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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from ga4gh.core import ga4gh_identify\n", | ||
| "from ga4gh.vrs import models" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 17, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "cpb = models.CisPhasedBlock(\n", | ||
| " members=[\n", | ||
| " models.Allele(\n", | ||
| " location=models.SequenceLocation(start=1, end=2),\n", | ||
| " state=models.LiteralSequenceExpression(sequence=\"C\")\n", | ||
| " ),\n", | ||
| " models.Allele(\n", | ||
| " location=models.SequenceLocation(start=3, end=4),\n", | ||
| " state=models.LiteralSequenceExpression(sequence=\"T\")\n", | ||
| " )\n", | ||
| " ],\n", | ||
| " sequenceReference=models.SequenceReference(\n", | ||
| " refgetAccession=\"SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU\"\n", | ||
| " )\n", | ||
| ")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "ename": "AttributeError", | ||
| "evalue": "This class does not support prior version identifiers.", | ||
| "output_type": "error", | ||
| "traceback": [ | ||
| "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", | ||
| "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", | ||
| "File \u001b[0;32m~/Documents/git/ga4gh/vrs-python/src/ga4gh/vrs/models.py:245\u001b[0m, in \u001b[0;36m_Ga4ghIdentifiableObject.compute_digest\u001b[0;34m(self, store, as_version)\u001b[0m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 245\u001b[0m digest \u001b[38;5;241m=\u001b[39m sha512t24u(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mga4gh_serialize_as_version\u001b[49m(as_version)\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m\"\u001b[39m))\n\u001b[1;32m 246\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mAttributeError\u001b[39;00m:\n", | ||
| "File \u001b[0;32m~/Documents/git/ga4gh/vrs-python/venv/lib/python3.10/site-packages/pydantic/main.py:828\u001b[0m, in \u001b[0;36mBaseModel.__getattr__\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m 826\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 827\u001b[0m \u001b[38;5;66;03m# this is the current error\u001b[39;00m\n\u001b[0;32m--> 828\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mAttributeError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mtype\u001b[39m(\u001b[38;5;28mself\u001b[39m)\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m object has no attribute \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mitem\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n", | ||
| "\u001b[0;31mAttributeError\u001b[0m: 'CisPhasedBlock' object has no attribute 'ga4gh_serialize_as_version'", | ||
| "\nDuring handling of the above exception, another exception occurred:\n", | ||
| "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", | ||
| "Cell \u001b[0;32mIn[18], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mga4gh_identify\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcpb\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mas_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m1.3\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n", | ||
| "File \u001b[0;32m~/Documents/git/ga4gh/vrs-python/src/ga4gh/core/identifiers.py:165\u001b[0m, in \u001b[0;36mga4gh_identify\u001b[0;34m(vro, in_place, as_version)\u001b[0m\n\u001b[1;32m 162\u001b[0m do_compute \u001b[38;5;241m=\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m vro\u001b[38;5;241m.\u001b[39mhas_valid_ga4gh_id()\n\u001b[1;32m 164\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m do_compute:\n\u001b[0;32m--> 165\u001b[0m obj_id \u001b[38;5;241m=\u001b[39m \u001b[43mvro\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_or_create_ga4gh_identifier\u001b[49m\u001b[43m(\u001b[49m\u001b[43min_place\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mas_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mas_version\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 167\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m obj_id\n\u001b[1;32m 169\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n", | ||
| "File \u001b[0;32m~/Documents/git/ga4gh/vrs-python/src/ga4gh/vrs/models.py:270\u001b[0m, in \u001b[0;36m_Ga4ghIdentifiableObject.get_or_create_ga4gh_identifier\u001b[0;34m(self, in_place, recompute, as_version)\u001b[0m\n\u001b[1;32m 251\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Sets and returns a GA4GH Computed Identifier for the object.\u001b[39;00m\n\u001b[1;32m 252\u001b[0m \u001b[38;5;124;03mOverwrites the existing identifier if overwrite is True.\u001b[39;00m\n\u001b[1;32m 253\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 267\u001b[0m \u001b[38;5;124;03mthe VRS version indicated by 'as_version'.\u001b[39;00m\n\u001b[1;32m 268\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m as_version \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 270\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcompute_ga4gh_identifier\u001b[49m\u001b[43m(\u001b[49m\u001b[43mas_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mas_version\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 272\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m in_place \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdefault\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 273\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mid \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", | ||
| "File \u001b[0;32m~/Documents/git/ga4gh/vrs-python/src/ga4gh/vrs/models.py:298\u001b[0m, in \u001b[0;36m_Ga4ghIdentifiableObject.compute_ga4gh_identifier\u001b[0;34m(self, recompute, as_version)\u001b[0m\n\u001b[1;32m 296\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mCURIE_NAMESPACE\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mCURIE_SEP\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mga4gh\u001b[38;5;241m.\u001b[39mprefix\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mGA4GH_PREFIX_SEP\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdigest\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 297\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 298\u001b[0m digest \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcompute_digest\u001b[49m\u001b[43m(\u001b[49m\u001b[43mas_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mas_version\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 299\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mCURIE_NAMESPACE\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mCURIE_SEP\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mga4gh\u001b[38;5;241m.\u001b[39mpriorPrefix[as_version]\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mGA4GH_PREFIX_SEP\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mdigest\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n", | ||
| "File \u001b[0;32m~/Documents/git/ga4gh/vrs-python/src/ga4gh/vrs/models.py:247\u001b[0m, in \u001b[0;36m_Ga4ghIdentifiableObject.compute_digest\u001b[0;34m(self, store, as_version)\u001b[0m\n\u001b[1;32m 245\u001b[0m digest \u001b[38;5;241m=\u001b[39m sha512t24u(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mga4gh_serialize_as_version(as_version)\u001b[38;5;241m.\u001b[39mencode(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mutf-8\u001b[39m\u001b[38;5;124m\"\u001b[39m))\n\u001b[1;32m 246\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mAttributeError\u001b[39;00m:\n\u001b[0;32m--> 247\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mAttributeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mThis class does not support prior version identifiers.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 248\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m digest\n", | ||
| "\u001b[0;31mAttributeError\u001b[0m: This class does not support prior version identifiers." | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "ga4gh_identify(cpb, as_version=\"1.3\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'ga4gh:SL.aoRy21xCtDozd151eDZmVTm6cejLNxt9'" | ||
| ] | ||
| }, | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "ga4gh_identify(sl)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "venv", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.10.14" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 2 | ||
| } |
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