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Squashed 'CRISPRessoWEB/CRISPRessoReports/' changes from ba01a8f..21f…
…63d0 21f63d0 Replace tabs with spaces and reindent template files a3bcfeb Fix hamburger menu and add -bs- to data-target and data-toggle bd0c0f1 Resize images and fix filepath 02f94fd Add spacing around body and footer tags e514cdc Final style fixes, color circles for style files a6700c0 Merge commit '6986c2ba2c6ea96db2498a1e5711dbba1f0d5d17' as 'CRISPRessoWEB/CRISPRessoReports' 7c6dfcd Removing CRISPRessoReport files 17d9ead Radio buttons, center buttons and inputs (login, register, new password), new div name for style dropdown fixes 202c31f Squashed 'CRISPRessoWEB/CRISPRessoReports/' content from commit ba01a8f 04558fb Remove extra files 8e3a590 Spacing changes, submission_compared fix, and submission_wgs file upload fix 980fdc4 Styling and bootstrap changes 9d40474 Centering issue and submit button fix e0c67a9 Subtree working ca7b25a Jinja choice loader e0b6d7b Path correction 5a9cd38 Bootstrap 5 and partials changes 49e4332 Layout.html for C2WEB and CLI b83bafa Fix error when rendering multi reports 99a8fa7 summaries partials and html updates bc5b3df fig_reports and replacement e4e482a Added a few changes from the selenium-tests branch on C2Web 2feadf4 Update indentation in report.html and extract log params into partial 480060c Update path to template directory to include `CRISPRessoReports` bbd49ed Use the `render_template` function for each report d9829c5 Add function to render template partials without using Flask 5941a02 Web updates refactoring done 452db8b Adding files ef333f0 Removing reports found in subtree 1bae0df Commit before adding subtree 1fbb427 Add server file to render js d1d6fdf Move styling to main.css file 1241569 Jinja partials for all submissions 0534637 New submission.js template file c5406d1 Changes to submission.js for bootstrap 5 and load file upload partial ecd03f6 Working file upload in partial. ce5d20f Working, missing custom label b30725e Bootstrap 5 changes e05d146 Layout and report update 70a0589 Replace sub, ins, del with Substitution, Insertion, Deletion 69c3656 Move where the style files are stored in Docker 7f03e98 Implement creating styles from the admin panel 9b27a2e Rename style_file references to style 5d3675f Add some default styles and rename the default to "Original" 43a8d29 Remove style file card from admin index page 1a8f332 Refactor saving style files when there is no name specified 64a7b1c Implement color pickers in style admin view 17c93c1 Succesfully implemented selecting default style fd79cdd Restyle the colors in the admin view 3cd94b8 Fix error when the default style can't be read from the database 5e626bd Refactor `style_handler` to read the style from the database 0f66d4a Refactor styles to be part of the database instead of files 9859812 Move style folder inside of server folder 9f71f21 Add margins around style file elements 2a28549 Restyle the color pickers 2c82c08 DEFAULTUSER can't see style_dropdown and variable for ALLOW_USER_STYLE_UPLOAD for users to upload style files dc4f2c7 Style dropdown - allow save json only for admin 15e7483 Style file check 7bd0e91 Remove style from Compare 0ab45f5 Colors function refactored and working for all types 2e24f8b Adding styling d6621f1 Debuging 0de02b5 Merge with master 5150f9b Adding style_files to partial 957a9ca Add style files to pooled and wgs b92c83e Changes to pooled and wgs, reset Dockerfile 7b56a89 Updated Docker file and style_files.html ee0fcfc Optional save file 229e21d Checkbox for custom colors that shows and hides color selectors, box on home page for style folder d906da9 Working style FileAdmin, access button, and further partial refactoring b3b70bd Rough framework for style admin page e4731d7 Style menu completed 1bb37bc New style menu with tabs 58f7e56 Tabs for different style options 8338067 Compare (#34) d4e9ef3 Update AWS EB instructions.docx 658a218 Fix bug when trying to send recovery password with bad email creds ee32e36 Adding color-picker partial to wgs and pooled 34ea688 Fix for responsiveness on cup and title f0c4d07 Adding color routes to other versions 110fe14 Color picker input added to cmd_to_run e732478 Names for color fields 036a229 Jinja partial for color picker and pip install in dockerfile 48bbf9c Cup animation (#33) 2905248 Selenium tests (#31) 5641fd3 Merge pull request #32 from edilytics/multi-amplicon-guides 570e42a Don't remove commas from amplicons or guides 0d70425 Add smallGenome.fa fc33197 Writing text for pooled dccfcb3 Files for testing 4cea67c Changes for WGS selenium tests. All tests functional. ff05713 Changes for WGS selenium test file loading 495a98d Changes for pooled testing 0ad86a5 Merge pull request pinellolab#30 from edilytics/pooled-upload-fix 127eb8f PopulatePooled error 30ff7a7 Merge remote-tracking branch 'origin/pooled-upload-fix' into selenium_tests 7847687 Add link to CRISPRessoWGS from profile page and change header 666f73b Remove example block from CRISPRessoWGS submission page 27fcc13 Fix bug where amplicon file isn't being uploaded properly in CRISPRessoPooled 8d979a4 Fix bug where files_to_delete was being replaced and standardize append 09e55fc Changes to make interleaved and pooled tests possible f89eca8 Changes necessary for selenium tests 3efe4f9 Clean up test files 6394dcd Merge pull request #28 from edilytics/s3 dcef708 Remove changes for CRISPRessoCompare e0c79cf Add demo config file for eb c9fc141 Update AWS EB instructions.docx a671c4e Set version to 2.6.3 3bb3a8d Pull out s3 javascript for use in crispresso and crispressopooled da5b15b Timezone for history is displayed in user local timezone e11691f Update history to show time of previous run 3e5f136 Update pooled with s3 4c7d429 Add data links to pooled report 353e88f Update admin portal landing page 712e828 Show run type in history 2802252 s3 and user updates efc3ed8 S3 error catching af68341 New S3 Validation f7d64e0 AWS validation before submission 8446093 Update s3 for batch and paired modes 0e7d327 S3_Upload function imrpvoed -JF b48e0dc Merge branch 's3' of https://github.com/edilytics/C2Web into s3 c991d52 added s3 user database model ab4aa54 add model for s3 bucket 853cda9 S3_Functionality improved -JF 8a4b554 Implemented front-end s3 browsing e082a5f stub out viewing method c5b6d13 Merge pull request #7 from edilytics/check-amplicon-length 222de5b Merge pull request #15 from edilytics/wgs-interface 712270a Add support for CRISPRessoWGS deaacee Extract out function to get server files in submit_routes 151eb15 Update crispresso2_info object fields d6b3789 Bump CRISPResso verion to 2.2.4 58ae313 Merge pull request #10 from edilytics/update-to-crispresso-2.2.2 7f2dc1c Stop trimming json error messages, fix #11 d28c03b Update reporting logic to use the new CRISPResso2_info schema ed8ea68 Bump CRISPResso version in Dockerfile and download release from Github 9151c5d Add CRISPRessoPooled report template 25a6e37 Merge pull request #6 from edilytics/pooled-interface b47d288 Check length of amplicons for hosted version, closes #4 54c28b6 Update submission file extension check 8fcadee Add a link to CRISPRessoPooled interface in user dashboard 7fd0283 Implement CRISPRessoPooled backend and report functionality 4063eb3 Modify submission.js to accept .txt and .tsv files b770323 Create template file for CRISPRessoPooled submission interface 396a7f5 Merge pull request #5 from edilytics/flask-modularization 8527384 Convert some celery configurations settings to new format ca1c175 Install less and vim in Dockerfile c693668 Read CRISPResso2_info from json files instead of pickle files a469e08 Move LoginManager to user_routes.py f62e67a Create db tables in init_db.py 0d85c90 Move login_required to user_routes 6f5e33e Reformatting of remaining __init__.py e615c0b Extract report routes out of __init__.py 20f2601 Extract user routes out from __init__.py 5582612 Extract status routes out from __init__.py 2406a10 Extract submit routes out from __init__.py b562fcd Extract celery tasks from __init__.py faa785d Extract views out from __init__.py ff44576 Extract model classes out from __init__.py f0c2e85 Merge pull request #3 from edilytics/2to3 8851603 Replace RabbitMQ with Redis bc1fcb5 Upgrade celery to version 5.0.5 244ec33 Convert from Python 2 to Python 3 cd3746b Refactor Docker image to use Python 3 via micromamba 2359800 Allow interleaved batches 926f84e Add features: Allow admin init, server discovery depth cb0146f Client and server-side checks for invalid characters on sgRNA and amplicon aa670f6 Update README.md c8faee0 Update README.md 84b2fed delete other images 0c007ee Update README.md 8a5d552 Update README.md ee5c151 Update README.md c8cd4f7 Trycatch pickle loads c1facd7 get rid of debug print of email e46a04e crispresso2.0.45 28c861c Update param descriptions 22b4a57 2.0.44 f4686be crispresso to 2.0.42 1a967a8 update report 265e796 2.4 70822d2 Job expiration d3e6d6e check progress on setinterval 2e8249b server-side files 4602c2d Update to crispresso 2.0.40 prime editing 21ed9d4 update errors and ignore email config 5bcb603 Update README.md a587444 initial commit 8ff1878 Initial commit git-subtree-dir: CRISPRessoWEB/CRISPRessoReports git-subtree-split: 21f63d05a15e1f48ec14db46fa0e5bc5f0ea5344
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