scout-browser 4.101.0__py3-none-any.whl → 4.102.0__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/clinvar.py +7 -7
- scout/adapter/mongo/hgnc.py +7 -2
- scout/adapter/mongo/omics_variant.py +8 -0
- scout/adapter/mongo/variant_loader.py +6 -2
- scout/constants/__init__.py +1 -0
- scout/constants/igv_tracks.py +6 -2
- scout/constants/phenotype.py +1 -0
- scout/load/hpo.py +8 -2
- scout/server/blueprints/alignviewers/controllers.py +8 -6
- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +2 -0
- scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
- scout/server/blueprints/cases/controllers.py +56 -28
- scout/server/blueprints/cases/templates/cases/case_report.html +9 -88
- scout/server/blueprints/cases/templates/cases/matchmaker.html +1 -1
- scout/server/blueprints/cases/templates/cases/phenotype.html +1 -1
- scout/server/blueprints/cases/templates/cases/utils.html +26 -24
- scout/server/blueprints/cases/views.py +32 -33
- scout/server/blueprints/clinvar/controllers.py +3 -2
- scout/server/blueprints/diagnoses/controllers.py +4 -8
- scout/server/blueprints/diagnoses/templates/diagnoses/diagnoses.html +1 -1
- scout/server/blueprints/diagnoses/templates/diagnoses/disease_term.html +1 -1
- scout/server/blueprints/diagnoses/views.py +2 -2
- scout/server/blueprints/institutes/controllers.py +107 -73
- scout/server/blueprints/institutes/templates/overview/cases.html +1 -1
- scout/server/blueprints/login/controllers.py +2 -1
- scout/server/blueprints/login/views.py +5 -2
- scout/server/blueprints/omics_variants/views.py +2 -2
- scout/server/blueprints/phenotypes/controllers.py +15 -2
- scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html +1 -1
- scout/server/blueprints/variant/controllers.py +10 -11
- scout/server/blueprints/variant/templates/variant/utils.html +1 -1
- scout/server/blueprints/variant/templates/variant/variant_details.html +68 -60
- scout/server/blueprints/variant/utils.py +25 -0
- scout/server/blueprints/variants/controllers.py +11 -42
- scout/server/blueprints/variants/views.py +9 -8
- scout/server/config.py +3 -0
- scout/server/extensions/beacon_extension.py +7 -2
- scout/server/templates/bootstrap_global.html +11 -1
- scout/server/templates/layout.html +6 -1
- scout/server/utils.py +24 -3
- {scout_browser-4.101.0.dist-info → scout_browser-4.102.0.dist-info}/METADATA +1 -1
- {scout_browser-4.101.0.dist-info → scout_browser-4.102.0.dist-info}/RECORD +45 -45
- {scout_browser-4.101.0.dist-info → scout_browser-4.102.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.101.0.dist-info → scout_browser-4.102.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.101.0.dist-info → scout_browser-4.102.0.dist-info}/licenses/LICENSE +0 -0
scout/server/utils.py
CHANGED
@@ -8,11 +8,21 @@ import zipfile
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from functools import wraps
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from io import BytesIO
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from typing import Dict, Optional, Tuple
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from urllib.parse import urlparse
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import pdfkit
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from bson.objectid import ObjectId
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from flask import
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from flask import (
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Response,
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abort,
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current_app,
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flash,
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redirect,
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render_template,
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request,
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)
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from flask_login import current_user
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from werkzeug.local import LocalProxy
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LOG = logging.getLogger(__name__)
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@@ -102,6 +112,17 @@ def public_endpoint(function):
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return function
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def safe_redirect_back(request: LocalProxy, link: Optional[str] = None) -> Response:
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"""Safely redirects the user back to the referring URL, if it originates from the same host.
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Otherwise, the user is redirected to a default '/'."""
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referrer = request.referrer
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if referrer:
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parsed_referrer = urlparse(referrer)
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if parsed_referrer.netloc == request.host:
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return redirect(link or referrer)
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return redirect("/")
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def variant_institute_and_case(
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store, variant_obj: dict, institute_id: Optional[str], case_name: Optional[str]
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) -> Tuple[dict, dict]:
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@@ -145,7 +166,7 @@ def institute_and_case(store, institute_id, case_name=None):
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return abort(404)
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# Make sure build is either "37" or "38"
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case_obj["genome_build"] =
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case_obj["genome_build"] = get_case_genome_build(case_obj)
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# validate that user has access to the institute
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@@ -208,7 +229,7 @@ def user_institutes(store, login_user):
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def get_case_genome_build(case_obj: dict) -> str:
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"""returns the genome build of a case, as a string."""
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return "38" if "38" in case_obj.get("genome_build", "37") else "37"
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return "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
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def get_case_mito_chromosome(case_obj: dict) -> str:
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.4
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Name: scout-browser
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Version: 4.
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Version: 4.102.0
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Summary: Clinical DNA variant visualizer and browser
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Project-URL: Repository, https://github.com/Clinical-Genomics/scout
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Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
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@@ -8,18 +8,18 @@ scout/adapter/mongo/case.py,sha256=Cqb_uWbW5gnAoOMoJVK9LYeCrJEE-M3fgI97-3t6gbc,6
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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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scout/adapter/mongo/clinvar.py,sha256=
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scout/adapter/mongo/clinvar.py,sha256=qaUrpO_eQfy2ZAAaNKOtLKxCgrMatEVhqHbJ__kXTI4,19462
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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=xC6VdfZUU8tIPKZrCklD-zX3wgfZD09ze5wrpyLbkIA,20245
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scout/adapter/mongo/filter.py,sha256=rIdjiDJCrNDeTNgssKm7n1HTxne72jvlX2I3FQjQGo8,9687
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scout/adapter/mongo/hgnc.py,sha256=
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scout/adapter/mongo/hgnc.py,sha256=S7CFw1DAP-jHGgybw-3H2Dozn5s1rYxnJMHnl8GArKU,16680
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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=SaA1mRxIZHtMfriMnd0yKiup-xSAG5g0ry9Achra9Tk,6646
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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=-Z4UCqeybbQQix1fWdOTKa6acuytPM2r8c-6pAv-gRY,8910
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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=zXAT5lWadRbhCNw5w161uCKzoUyTuUSlCm32P8aBa_M,36315
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@@ -28,7 +28,7 @@ scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt
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scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
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scout/adapter/mongo/variant.py,sha256=IMZcRr43b3XsDqi9kpymobAj_CPVQkN_rxLMfxQ75LI,36267
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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=u7XNy3-RjMg80c4iUV2FLfIjfCm286uC0HzHFeiJmh4,28674
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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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@@ -125,7 +125,7 @@ scout/commands/view/intervals.py,sha256=8Pofxy0DwL2Euh3SdnTLLWsU6DjLNOwIGdxeCS83
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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/__init__.py,sha256=nUd4T3RwBSNcxiU8rXZDOd8nPRl2gqWILY-C0SflnzE,5969
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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/file_types.py,sha256=3N3TReXVkhxbpvYupsENVFAHEGQyZ1S7efP7wZEqs44,2890
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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=
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scout/constants/igv_tracks.py,sha256=rhCrmPGLVUMcFrLfjswzeO2UeKIsf3dgjgyepKjh3sM,4777
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scout/constants/indexes.py,sha256=qe-1ntYqlwqLEDqsJDX6RhAnCYt_2tVZ9ZJ4nWoTIkQ,5843
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scout/constants/panels.py,sha256=1N2Ys94IxoEWxySTJDW-rFJ55vtCkqnn6bRWjkw61J4,876
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scout/constants/phenotype.py,sha256=
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scout/constants/phenotype.py,sha256=FqTZJOmBE5vxWU_XPrLi1nkPix5d5WAxLEpjw9Hz4Ak,2381
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scout/constants/query_terms.py,sha256=tuHYdV0nNKCw4UpypOwUgKImaWFimOyn-evAEGdxz-E,1615
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scout/constants/so_terms.py,sha256=aJcQv3wgpZylVhqSJH854WS8xSARDxWGnW6I5mG1egE,4321
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scout/constants/variant_tags.py,sha256=NnpcJGRDycq3PIrDQsd57ynJ8NzmJETICBVjzGKZlSg,17907
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scout/load/disease.py,sha256=eZ-RDTtfO6-YCk0tCHuhCWxw1FSCwHNZEemWXCC4P_w,2747
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scout/load/exon.py,sha256=ONaWJ9EfbhGV8KGXxwlq_jYCoU-JkBpv4r9zDaCjtls,2070
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scout/load/hgnc_gene.py,sha256=GcSQ01CioYIshAzXAv4msIGDPjTjGBBPBnLX2GvaZJ4,4507
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scout/load/hpo.py,sha256=
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scout/load/hpo.py,sha256=UAUbklr_KIHLutBBW2N3KwInPLFuiufjh8Ke-38m_Pc,2679
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scout/load/institute.py,sha256=etmZ0CZRHOVi3f9R-wn5BK1pZPhtZwq2QYbh2RXXxDc,625
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scout/load/panel.py,sha256=MY5M7-lDzVXt5RJH87N28TB7awdM6s-SoawholTl2GM,4776
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scout/load/panelapp.py,sha256=b37hLLpUNhXPz5SOYnhnRhb1OmSX-z2k7FtKMm9pXE8,5319
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scout/server/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
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scout/server/app.py,sha256=0Vmhzl7BviwbFA6ZsnXDM-E_KM6kEEWraCUxm8qMvc4,12011
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scout/server/auto.py,sha256=8B6GwfOaUChkTLuLgYQDFMWlxGuHkEegF1argH2G2Ik,401
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scout/server/config.py,sha256=
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scout/server/config.py,sha256=JcT9rUDcAdm9oSk7Wwbu-Aut96-xvBQnMeQTt_-6rXs,6401
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scout/server/links.py,sha256=aFCvrtXrc1gnhNhnifapVdUZOZKEpBD2zSxWXdvQLEk,28154
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scout/server/utils.py,sha256=
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scout/server/utils.py,sha256=gNPPtbIXKenxprg1b240pkEbJZowfY4xjH9lctbpeEs,14584
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scout/server/blueprints/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
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scout/server/blueprints/alignviewers/__init__.py,sha256=XMVed2ekVUAvroqENDHSr2pwM8otqau8ZA-rbH1T2U8,59
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scout/server/blueprints/alignviewers/controllers.py,sha256=
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scout/server/blueprints/alignviewers/controllers.py,sha256=s8fvqOewsR9bSf-tbZFGe1ePvz5zfoMrVvEzZBe6Cmw,15268
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scout/server/blueprints/alignviewers/partial.py,sha256=9hpI00yhvZZCcPVUHlVDp488r1j7vYU5YDXYA6OkWQM,2005
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scout/server/blueprints/alignviewers/views.py,sha256=Qa9VOPbqh2MC-L_x1Yp6n8hfr6mIm9EPIUdN_0itJRU,5092
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scout/server/blueprints/alignviewers/templates/alignviewers/igv_sashimi_viewer.html,sha256=37ArJCraTajqWlCvyQYVfSvWCg94pRDIMvf2Y7Oe_j4,5545
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scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html,sha256=
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scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=
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scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html,sha256=1DUcfgoFMJDBYHuZ5IwNvbs0fHSDjWJdmNS_GxIbSjE,10891
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scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=jaf4fba_RHVRymWxP32wCkR0GSZKD7PS8hYjqO8GVFI,336
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scout/server/blueprints/api/__init__.py,sha256=HR6HjS7ot1K_8Lt5eQdNT154z_FCdHGSigy8r2LpNCI,26
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scout/server/blueprints/api/views.py,sha256=pbl78wfhrm1T8JmiJDYF3BbTbfFrlF-hQRbuv2GWI0s,3729
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scout/server/blueprints/cases/__init__.py,sha256=_c17kPFITFYcIVphF4V9bf0PZBer8bU3rtVWQnljKDU,52
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scout/server/blueprints/cases/controllers.py,sha256=
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scout/server/blueprints/cases/views.py,sha256=
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scout/server/blueprints/cases/controllers.py,sha256=O3Emj0WOdVbsZBuGNbnNIow7qudYHBob3ATcNhOGniY,57728
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scout/server/blueprints/cases/views.py,sha256=qYnmXi5DpmuLEztQ9DgoOMfe-oOaGAe8JCzZ6tvormw,43092
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scout/server/blueprints/cases/static/case_images.js,sha256=pb_gG7DNQc-1lADqSII8YvjBwmHyeQWYVtuu2jyrTlU,14997
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scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAjaRWhjL-bK5bsQnLpH54HZak,541
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scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkke1UHxjiYWY_gBzWcIkGpdJUA,2978
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scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
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scout/server/static/robots.txt,sha256=fFX0beQN4x3mzR3evnZjrOUYOTNkezYAwqMowTUpmxM,106
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667
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-
scout/server/templates/bootstrap_global.html,sha256=
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668
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scout/server/templates/layout.html,sha256=
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667
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+
scout/server/templates/bootstrap_global.html,sha256=6JrQGCdrSM17VJhcUTPBMSEHRkaOAo1w8Hcsvg6uhRE,2897
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668
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+
scout/server/templates/layout.html,sha256=JeUfKYL7R-8-eaZndV4WukpSiIlWga_qYghpOuwq594,5115
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669
669
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scout/server/templates/report_base.html,sha256=bNYzoJFgtYMnfxQYeguwQK9c15ZASdmXd72DaiCfZto,2281
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670
670
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scout/server/templates/utils.html,sha256=0FpSmFLBAOTApGntcIW9YKhqXn6ABDt51aOidx3QtYM,12818
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671
671
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scout/server/translations/sv/LC_MESSAGES/messages.mo,sha256=eI53pCtlYj1MXduDicMZRxBhgOV_TlmMUpH7IhncgDY,4452
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@@ -689,8 +689,8 @@ scout/utils/link.py,sha256=HpQvwu0hmuCrs7TcAExLmOzEGr3glWuu8iaW0ao5pEA,9011
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689
689
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scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
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690
690
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scout/utils/scout_requests.py,sha256=6R8boknrfwlmrRQ2txD81lfVtqUK_iabywEiVyIiZfQ,12685
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691
691
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scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
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692
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-
scout_browser-4.
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693
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scout_browser-4.
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694
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scout_browser-4.
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695
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scout_browser-4.
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scout_browser-4.
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692
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+
scout_browser-4.102.0.dist-info/METADATA,sha256=Dzeha9Ho1ykmvcAzIodqT_hxJeNAqr333lP4-g3iSzY,15527
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693
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+
scout_browser-4.102.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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694
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+
scout_browser-4.102.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
|
695
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+
scout_browser-4.102.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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696
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+
scout_browser-4.102.0.dist-info/RECORD,,
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File without changes
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File without changes
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