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+ { "syntax": "hgvs.c", "value": "NM_000321.2:c.958C>T" }
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+ ],
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+ "allelicState": { "id": "GENO:0000135" },
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+ "extensions": [
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+ { "name": "test-type", "value": "Exome, short read" }
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+ ]
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+ }
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+ }
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+ },
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+ {
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+ "variantInterpretation": {
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+ "acmgPathogenicityClassification": "LIKELY_PATHOGENIC",
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+ "variationDescriptor": {
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+ "geneContext": { "valueId": "HGNC:9884", "symbol": "RB1" },
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+ "expressions": [
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+ { "syntax": "hgvs.c", "value": "NM_000321.2:c.1234A>G" }
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+ ],
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+ "allelicState": { "label": "heterozygous" },
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+ "extensions": [
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+ { "name": "test-type", "value": "Exome, short read" }
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+ ]
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+ }
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+ }
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+ }
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+ ]
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+ }
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+ }
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+ ],
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+ "metaData": {
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+ "created": "2021-05-14T10:35:00Z",
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+ "createdBy": "mgz",
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+ "submittedBy": "a_clinician@mgz-muenchen.de",
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+ "phenopacketSchemaVersion": "2.0"
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+ },
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+ "compressedFeatures": {
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+ "includes": [
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+ "HP:0030084",
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+ "HP:0000555",
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+ "HP:0000486",
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+ "HP:0000541",
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+ "HP:0084369",
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+ "HP:0112358",
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+ "HP:0000145",
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+ "HP:1234567",
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+ "HP:9876543",
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+ "HP:5678912"
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+ ],
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+ "excludes": ["HP:0031360", "HP:0001234"]
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+ },
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+ "credentials": {
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+ "key": "QhcoRruGBVP39XCh8BujCE+q42qCRy/tu2CQ4YmRBgg=",
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+ "keyId": "mgz",
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+ "user": "a_clinician@mgz-muenchen.de"
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+ }
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+ }
package/demos/demo_from_gui.json ADDED
@@ -0,0 +1,64 @@
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+ {
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+ "subject": {
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+ "dateOfBirth": "2000-01-01",
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+ "sex": 1
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+ },
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+ "compressedFeatures": {
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+ "included": [
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+ "HP:0001250",
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+ "HP:0001249",
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+ "HP:0003155"
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+ ],
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+ "excluded": [
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+ "HP:0031360"
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+ ]
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+ },
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+ "interpretations": [
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+ {
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+ "id": "first",
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+ "progressStatus": 3,
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+ "diagnosis": {
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+ "disease": {
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+ "id": "OMIM:614207"
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+ },
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+ "genomicInterpretations": [
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+ {
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+ "subjectOrBiosampleId": "0.0",
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+ "variantInterpretation": {
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+ "acmgPathogenicityClassification": "Pathogenic",
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+ "variationDescriptor": {
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+ "geneContext": {
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+ "valueId": "26031",
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+ "symbol": "PIGV",
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+ "alternateIds": [
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+ "55650"
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+ ]
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+ },
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+ "expressions": [
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+ {
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+ "syntax": "hgvs.c",
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+ "value": "NM_017837.4(PIGV):c.1022C>A (p.Ala341Glu)"
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+ }
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+ ],
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+ "allelicState": {
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+ "id": "GENO_0000136"
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+ },
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+ "extensions": [
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+ {
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+ "name": "test-type"
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+ }
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+ ]
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+ }
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+ }
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+ }
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+ ]
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+ }
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+ }
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+ ],
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+ "metaData": {
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+ "created": "2022-10-17",
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+ "createdBy": "ACME Genetics",
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+ "submittedBy": "genetics@acme.org",
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+ "pseudonym": "PINKYANDTHEBRAIN"
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+ }
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+ }
package/demos/rxome.decrypt.json ADDED
@@ -0,0 +1 @@
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+ {"key":"\n-----BEGIN PGP PRIVATE KEY BLOCK-----\n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\nyOcQrcylWRQ4NvdK9SqsEomwxTwHkQQ=\n=YCih\n-----END PGP PRIVATE KEY BLOCK-----\n","cipher":"\n-----BEGIN PGP MESSAGE-----\n\nwV4Dhx/ATfJT0nQSAQdAkPgYRHClE5eUyl58gXBQrmZoiTtkvrOZLjnaLvFq\ncicw/28IAdW/0wuYtbd0CQf6gFMMLVmF+4Qx6OeQHehI8t+5mi7Keve1eaJp\nj2WL1TiN0lsBBbYvVdInUt3VbiywTxa+sMvfT+0crmTtsfJ6FrbD7nR22L/v\n9RgUEaY6cDrNu+PzcKGVYQj/WCqhlFflcAn+/cfcu0mRkllmbghN2uYbymff\n4M44RC1yZ0j1\n=x+N1\n-----END PGP MESSAGE-----\n"}
package/demos/rxome.encrypt.json ADDED
@@ -0,0 +1 @@
1
+ {"key":"\n-----BEGIN PGP PRIVATE KEY BLOCK-----\n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\nyOcQrcylWRQ4NvdK9SqsEomwxTwHkQQ=\n=YCih\n-----END PGP PRIVATE KEY BLOCK-----\n","message":"answer to life the universe and everything"}
package/demos/testmessage_cipher ADDED
@@ -0,0 +1,19 @@
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+ -----BEGIN PGP MESSAGE-----
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+
3
+ wV4DruMxOlc0LJISAQdAlDfQLOtEYb9sQXbZlnpT32SVLEyQv7zQW79K56oz
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+ c2owA0yACb84SftSGY83ziiruubKOOBIA1l9ItThQIeFMq+ZEFMLijiszPA6
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+ FUnEZt6m0sFoARYpdpO8fdAhOevZ3Yc8gOsyT9NUZdFKsrmyZFYwY8/tDN3i
6
+ UOwCtYgYwREKBpPCo6hN4UTASlr927i03YCvgkehnCWVnt5keAOb5bfWM8S3
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+ P/sgRfwaosvNL+UJ83ZKvRwiXMVxt4DGpI9gC9IjuKEiWygMzgBIlZQJ9qQ4
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+ uzGEH1Pqbk04iNnVUpR5KE5Fao4Dc19sy3EVSfYcsG2rkENq65hpdhhyo+9T
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+ AtW7BhzspvOCYDyCiGq1d/EhYSPtqKfnfOt3JeyWLydR8PFwKM3Y4Z3zWf9g
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+ Cum7YHwdbLmwI6xFzcIY7gc1HXoTTrEGd+3GDYL74hgj4hWOo2/A22lhDO7R
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+ yi+XnsxZwEmJqGwY75oEfh8oDzV+p4KgIibDMGv98n/1u/fVn5zpIbS44rsx
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+ mNq72ZQ3u4dEMhVIsCi5Jarf+FT3wfGemUOG0L6BENqrtfXffmuOrKOVx4eY
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+ J2+HPilGy8xrj3urzWsc9J54YyHJQW+t6Pqy30syggFPQW8ks8QdOZ/pCfMX
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+ gJbNocnvPpb/SFVXxhVw1L4D48p+ADbDYiKesmy6z3jpD2d6/4GRDuE5l/Ms
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+ U16dvH979Z/ZWMmjTrTMs8prUi8ZDp1fTN90E5ygcvi5QF0LqsevW/JJ0x4t
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+ FhPFyiXaHOzRjxJOE9DqAaDzPIRpLoGgqt8xdJdcq2FzCRz96bzdZHXRpRT8
17
+ +8Zs+/A9Ob4rYgxyG6UXpaJwzxQF
18
+ =vJT6
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+ -----END PGP MESSAGE-----
package/index.js ADDED
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+ export * from './lib/rxome-api';
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+ export * from './lib/rxome-api-demo';
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+ export * from './lib/rxome-generator';