scout-browser 4.96.0__py3-none-any.whl → 4.98.0__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/adapter/mongo/case.py +51 -47
- scout/adapter/mongo/filter.py +28 -11
- scout/adapter/mongo/institute.py +2 -0
- scout/adapter/mongo/omics_variant.py +20 -5
- scout/adapter/mongo/query.py +104 -95
- scout/adapter/mongo/variant.py +0 -5
- scout/adapter/mongo/variant_loader.py +10 -12
- scout/build/individual.py +3 -11
- scout/commands/delete/delete_command.py +87 -49
- scout/commands/load/research.py +4 -4
- scout/commands/load/variants.py +25 -8
- scout/commands/setup/setup_scout.py +1 -1
- scout/commands/update/case.py +12 -0
- scout/commands/update/individual.py +1 -2
- scout/constants/__init__.py +7 -2
- scout/constants/file_types.py +68 -119
- scout/constants/filters.py +2 -1
- scout/constants/gene_tags.py +3 -3
- scout/constants/igv_tracks.py +7 -11
- scout/constants/query_terms.py +2 -2
- scout/demo/643594.config.yaml +6 -0
- scout/demo/643594.peddy.ped +1 -1
- scout/demo/643594.somalier.ancestry.tsv +4 -0
- scout/demo/643594.somalier.pairs.tsv +4 -0
- scout/demo/643594.somalier.samples.tsv +4 -0
- scout/demo/cancer.load_config.yaml +1 -0
- scout/demo/resources/__init__.py +1 -1
- scout/demo/resources/gnomad.v4.1.constraint_metrics_reduced.tsv +3755 -0
- scout/exceptions/database.py +1 -1
- scout/load/all.py +8 -16
- scout/models/case/case.py +1 -0
- scout/models/case/case_loading_models.py +12 -5
- scout/models/managed_variant.py +3 -3
- scout/models/omics_variant.py +3 -3
- scout/parse/case.py +112 -5
- scout/parse/pedqc.py +127 -0
- scout/parse/variant/frequency.py +9 -6
- scout/parse/variant/variant.py +71 -39
- scout/server/app.py +2 -0
- scout/server/blueprints/alignviewers/controllers.py +2 -0
- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +3 -0
- scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
- scout/server/blueprints/cases/controllers.py +23 -3
- scout/server/blueprints/cases/templates/cases/case.html +3 -0
- scout/server/blueprints/cases/templates/cases/chanjo2_form.html +2 -2
- scout/server/blueprints/cases/templates/cases/gene_panel.html +9 -3
- scout/server/blueprints/cases/templates/cases/individuals_table.html +4 -1
- scout/server/blueprints/cases/templates/cases/utils.html +23 -19
- scout/server/blueprints/cases/views.py +5 -9
- scout/server/blueprints/clinvar/controllers.py +11 -11
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +15 -7
- scout/server/blueprints/institutes/controllers.py +20 -1
- scout/server/blueprints/institutes/forms.py +5 -1
- scout/server/blueprints/institutes/templates/overview/filters.html +14 -1
- scout/server/blueprints/institutes/templates/overview/institute_settings.html +7 -0
- scout/server/blueprints/institutes/templates/overview/utils.html +20 -1
- scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +9 -2
- scout/server/blueprints/omics_variants/views.py +8 -10
- scout/server/blueprints/variant/controllers.py +30 -1
- scout/server/blueprints/variant/templates/variant/cancer-variant.html +19 -3
- scout/server/blueprints/variant/templates/variant/components.html +26 -9
- scout/server/blueprints/variant/templates/variant/variant.html +4 -2
- scout/server/blueprints/variant/utils.py +2 -0
- scout/server/blueprints/variants/controllers.py +29 -3
- scout/server/blueprints/variants/forms.py +37 -10
- scout/server/blueprints/variants/templates/variants/components.html +12 -10
- scout/server/blueprints/variants/templates/variants/utils.html +59 -36
- scout/server/blueprints/variants/views.py +45 -60
- scout/server/extensions/beacon_extension.py +1 -1
- scout/server/extensions/bionano_extension.py +5 -5
- scout/server/extensions/chanjo2_extension.py +40 -1
- scout/server/extensions/chanjo_extension.py +1 -1
- scout/server/extensions/matchmaker_extension.py +1 -1
- scout/server/static/bs_styles.css +2 -0
- scout/server/templates/layout.html +1 -0
- scout/server/utils.py +5 -0
- scout/utils/ensembl_biomart_clients.py +2 -11
- scout/utils/scout_requests.py +1 -1
- {scout_browser-4.96.0.dist-info → scout_browser-4.98.0.dist-info}/METADATA +1 -1
- {scout_browser-4.96.0.dist-info → scout_browser-4.98.0.dist-info}/RECORD +83 -81
- scout/demo/resources/gnomad.v4.0.constraint_metrics_reduced.tsv +0 -3755
- scout/parse/peddy.py +0 -149
- scout/utils/sort.py +0 -21
- {scout_browser-4.96.0.dist-info → scout_browser-4.98.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.96.0.dist-info → scout_browser-4.98.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.96.0.dist-info → scout_browser-4.98.0.dist-info}/licenses/LICENSE +0 -0
@@ -4,7 +4,7 @@ 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=iIa2AjGNztKHcZzolY0T6r7Oh0guj6R1putztp4OTNY,4427
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scout/adapter/mongo/case.py,sha256=
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scout/adapter/mongo/case.py,sha256=Z1RuWHRm_5sddOujntFbj8fGhg9AdgUgrUb2Qqapiug,65353
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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/ccv.py,sha256=VIz-Yqzm-1UVPDKvZkBllO4BOKXzvKCXcQUjTtZCHTI,4165
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@@ -12,30 +12,30 @@ scout/adapter/mongo/clinvar.py,sha256=tczC39O3DFDkYgjt2RDgkkG-x1Mvx_99Hw7dAbIQ5g
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scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7uQ,2622
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scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
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scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
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scout/adapter/mongo/filter.py,sha256=
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scout/adapter/mongo/filter.py,sha256=rIdjiDJCrNDeTNgssKm7n1HTxne72jvlX2I3FQjQGo8,9687
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scout/adapter/mongo/hgnc.py,sha256=P80WdIFkpFDeR6Pa0H-pgeScGrZdCviWVL4rqR5Aqvk,16547
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scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
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scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
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scout/adapter/mongo/institute.py,sha256=
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scout/adapter/mongo/institute.py,sha256=X_lQHSqSfMvE4PUb-txLvdjWqwdkEcNwUAq_9p6ay8A,7112
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scout/adapter/mongo/managed_variant.py,sha256=mPbp64nMDwAij8zvBbFGjI3MLbk6CC-OO9RTwtEIi44,8451
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scout/adapter/mongo/matchmaker.py,sha256=amTvFOlUbrt1RmecY_8hPY6bO3j79lc2UbmzlCQcRuk,6378
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scout/adapter/mongo/omics_variant.py,sha256=
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scout/adapter/mongo/omics_variant.py,sha256=rgfHZYElFDNeh9Atx-oNhS3PbKbiDWn4JABGPZ33Vzk,8024
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scout/adapter/mongo/panel.py,sha256=d1oMEYAiDGybLmlbbf3-fQdCdU0-T7x2XdIUwZGthYk,20031
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scout/adapter/mongo/phenomodel.py,sha256=cypSS8YRzu98Bf1kC0orfrLNn_ZQSYCK8e4mNR5PaPY,2572
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scout/adapter/mongo/query.py,sha256=
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scout/adapter/mongo/query.py,sha256=DqgpPGm9n3lmReHfVMGUNVCTvvMltRXSzaeYW5tDaXc,35327
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scout/adapter/mongo/rank_model.py,sha256=wvDNI4OLf-f7ZYZ_Q_6qi0myxOJCNNJR_-2-_0u2K2M,5712
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scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt8NMY,7417
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scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
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scout/adapter/mongo/variant.py,sha256=
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scout/adapter/mongo/variant.py,sha256=r4CJ3yus3HKTdIHHKtrRitQkN3syuMy8pkWPgR7XyAc,35044
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scout/adapter/mongo/variant_events.py,sha256=yNnMM58P1LbYFw73rWzti6l2zWa_G93ozUTbVkcz4_I,33475
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scout/adapter/mongo/variant_loader.py,sha256=
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scout/adapter/mongo/variant_loader.py,sha256=qay1v-LNYTAkOVeeKSuJhU6abYO_U26woAdvoyAgGsI,28205
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scout/build/__init__.py,sha256=GUWEaXTpwsJil_KtrXBQJpZIwCQFSgo8NlK49R9IkA8,521
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scout/build/acmg.py,sha256=M21MrrP_dtEyOuu6t-jBDdaqYcHPMLcwJlt9fHG2ycE,1523
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scout/build/case.py,sha256=LtYx6zQcCoGCss48qf7uluzTlXVH0Pl-WhqYzkbIcZ8,11510
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scout/build/ccv.py,sha256=cfAWSQ5cSBWURkL9_fPm1Y5aRcTIDOE9ieSWaYLufB4,1660
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scout/build/disease.py,sha256=Zew9AF_z1NbbKcO3uJZ2wgni501SkfnYRgnaCZ4m8FY,2020
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scout/build/hpo.py,sha256=LJBCTq-x09D0CSKcUHB8a6ynuUrVh_7Ia0ooA1BxMys,1207
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scout/build/individual.py,sha256=
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scout/build/individual.py,sha256=pLImS_cTrDSaSPlBT6sonGUZCeWUik3jni4X81CQfsE,5132
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scout/build/institute.py,sha256=CZKn-cFbh0cWO2ySoRV_P1nYFizlyvu50LKrtAz-PLo,1330
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scout/build/managed_variant.py,sha256=krcQBc4LLxlnUQwXuV2FxNLiSkMoIkLxQueYFl04Vyo,1666
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scout/build/panel.py,sha256=smhtynG_ggNgUyuAGqg_-m1UMnBHhrk2ALutYoNTTec,4273
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@@ -59,7 +59,7 @@ scout/commands/serve.py,sha256=OZRHJrvlIXz1NQ1NHB175TxTxgpblybIPIob0PIvDXk,1554
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scout/commands/utils.py,sha256=T29f-1wTq3uoxqtv6QOqBdMBl7tLeEn8DYXnnv3gowI,306
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scout/commands/wipe_database.py,sha256=TvCoXZCT-mvTqsZaFstV5u5FM8KAQstB3JxyGHYMLtg,1005
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scout/commands/delete/__init__.py,sha256=6Z97FsWMqyKqF64Anl1zwljVNTfjJUCI7yylxIEnsUY,35
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scout/commands/delete/delete_command.py,sha256=
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scout/commands/delete/delete_command.py,sha256=c-cWdtc0VCLVLL5hpMxSuyaBiYCppm403eRoLhD1SSo,14568
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scout/commands/download/__init__.py,sha256=mfDzxqKzJ0LgfPBN_fehkdX5BPy1FJ3rauA3ORLIjCM,39
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scout/commands/download/download_command.py,sha256=m5CKefst3qhs4urfNu1A2TERisUb_5WPn-wn9bGCDr0,736
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scout/commands/download/ensembl.py,sha256=CsTMjYihBtXyfofNIQ2riL9UBzydDbqoNZ7jJVQ15ak,2112
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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=
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scout/commands/load/research.py,sha256=7B-Xo5oAHB69szKp4nQM-vITVKstLQ8zLkaQ3TtiMiw,4458
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scout/commands/load/user.py,sha256=eDHt_byU3DVhI9D-3GwEW_VpQbIF6bPEORAieCTcdUc,1412
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scout/commands/load/variants.py,sha256=
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scout/commands/load/variants.py,sha256=XnF5p_ZAltPgOnmGYtS4tuvJcVEZf7L6K9p6IdYfuEQ,9972
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scout/commands/setup/__init__.py,sha256=uiuizwirbfLqp93K4__b982obk1stkzwpvXHi51OAbE,31
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scout/commands/setup/setup_scout.py,sha256=txS4tRwk1FMlS_qkyJl0XaZU0rFivqVCMqMi7iZtw78,9254
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scout/commands/update/__init__.py,sha256=yKNjRTVFsSTko8T7znfMqSI_HsGPN2-z1c0twkwO5uE,25
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scout/commands/update/base.py,sha256=XxxBGzn9JdFfk39jsZbU5eAZhE41MLq73WwLqa_u4Rc,1179
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scout/commands/update/case.py,sha256=
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scout/commands/update/case.py,sha256=8g-vLnjBCAL5hB-btQOFmzn2fVJM6OHILCgP1nDqKYo,7737
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scout/commands/update/compounds.py,sha256=vwCtb6045tGovKWHqY_uL8w1l9rZ_Hxlt0gUU0cKXUk,753
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scout/commands/update/disease.py,sha256=AajPLoEtd9YeU3jf7S7ZQRs3_o1H3GSxHsST_sVaIZQ,3846
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scout/commands/update/genes.py,sha256=GhYIn2zWrAZMhdJjzzrpo8AquFqr7XOvosOk8lg4Zwk,6989
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scout/commands/update/hpo.py,sha256=eyCuUlUwPmyP0oLh1olXhdqInlUXDdLe8ylgTlHWi-g,1339
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scout/commands/update/individual.py,sha256=
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scout/commands/update/individual.py,sha256=0xaqWeTWqs8wW3T2j-v3MNkVE4a1eY-NpF6NiazhN_Q,4080
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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/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=QsXeGXaS58SpLCLxVvf1BxZB2YfPZWzI-7BmMyJ8hBw,5891
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scout/constants/acmg.py,sha256=N9X2sJLbK6g6tDPhW0gYQifImzaowb4F6jfTYUBr-Z0,18717
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scout/constants/case_tags.py,sha256=O-BwEzU36MSpN7qqd-aSvoi4-VDRY8rM5hQ7Jg7DMgs,9447
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scout/constants/ccv.py,sha256=YP82qWCrjv3JB8d2LkUdBlBZolk0uF3nhNmkNgmebiI,9734
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scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
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scout/constants/clnsig.py,sha256=TSeZjUno2jEvQTenrltZ900ZFYIRNoul_Wm2qRjvpPA,1493
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scout/constants/disease_parsing.py,sha256=M9_OgsN88oXwKH_XpxdDma0zuWPRoHFQjL19tzojBPo,686
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scout/constants/file_types.py,sha256=DoXe34PJLYYHRH8-VqU1u1sd13lckl3nPckweXltKE4,2669
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scout/constants/filters.py,sha256=ZgVGt6No5D7PiN1o1wWDm3E5SCRk7YLya87_4QtIMPs,979
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scout/constants/gene_tags.py,sha256=yBrMu9qXyYaQ13l3XMakooyd2ZtPXm1XgpSSH_bC-5U,4513
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scout/constants/igv_tracks.py,sha256=uh8x1EqkXXVEBEGPi34Dxr_qztooQhZ0ZNmt2vpxzDo,4474
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scout/constants/indexes.py,sha256=mCj_ih9Sv7Qv4DrzLRH30EQZ-Tgyn_Sf6NYapCOlMOc,5793
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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=3t8JlqaM18-7t1Zd_dEv34hsIyxX_Yd6kjIbw5ZjjV8,1596
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