scout-browser 4.90.1__py3-none-any.whl → 4.91.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scout/__version__.py +1 -1
- scout/adapter/mongo/case.py +27 -38
- scout/commands/export/variant.py +14 -4
- scout/commands/load/panel.py +2 -1
- scout/commands/update/panelapp.py +11 -3
- scout/commands/view/case.py +2 -2
- scout/constants/__init__.py +1 -2
- scout/constants/acmg.py +15 -15
- scout/constants/case_tags.py +0 -46
- scout/constants/clnsig.py +2 -1
- scout/constants/gene_tags.py +0 -6
- scout/constants/panels.py +16 -0
- scout/constants/variants_export.py +2 -0
- scout/demo/__init__.py +4 -1
- scout/demo/panelapp_panel.json +463 -0
- scout/demo/panelapp_panels_reduced.json +37 -0
- scout/load/panel.py +3 -142
- scout/load/panelapp.py +138 -0
- scout/models/case/case_loading_models.py +5 -4
- scout/parse/panel.py +3 -117
- scout/parse/panelapp.py +112 -0
- scout/parse/variant/clnsig.py +26 -21
- scout/parse/variant/genotype.py +6 -5
- scout/server/blueprints/alignviewers/controllers.py +7 -5
- scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
- scout/server/blueprints/cases/templates/cases/case_sma.html +49 -42
- scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +27 -12
- scout/server/blueprints/cases/views.py +18 -7
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +7 -7
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +2 -2
- scout/server/blueprints/dashboard/controllers.py +128 -165
- scout/server/blueprints/dashboard/forms.py +3 -13
- scout/server/blueprints/dashboard/templates/dashboard/dashboard_general.html +17 -22
- scout/server/blueprints/institutes/forms.py +1 -2
- scout/server/blueprints/institutes/templates/overview/cases.html +2 -133
- scout/server/blueprints/institutes/templates/overview/utils.html +135 -0
- scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +5 -0
- scout/server/blueprints/panels/templates/panels/panel.html +5 -1
- scout/server/blueprints/panels/templates/panels/panel_pdf_simple.html +5 -1
- scout/server/blueprints/variant/controllers.py +6 -1
- scout/server/blueprints/variant/templates/variant/buttons.html +11 -10
- scout/server/blueprints/variant/templates/variant/components.html +63 -44
- scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html +1 -1
- scout/server/blueprints/variant/templates/variant/utils.html +38 -10
- scout/server/blueprints/variant/templates/variant/variant.html +1 -1
- scout/server/blueprints/variants/controllers.py +9 -4
- scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html +10 -6
- scout/server/blueprints/variants/templates/variants/cancer-variants.html +6 -17
- scout/server/blueprints/variants/templates/variants/str-variants.html +2 -2
- scout/server/blueprints/variants/templates/variants/sv-variants.html +7 -4
- scout/server/blueprints/variants/templates/variants/utils.html +14 -0
- scout/server/extensions/__init__.py +2 -0
- scout/server/extensions/panelapp_extension.py +75 -0
- scout/server/links.py +19 -1
- scout/server/utils.py +25 -33
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.1.dist-info}/METADATA +1 -1
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.1.dist-info}/RECORD +61 -57
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.1.dist-info}/WHEEL +1 -1
- scout/demo/panelapp_test_panel.json +0 -79
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.1.dist-info}/LICENSE +0 -0
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.1.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.90.1.dist-info → scout_browser-4.91.1.dist-info}/top_level.txt +0 -0
scout/server/utils.py
CHANGED
@@ -297,51 +297,43 @@ def _check_path_name(ind: Dict, path_name: str) -> bool:
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return False
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def case_append_alignments(case_obj):
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def case_append_alignments(case_obj: dict):
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"""Deconvolute information about files to case_obj.
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This function prepares
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the templates.
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Loops over the the individuals and gather bam/cram files, indexes and sample display names in
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lists
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Args:
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case_obj(scout.models.Case)
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This function prepares bam/cram files and their indexes for easy access in templates.
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"""
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unwrap_settings = [
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{"path": "bam_file", "append_to": "bam_files", "index": "bai_files"},
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{"path": "mt_bam", "append_to": "mt_bams", "index": "mt_bais"},
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{"path": "rhocall_bed", "append_to": "rhocall_beds", "index":
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{"path": "rhocall_wig", "append_to": "rhocall_wigs", "index":
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{
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"index": "no_index",
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},
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{"path": "upd_sites_bed", "append_to": "upd_sites_beds", "index": "no_index"},
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{
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"path": "tiddit_coverage_wig",
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"append_to": "tiddit_coverage_wigs",
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"index": "no_index",
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},
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{"path": "rhocall_bed", "append_to": "rhocall_beds", "index": None},
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{"path": "rhocall_wig", "append_to": "rhocall_wigs", "index": None},
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{"path": "upd_regions_bed", "append_to": "upd_regions_beds", "index": None},
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{"path": "upd_sites_bed", "append_to": "upd_sites_beds", "index": None},
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{"path": "tiddit_coverage_wig", "append_to": "tiddit_coverage_wigs", "index": None},
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]
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def process_file(case_obj, individual, setting):
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"""Process a single file and its optional index."""
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file_path = individual.get(setting["path"])
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append_safe(
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case_obj,
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"
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setting["append_to"],
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file_path if file_path and os.path.exists(file_path) else "missing",
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)
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if setting["index"]:
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index_path = (
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find_index(file_path) if file_path and os.path.exists(file_path) else "missing"
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)
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append_safe(case_obj, setting["index"], index_path)
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for individual in case_obj["individuals"]:
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# Add sample name
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sample_name = f"{case_obj.get('display_name', '')} - {individual.get('display_name', '')}"
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append_safe(case_obj, "sample_names", sample_name)
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# Process all file settings
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for setting in unwrap_settings:
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if not (file_path and os.path.exists(file_path)):
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continue
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append_safe(case_obj, setting["append_to"], file_path)
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if not setting["index"] == "no_index":
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append_safe(
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case_obj, setting["index"], find_index(file_path)
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) # either bai_files or mt_bais
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process_file(case_obj, individual, setting)
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def append_safe(obj, obj_index, elem):
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scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
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scout/__version__.py,sha256=
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scout/__version__.py,sha256=UEW2jG2n4LaWe4lbBdEuuVDJFg2ITmLfH-vIghRM4ms,23
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scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
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scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
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scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
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scout/adapter/mongo/acmg.py,sha256=v2Zuw-6APVmcnBnNXa18WJEu2vj5GUhZNiKMkruJsBI,4170
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scout/adapter/mongo/base.py,sha256=yiaEmybAjLiCdAKouT0TET9aM2U-PtQm3En52MHR7Zs,4340
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scout/adapter/mongo/case.py,sha256=
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scout/adapter/mongo/case.py,sha256=mNqtFwmFcdAHNTjiIrRNzbXbPvYeUA_yCjMt9d2K2xw,63931
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scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
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scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
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scout/adapter/mongo/clinvar.py,sha256=tczC39O3DFDkYgjt2RDgkkG-x1Mvx_99Hw7dAbIQ5gk,19838
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@@ -80,14 +80,14 @@ scout/commands/export/mitochondrial_report.py,sha256=vglirazMK0gVgl6FMzls4ZhMQI_
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scout/commands/export/panel.py,sha256=Tt4wPxptpNKHHwKrYyPIkR0eIz6ad6-MB98_PRFFYW4,1336
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scout/commands/export/transcript.py,sha256=J92-ZIyVaarPFyajiqr9_RlpCbdWtTpbPd5VpRWyYLs,1024
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scout/commands/export/utils.py,sha256=kvm7OaLCzPVaC0HnQLO_034akDc0nlPFWLtLe8P2a10,300
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scout/commands/export/variant.py,sha256=
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scout/commands/export/variant.py,sha256=p7H6KMR_Ysr2GF66RnXYjZ9yPB_B3K8ofyOYNFDoAW4,7502
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scout/commands/load/__init__.py,sha256=qwXkYqeL2oNJ1zoWh_83Np4JjwWWwQqp5L9vTOC6VS0,23
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scout/commands/load/base.py,sha256=4dU7CdTPpAhsLaw20eRTJ2MRyEsPGJK33F6em0TxDnI,1406
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scout/commands/load/case.py,sha256=BD-qoDp5GjVBfTgUM8MihCoNWVgOysOviHO6kqkfcWY,4150
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scout/commands/load/cytoband.py,sha256=mPIL7RrcENUtY8oXpKp_Ej69jdvk6M5ax3KlWEvXWeA,935
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scout/commands/load/exons.py,sha256=isxBFR0is5TFvv4j0PHB4KqmHFJHQ0TLQBudrjKmuUI,1887
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scout/commands/load/institute.py,sha256=EYbDeWmpeRl0_jBnsckAp6qua5VyZKpczoHfADfYIDQ,1060
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scout/commands/load/panel.py,sha256=
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scout/commands/load/panel.py,sha256=kx6HpFYcYgPwTLsgarjM7eL43bkZwpPj__I_gqjGN60,2925
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scout/commands/load/region.py,sha256=psICLlMf5WBdSCgXsJZUsM8fICsTJB3Q6U6dB5S6w_8,869
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scout/commands/load/report.py,sha256=DrnyOJcLbOUUJHzI3jwlj955zYohvjuTeeoeUS_ZU8Q,3564
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scout/commands/load/research.py,sha256=6GBKJY3POQyGxfPwcfj06tcCX48CBTZqq8MSdjevBjM,4426
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scout/commands/update/institute.py,sha256=ms8mmTGfCXqxeh_vSB1cdNDGrdHoSSgh9ryhB5GrJQc,1727
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scout/commands/update/omim.py,sha256=s39qterBGhtBfW7Uc-IJabni93PIhT8shqVbkmQBb9k,2309
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scout/commands/update/panel.py,sha256=990shZ15k5pwHUkd767o8oQ5iqVIpgRA7N_9yv1_eqc,2912
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scout/commands/update/panelapp.py,sha256=
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scout/commands/update/panelapp.py,sha256=UZ-k0UpVTM-scSg_pZdih84ZbYdTBtllouM87iMDx_0,1460
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scout/commands/update/phenotype_groups.py,sha256=Ll0COlEckn1Z7VAJbFbG2EZ5FKFVEcff0sWiUsx-D-g,1980
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scout/commands/update/user.py,sha256=s5s7nh9UABBO9P6L11_j5tsi4iPxzieHw40yDhc4PWM,2497
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scout/commands/view/__init__.py,sha256=ZtRW7UBNf1rPnlCslBVcmjafOPg9WTPpn4xxlAA0wMo,23
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scout/commands/view/aliases.py,sha256=M0hTBHk_cyW-BG0cNz5T3q20waYP4ktTfTCzCtkTUs0,1995
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scout/commands/view/base.py,sha256=Lz2cB7yTPjHXLgDu3aumHm6d4ozAKEA5V5ff1NAT4wA,1000
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scout/commands/view/case.py,sha256=
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scout/commands/view/case.py,sha256=O66_4bk7GOipdqP0Eza0xw9DFkh6e7wIAc7_egC2o8A,3266
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scout/commands/view/collections.py,sha256=RsO941NK29TJs1mWtof2qGhxqWlj7oBTu8WFIjzxnxs,453
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scout/commands/view/diseases.py,sha256=XJWz6xrIsyCbdA9-6XDXyRiSnv1oQ-eRZur3BdQ8Tr8,704
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scout/commands/view/hgnc.py,sha256=VQcDnYuDbcfkh9mxUJgZwXMAymj449By4NjXNwRfb18,1304
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scout/commands/view/panels.py,sha256=a0fQcP9-SDPuRYV7aEgIGUCYaMN6V47h6finpcdoomU,1098
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scout/commands/view/transcripts.py,sha256=59WyNNp7zHPJIz9QgzrkoeKaSXTtuLli0VuL8IidEmY,1277
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scout/commands/view/users.py,sha256=MKlmhDYRM7Yf-Trmi1ijEuqsDIUn326bdFADyDs7XYg,832
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scout/constants/__init__.py,sha256=
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scout/constants/acmg.py,sha256=
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scout/constants/case_tags.py,sha256=
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scout/constants/__init__.py,sha256=HZvAMX-37ugK0fRwa8xKGvnZkicyUJH-SH2pqw7rm-g,5760
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scout/constants/acmg.py,sha256=hYPzoLUqpuTjGXfIN80Nb1njriesH9oAELu1scp-ByU,18083
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scout/constants/case_tags.py,sha256=EvLYtbZADyFEngeY8rvPsJ_1NdLmHrlnrGTlnj7tGGs,9336
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scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
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scout/constants/clnsig.py,sha256=
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scout/constants/clnsig.py,sha256=5Z4fZU__ej9teXK4hD9vGhIGmaGL6PoJqK5GuzLWxpE,1414
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scout/constants/disease_parsing.py,sha256=M9_OgsN88oXwKH_XpxdDma0zuWPRoHFQjL19tzojBPo,686
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scout/constants/file_types.py,sha256=3BU2cw40cHMT5IzEGEF_SsIhgYUbnIlUCRmwmB01fzI,3046
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scout/constants/filters.py,sha256=1bcj-z7__yv5eQpjB60wqSHZ3U5U0CVyNbcYT-Wn-vc,957
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scout/constants/gene_tags.py,sha256=
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scout/constants/gene_tags.py,sha256=pRRsjn9zYGR3nLFKxe1gOYqWm4uQbpfxYzfRxcptxqA,3856
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scout/constants/igv_tracks.py,sha256=NbBBnM3s1S8cJM_S36qi7SU2ACW_lJVS6EP2W0kCTIQ,4697
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scout/constants/indexes.py,sha256=-rb5VP68Arl2t-bFDYWiQswAF3YxjrAJVuMtQWrT__8,5497
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scout/constants/panels.py,sha256=
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scout/constants/panels.py,sha256=X38XGPlNgOGhXHt5mSpryOS7gMeP-tUD1t1WIT2G5wM,785
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scout/constants/phenotype.py,sha256=MrbXirisR_7GPnxV3NOj3-BoM9CvtGgFZj7PfJu85RM,2331
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scout/constants/query_terms.py,sha256=2A4CuTgc7W_VMj4atkJdZFfvBATu7OQg51udFM0rMOo,1574
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scout/constants/so_terms.py,sha256=aJcQv3wgpZylVhqSJH854WS8xSARDxWGnW6I5mG1egE,4321
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scout/constants/variant_tags.py,sha256=LxE_jTF5hk9M-lU7nAl1mdhpctatYwO91BLfVgN3qCQ,17919
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scout/constants/variants_export.py,sha256=
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scout/constants/variants_export.py,sha256=uQvFsbRMdbgl39HUdGWzFAEe1KOHp5OgvhjbGMD3O_Q,1969
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scout/demo/643594.clinical.SV.vcf.gz,sha256=Y5CcTI7vJAS53ch8OHPR80X44rArHZoQeQZGl8AHmq0,11927
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scout/demo/643594.clinical.SV.vcf.gz.tbi,sha256=1CPB8ftoYF3gjRfqG0xMQlVMD1lY0xSdXp_KrJbfzac,1284
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scout/demo/ADM1059A2.test.cgh,sha256=29YOnGgPB3wxWwxVwf_mCLrhZ4Cf5hqVxw_DUggBe7Y,29
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scout/demo/__init__.py,sha256=ggXVz3_6ZUAzIZtuaK8kz3C6BuxSfaQ56PAzinJcYoI,2061
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{
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