Squashed 'CRISPRessoWEB/CRISPRessoReports/' changes from 21f63d0..418…

…d811

418d811 Fix command used and parameters elements. Increase print width and height to 100%
40330d5 Adding styling for print-only and screen only
REVERT: 21f63d0 Replace tabs with spaces and reindent template files
REVERT: a3bcfeb Fix hamburger menu and add -bs- to data-target and data-toggle
REVERT: bd0c0f1 Resize images and fix filepath
REVERT: 02f94fd Add spacing around body and footer tags
REVERT: e514cdc Final style fixes, color circles for style files
REVERT: a6700c0 Merge commit '6986c2ba2c6ea96db2498a1e5711dbba1f0d5d17' as 'CRISPRessoWEB/CRISPRessoReports'
REVERT: 7c6dfcd Removing CRISPRessoReport files
REVERT: 17d9ead Radio buttons, center buttons and inputs (login, register, new password), new div name for style dropdown fixes
REVERT: 202c31f Squashed 'CRISPRessoWEB/CRISPRessoReports/' content from commit ba01a8f
REVERT: 04558fb Remove extra files
REVERT: 8e3a590 Spacing changes, submission_compared fix, and submission_wgs file upload fix
REVERT: 980fdc4 Styling and bootstrap changes
REVERT: 9d40474 Centering issue and submit button fix
REVERT: e0c67a9 Subtree working
REVERT: ca7b25a Jinja choice loader
REVERT: e0b6d7b Path correction
REVERT: 5a9cd38 Bootstrap 5 and partials changes
REVERT: 49e4332 Layout.html for C2WEB and CLI
REVERT: b83bafa Fix error when rendering multi reports
REVERT: 99a8fa7 summaries partials and html updates
REVERT: bc5b3df fig_reports and replacement
REVERT: e4e482a Added a few changes from the selenium-tests branch on C2Web
REVERT: 2feadf4 Update indentation in report.html and extract log params into partial
REVERT: 480060c Update path to template directory to include `CRISPRessoReports`
REVERT: bbd49ed Use the `render_template` function for each report
REVERT: d9829c5 Add function to render template partials without using Flask
REVERT: 5941a02 Web updates refactoring done
REVERT: 452db8b Adding files
REVERT: ef333f0 Removing reports found in subtree
REVERT: 1bae0df Commit before adding subtree
REVERT: 1fbb427 Add server file to render js
REVERT: d1d6fdf Move styling to main.css file
REVERT: 1241569 Jinja partials for all submissions
REVERT: 0534637 New submission.js template file
REVERT: c5406d1 Changes to submission.js for bootstrap 5 and load file upload partial
REVERT: ecd03f6 Working file upload in partial.
REVERT: ce5d20f Working, missing custom label
REVERT: b30725e Bootstrap 5 changes
REVERT: e05d146 Layout and report update
REVERT: 70a0589 Replace sub, ins, del with Substitution, Insertion, Deletion
REVERT: 69c3656 Move where the style files are stored in Docker
REVERT: 7f03e98 Implement creating styles from the admin panel
REVERT: 9b27a2e Rename style_file references to style
REVERT: 5d3675f Add some default styles and rename the default to "Original"
REVERT: 43a8d29 Remove style file card from admin index page
REVERT: 1a8f332 Refactor saving style files when there is no name specified
REVERT: 64a7b1c Implement color pickers in style admin view
REVERT: 17c93c1 Succesfully implemented selecting default style
REVERT: fd79cdd Restyle the colors in the admin view
REVERT: 3cd94b8 Fix error when the default style can't be read from the database
REVERT: 5e626bd Refactor `style_handler` to read the style from the database
REVERT: 0f66d4a Refactor styles to be part of the database instead of files
REVERT: 9859812 Move style folder inside of server folder
REVERT: 9f71f21 Add margins around style file elements
REVERT: 2a28549 Restyle the color pickers
REVERT: 2c82c08 DEFAULTUSER can't see style_dropdown and variable for ALLOW_USER_STYLE_UPLOAD for users to upload style files
REVERT: dc4f2c7 Style dropdown - allow save json only for admin
REVERT: 15e7483 Style file check
REVERT: 7bd0e91 Remove style from Compare
REVERT: 0ab45f5 Colors function refactored and working for all types
REVERT: 2e24f8b Adding styling
REVERT: d6621f1 Debuging
REVERT: 0de02b5 Merge with master
REVERT: 5150f9b Adding style_files to partial
REVERT: 957a9ca Add style files to pooled and wgs
REVERT: b92c83e Changes to pooled and wgs, reset Dockerfile
REVERT: 7b56a89 Updated Docker file and style_files.html
REVERT: ee0fcfc Optional save file
REVERT: 229e21d Checkbox for custom colors that shows and hides color selectors, box on home page for style folder
REVERT: d906da9 Working style FileAdmin, access button, and further partial refactoring
REVERT: b3b70bd Rough framework for style admin page
REVERT: e4731d7 Style menu completed
REVERT: 1bb37bc New style menu with tabs
REVERT: 58f7e56 Tabs for different style options
REVERT: 8338067 Compare (#34)
REVERT: d4e9ef3 Update AWS EB instructions.docx
REVERT: 658a218 Fix bug when trying to send recovery password with bad email creds
REVERT: ee32e36 Adding color-picker partial to wgs and pooled
REVERT: 34ea688 Fix for responsiveness on cup and title
REVERT: f0c4d07 Adding color routes to other versions
REVERT: 110fe14 Color picker input added to cmd_to_run
REVERT: e732478 Names for color fields
REVERT: 036a229 Jinja partial for color picker and pip install in dockerfile
REVERT: 48bbf9c Cup animation (#33)
REVERT: 2905248 Selenium tests (#31)
REVERT: 5641fd3 Merge pull request #32 from edilytics/multi-amplicon-guides
REVERT: 570e42a Don't remove commas from amplicons or guides
REVERT: 0d70425 Add smallGenome.fa
REVERT: fc33197 Writing text for pooled
REVERT: dccfcb3 Files for testing
REVERT: 4cea67c Changes for WGS selenium tests. All tests functional.
REVERT: ff05713 Changes for WGS selenium test file loading
REVERT: 495a98d Changes for pooled testing
REVERT: 0ad86a5 Merge pull request pinellolab#30 from edilytics/pooled-upload-fix
REVERT: 127eb8f PopulatePooled error
REVERT: 30ff7a7 Merge remote-tracking branch 'origin/pooled-upload-fix' into selenium_tests
REVERT: 7847687 Add link to CRISPRessoWGS from profile page and change header
REVERT: 666f73b Remove example block from CRISPRessoWGS submission page
REVERT: 27fcc13 Fix bug where amplicon file isn't being uploaded properly in CRISPRessoPooled
REVERT: 8d979a4 Fix bug where files_to_delete was being replaced and standardize append
REVERT: 09e55fc Changes to make interleaved and pooled tests possible
REVERT: f89eca8 Changes necessary for selenium tests
REVERT: 3efe4f9 Clean up test files
REVERT: 6394dcd Merge pull request #28 from edilytics/s3
REVERT: dcef708 Remove changes for CRISPRessoCompare
REVERT: e0c79cf Add demo config file for eb
REVERT: c9fc141 Update AWS EB instructions.docx
REVERT: a671c4e Set version to 2.6.3
REVERT: 3bb3a8d Pull out s3 javascript for use in crispresso and crispressopooled
REVERT: da5b15b Timezone for history is displayed in user local timezone
REVERT: e11691f Update history to show time of previous run
REVERT: 3e5f136 Update pooled with s3
REVERT: 4c7d429 Add data links to pooled report
REVERT: 353e88f Update admin portal landing page
REVERT: 712e828 Show run type in history
REVERT: 2802252 s3 and user updates
REVERT: efc3ed8 S3 error catching
REVERT: af68341 New S3 Validation
REVERT: f7d64e0 AWS validation before submission
REVERT: 8446093 Update s3 for batch and paired modes
REVERT: 0e7d327 S3_Upload function imrpvoed -JF
REVERT: b48e0dc Merge branch 's3' of https://github.com/edilytics/C2Web into s3
REVERT: c991d52 added s3 user database model
REVERT: ab4aa54 add model for s3 bucket
REVERT: 853cda9 S3_Functionality improved -JF
REVERT: 8a4b554 Implemented front-end s3 browsing
REVERT: e082a5f stub out viewing method
REVERT: c5b6d13 Merge pull request #7 from edilytics/check-amplicon-length
REVERT: 222de5b Merge pull request #15 from edilytics/wgs-interface
REVERT: 712270a Add support for CRISPRessoWGS
REVERT: deaacee Extract out function to get server files in submit_routes
REVERT: 151eb15 Update crispresso2_info object fields
REVERT: d6b3789 Bump CRISPResso verion to 2.2.4
REVERT: 58ae313 Merge pull request #10 from edilytics/update-to-crispresso-2.2.2
REVERT: 7f2dc1c Stop trimming json error messages, fix #11
REVERT: d28c03b Update reporting logic to use the new CRISPResso2_info schema
REVERT: ed8ea68 Bump CRISPResso version in Dockerfile and download release from Github
REVERT: 9151c5d Add CRISPRessoPooled report template
REVERT: 25a6e37 Merge pull request #6 from edilytics/pooled-interface
REVERT: b47d288 Check length of amplicons for hosted version, closes #4
REVERT: 54c28b6 Update submission file extension check
REVERT: 8fcadee Add a link to CRISPRessoPooled interface in user dashboard
REVERT: 7fd0283 Implement CRISPRessoPooled backend and report functionality
REVERT: 4063eb3 Modify submission.js to accept .txt and .tsv files
REVERT: b770323 Create template file for CRISPRessoPooled submission interface
REVERT: 396a7f5 Merge pull request #5 from edilytics/flask-modularization
REVERT: 8527384 Convert some celery configurations settings to new format
REVERT: ca1c175 Install less and vim in Dockerfile
REVERT: c693668 Read CRISPResso2_info from json files instead of pickle files
REVERT: a469e08 Move LoginManager to user_routes.py
REVERT: f62e67a Create db tables in init_db.py
REVERT: 0d85c90 Move login_required to user_routes
REVERT: 6f5e33e Reformatting of remaining __init__.py
REVERT: e615c0b Extract report routes out of __init__.py
REVERT: 20f2601 Extract user routes out from __init__.py
REVERT: 5582612 Extract status routes out from __init__.py
REVERT: 2406a10 Extract submit routes out from __init__.py
REVERT: b562fcd Extract celery tasks from __init__.py
REVERT: faa785d Extract views out from __init__.py
REVERT: ff44576 Extract model classes out from __init__.py
REVERT: f0c2e85 Merge pull request #3 from edilytics/2to3
REVERT: 8851603 Replace RabbitMQ with Redis
REVERT: bc1fcb5 Upgrade celery to version 5.0.5
REVERT: 244ec33 Convert from Python 2 to Python 3
REVERT: cd3746b Refactor Docker image to use Python 3 via micromamba
REVERT: 2359800 Allow interleaved batches
REVERT: 926f84e Add features: Allow admin init, server discovery depth
REVERT: cb0146f Client and server-side checks for invalid characters on sgRNA and amplicon
REVERT: aa670f6 Update README.md
REVERT: c8faee0 Update README.md
REVERT: 84b2fed delete other images
REVERT: 0c007ee Update README.md
REVERT: 8a5d552 Update README.md
REVERT: ee5c151 Update README.md
REVERT: c8cd4f7 Trycatch pickle loads
REVERT: c1facd7 get rid of debug print of email
REVERT: e46a04e crispresso2.0.45
REVERT: 28c861c Update param descriptions
REVERT: 22b4a57 2.0.44
REVERT: f4686be crispresso to 2.0.42
REVERT: 1a967a8 update report
REVERT: 265e796 2.4
REVERT: 70822d2 Job expiration
REVERT: d3e6d6e check progress on setinterval
REVERT: 2e8249b server-side files
REVERT: 4602c2d Update to crispresso 2.0.40 prime editing
REVERT: 21ed9d4 update errors and ignore email config
REVERT: 5bcb603 Update README.md
REVERT: a587444 initial commit
REVERT: 8ff1878 Initial commit

git-subtree-dir: CRISPRessoWEB/CRISPRessoReports
git-subtree-split: 418d811a007d782bef7c319358bb13702e97b1bf

templates/batchReport.html

@@ -148,7 +148,7 @@ <h5>{{report_data['titles'][plot_name]}}</h5>
 
     {# data bit for web version: #}
     {#
-        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-bs-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
+        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
     #}
 	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
 </div> {# jumbrotron #} <!-- end jumbotron -->

templates/pooledReport.html

@@ -86,7 +86,7 @@ <h5 id="modification_summary_title">{{report_data['titles'][plot_name]}}</h5>
             </div>
     {# data bit for web version: #}
     {#
-        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-bs-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
+        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
     #}
 	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
 </div> {# jumbrotron #} <!-- end jumbotron -->

templates/shared/partials/fig_reports.html

@@ -1,10 +1,13 @@
 <div id="fig_{{fig_name}}">
-    <div class="d-flex flex-column">
     {% if amplicon_name is defined %}
         {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'][amplicon_name] %}
             {{report_data['figures']['htmls'][amplicon_name][fig_name]|safe}}
         {% else %}
-            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.png" width={{width}} ></a>
+        {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %}
+            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.png" width='40%' height='40%' ></a>
+            {% else %}
+            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][amplicon_name][fig_name]}}.png" width='100%' height='100%' ></a>
+            {% endif %} 
         {% endif %}
         <label class="labelpadding">{{report_data['figures']['captions'][amplicon_name][fig_name]}}</label>
         {% for (data_label,data_path) in report_data['figures']['datas'][amplicon_name][fig_name] %}
@@ -14,12 +17,15 @@
         {% if 'htmls' in report_data['figures'] and fig_name in report_data['figures']['htmls'] %}
             {{report_data['figures']['htmls'][fig_name]|safe}}
         {% else %}
-            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.png" width={{width}} ></a>      
+            {% if fig_name in ['plot_1a', 'plot_1b', 'plot_1c', 'plot_3a', 'plot_4a', 'plot_4b', 'plot_4c'] %}
+            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.png" width='40%' height='40%' ></a>
+            {% else %}
+            <a href="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.pdf"><img src="{{report_data['crispresso_data_path']}}{{report_data['figures']['locs'][fig_name]}}.png" width='100%' height='100%' ></a>
+            {% endif %}        
         {% endif %}
         <label class="labelpadding">{{report_data['figures']['captions'][fig_name]}}</label>
         {% for (data_label,data_path) in report_data['figures']['datas'][fig_name] %}
             <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a></small></p>
         {% endfor %}
     {% endif %}
-    </div>
 </div>

templates/shared/partials/log_params.html

@@ -1,11 +1,23 @@
-<div class="tab-pane fade text-start" id="log_params" role="tabpanel">
+<div class="tab-pane fade text-start screen-only" id="log_params" role="tabpanel">
   <p>CRISPResso version: {{report_data['run_data']['running_info']['version']}}</p>
   <p>Run completed: {{report_data['run_data']['running_info']['end_time_string']}}</p>
   <p>Amplicon sequence: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args']['amplicon_seq']}}</pre></p>
   {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %}
-  <p>Guide sequence: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args']['guide_seq']}}</pre></p>
+    <p>Guide sequence: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args']['guide_seq']}}</pre></p>
   {% endif %}
   <p>Command used: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['command_used']}}</pre></p>
   <p>Parameters: <pre class='pre-scrollable'>{{report_data['run_data']['running_info']['args_string']}}</pre></p>
   <p class='text-center m-0'><small><a href="{{report_data['crispresso_data_path']}}{{report_data['run_data']['running_info']['log_filename']}}">Running log</a></small></p>
 </div>
+
+<div class="tab-pane fade text-left print-only" id="log_params" role="tabpanel">
+  <p>CRISPResso version: {{report_data['run_data']['running_info']['version']}}</p>
+  <p>Run completed: {{report_data['run_data']['running_info']['end_time_string']}}</p>
+  <p>Amplicon sequence: {{report_data['run_data']['running_info']['args']['amplicon_seq']}}</p>
+  {% if report_data['run_data']['running_info']['args']['guide_seq'] != '' %}
+    <p>Guide sequence: {{report_data['run_data']['running_info']['args']['guide_seq']}}</p>
+  {% endif %}
+  <p>Command used: {{report_data['run_data']['running_info']['command_used']}}</p>
+  <p>Parameters: {{report_data['run_data']['running_info']['args_string']}}</p>
+  <p class='text-center m-0'><small><a href="{{report_data['crispresso_data_path']}}{{report_data['run_data']['running_info']['log_filename']}}">Running log</a></small></p>
+</div>

templates/wgsReport.html

@@ -84,7 +84,7 @@ <h5>{{report_data['titles'][plot_name]}}</h5>
             </div>
     {# data bit for web version: #}
     {#
-        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-bs-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
+        			  <p class="m-0"><small>Data: <a href="{{report_data['crispresso_data_path']}}{{data_path}}">{{data_label}}</a> <a href="{{report_data['crispresso_data_path']}}{{data_path}}" title="{{data_label}}" download> <span class="fas fa-download" data-toggle='tooltip' title='Download {{data_label}}'><span></a></small></p>
     #}
 	</div> {# jumbotron_content #} <!-- end jumbotron_content -->
 </div> {# jumbrotron #} <!-- end jumbotron -->