File: api/app/routers/sessions.py:37 | Severity: Critical
_get_status_payload queries ComparisonSession by session_id alone, with no organization_id filter:
async def _get_status_payload(session_id: int, db: AsyncSession):
Ian ionox0
ionox0
/ triplanar_mapping_threejs_nodes.ts
Last active
September 5, 2024 00:15
triplanar_mapping_threejs_nodes.ts
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| import { abs, float, vec3, tslFn, vec2, vec4, sin, fract, max, normalize, mul, texture, floor, sub, min, smoothstep, mix, storage, instanceIndex, uint, uv, normalLocal, positionLocal, positionWorld, normalWorld } from '../../../three.js/examples/jsm/nodes/Nodes'; | |
| import StorageInstancedBufferAttribute from '../../../three.js/examples/jsm/renderers/common/StorageInstancedBufferAttribute'; | |
| function _PS(data: any, diffuseTex: THREE.TextureAtlas, noiseTexture: THREE.Texture ) { | |
| const TRI_SCALE = float(10.0); | |
| const TerrainBlend_4 = (d0: any, d1: any, d2: any, d3: any) => { | |
| const depth = float( 0.2 ).toVar(); |
ionox0
/ SUB1-FGFR2.tsv
Last active
August 24, 2022 20:00
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| fusion_id | direct_support | discordant_support | total_support | effect | topo | chr3 | exon3 | gene3 | transcript3 | bp3 | chr5 | exon5 | gene5 | transcript5 | bp5 | new_whitelist | new_reportable | self_fusion | is_hard_filtered | meets_support_criteria | contains_relevant_domains_3 | contains_relevant_domains_5 | fusion_domains | order_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| be1f8268-44ee-4c99-b0db-e4766db2c977 | 30 | 28 | 58 | in-frame | NaN | 10 | 18.0 | FGFR2 | ENST00000457416 | 123242706 | 5 | 2.0 | SUB1 | ENST00000265073 | 32589733 | False | False | False | False | False | False | False | [] | 22fwudfy | |
| 24a800ce-1d7b-4ce8-9c9a-041508bbbc99 | 30 | 28 | 58 | in-frame | NaN | 5 | 3.0 | SUB1 | ENST00000265073 | 32589733 | 10 | 17.0 | FGFR2 | ENST00000457416 | 123242706 | False | False | False | False | False | False | True | [] | 22fwudfy |
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| class: Workflow | |
| cwlVersion: v1.0 | |
| id: access_qc_aggregator | |
| label: access_qc_aggregator | |
| $namespaces: | |
| sbg: 'https://www.sevenbridges.com/' | |
| inputs: | |
| - id: duplex_extraction_files | |
| type: | |
| type: array |
ionox0
/ find_duplicate_fastq_requests.py
Last active
April 7, 2021 20:15
find_duplicate_fastq_requests
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| access_filems = FileMetadata.objects.filter(metadata__recipe='MSK-ACCESS_v1', file__file_type__name='fastq') | |
| access_request_ids = set([f.metadata['requestId'] for f in access_filems]) | |
| # --> 103 ACCESS request IDs total | |
| duplicates = File.objects\ | |
| .filter( | |
| filemetadata__metadata__requestId__in=access_request_ids, | |
| file_type__name='fastq' |
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| /work/access/production/runs/voyager/staging/small_variants/50948a4f-c4b8-4856-97e5-ece000ddc3d4 | |
| /work/access/production/runs/voyager/staging/small_variants/7511548f-f695-497e-9558-51b3d63d27ac | |
| /work/access/production/runs/voyager/staging/small_variants/a99cf55e-ad09-44f6-b50e-44cf4169960b | |
| /work/access/production/runs/voyager/staging/small_variants/fcee2eec-7a7f-4eba-9bfa-841e5234f49f | |
| /work/access/production/runs/voyager/staging/small_variants/7cc7c0c1-b1d5-477a-909e-897362ba3cb5 | |
| /work/access/production/runs/voyager/staging/small_variants/547fc37c-fd79-4de1-9013-86f69fb89c27 | |
| /work/access/production/runs/voyager/staging/small_variants/85189928-d546-4be0-8542-983d556c16a1 | |
| /work/access/production/runs/voyager/staging/small_variants/430b9606-2583-441e-8a2d-f216a4ed97e5 | |
| /work/access/production/runs/voyager/staging/small_variants/eabeb028-0d6e-48e8-aff5-33d1f0be99ce | |
| /work/access/production/runs/voyager/staging/small_variants/f44cfe07-e633-4c48-92dd-2a22ccc6a83e |
ionox0
/ import_access_cnv_and_msi_resources.py
Last active
January 4, 2021 20:57
import_access_cnv_and_msi_resources.py
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| import json | |
| import requests | |
| paths = [ | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/curated_normal_manifest.txt", | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/ACCESS_targets_coverage.bed", | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/ACCESS_targets_coverage.txt", | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/microsatellites.list", | |
| "/juno/work/access/production/resources/admie/versions/v1.0/ADMIE.joblib" | |
| ] |
ionox0
/ import_access_reference_files.py
Last active
January 27, 2021 19:23
import_access_reference_files.py
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| import requests | |
| gene_list = { | |
| 'path': '/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/juber-hg19-gene-list.bed', | |
| 'file_type': 'bed', | |
| } | |
| hotspots = { | |
| 'path': '/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/hotspot-list-union-v1-v2_with_TERT.txt', | |
| 'file_type': 'txt', |
ionox0
/ ACCESS_variant_calling_parameters.yaml
Last active
September 22, 2020 20:53
ACCESS_variant_calling_parameters.yaml
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| # Params | |
| mutect_params: | |
| dcov: 5000 | |
| read_filter: ['BadCigar'] | |
| fraction_contamination: 0.0005 | |
| minimum_mutation_cell_fraction: 0.0005 | |
| vardict_params: | |
| allele_freq_thres: 0.0005 | |
| min_num_variant_reads: 1 |
ionox0
/ optimize_meetings_dp.py
Created
March 16, 2020 17:22
dynamic programming for scheduling meetings of varying length given max available time
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| def optimize_meetings(meetings, max_time): | |
| memo = [[0] * (max_time + 1) for _ in range(len(meetings) + 1)] | |
| for i in range(len(meetings) + 1): | |
| if i == 0: continue | |
| for j in range(max_time + 1): | |
| cur_mtg = meetings[i - 1] | |
| index = j - cur_mtg |
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