Automate NCCAT reports

[leginonbot]

---

Author Name: Sargis Dallakyan (@dallakyan)
Original Redmine Issue: 6839, https://emg.nysbc.org/redmine/issues/6839
Original Date: 2019-03-14

---

None

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-04-05T23:15:25Z

---

Searched for an editor to add to this page with an option to upload images. Found https://ckeditor.com which comes with CKFinder but it costs $$. Looked at https://alternativeto.net/software/ckfinder/ and decided to go with https://responsivefilemanager.com and tinymce. I have not committed their code to our git repo since it's not clear what their redistribution policy is. Instead, I'm writing install notes below so we can redo it if needed.

Install Notes

Download tinymce and filemanager copy them to myamiweb root. Login to emgweb and do:

mkdir thumbs
chown apache thumbs
ln -s /gpfs/uploads

File manager doesn't come with security option, meaning everyone can upload and view images. To secure it, edit filemanager/config/config.php and add the following code at the beginning:

require_once "inc/dbemauth.inc";
require_once "inc/admin.inc";
require_once "inc/user.inc.php";

$login_check = $dbemauth->is_logged();
$is_admin = (privilege('users')>3);
if (!$is_admin)
        redirect(BASE_URL.'accessdeny.php?text=You do not have administrator privilege');

This way only admin users can upload images. I suggest we make /gpfs/uploads/$user/$session to store images similar to /gpfs/leginon.

This will be live on emgweb tomorrow.

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-04-05T23:34:57Z

---

Also deny directory listing with htaccess for thumbs and uploads using https://stackoverflow.com/questions/5932641/deny-directory-listing-with-htaccess

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-04-08T23:10:35Z

---

Added "Download PDF" at the bottom thanks to https://github.com/MrRio/jsPDF

[leginonbot]

---

Original Redmine Comment
Author Name: Bridget Carragher (@bcarr-czi)
Original Date: 2019-04-17T02:59:53Z

---

I really like these:
Can I suggest a few changes:

• Please change the link tho test from "Poster" to "Report"
• Can we make the blue splash banned extend across te whole report at the top; looks a little strangled otherwise.
• Can we include the usual blurb that described in text the data collection parameters in the version required by a journal.
  I think this is in the other reports (I would look it up but google chrome has eaten all y bookmarks!)
  Thanks,
  Bridget

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-04-17T21:51:01Z

---

• Changed the link from [poster] to [report].
• The blue splash banner now extends across the whole report at the top.
  This will be available tomorrow after nightly updates.

Please email me a report with a blurb that describes in text the data collection parameters in the version required by a journal. I'll implement it as well. Thank you.

[leginonbot]

---

Original Redmine Comment
Author Name: Bridget Carragher (@bcarr-czi)
Original Date: 2019-04-18T00:05:20Z

---

Thanks Sargis _ I will check these out tomorrow.
The section I want added to the Report is the "Experimental Method" section that is already part of the User Results page - you can click on any of these and you will find it near the end.

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-04-18T00:15:20Z

---

Ok, got it. I'll copy "Experimental Method" section from User Results page. Some of it is in "Experimental setup" table. I'll remove them from there to avoid repetition.

[leginonbot]

---

Original Redmine Comment
Author Name: Bridget Carragher (@bcarr-czi)
Original Date: 2019-04-18T00:38:10Z

---

Hmmm... I think I like both though - they serve different purposes.. Ed, can you weigh on on this please.

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-04-18T22:52:44Z

---

Copied over Experimental Methods section. Left the rest unchanged. This will be available tomorrow after nightly updates.

[leginonbot]

---

Original Redmine Comment
Author Name: Bridget Carragher (@bcarr-czi)
Original Date: 2019-04-18T23:43:00Z

---

Excellent, thank you.

[leginonbot]

---

Original Redmine Comment
Author Name: Ed Eng (Ed Eng)
Original Date: 2019-04-19T01:44:09Z

---

In terms of the previous query the context is slightly different and the user would glean different information.

An issue I have is that there may have several grid Atlases or parameters within a session.

Questions:

1. Is there a way to specify which grid Atlas to show in the report if there are multiple ones in the session?
2. Is there a way to designate the table to show the information from the last entries of each preset? Meaning during setup a particular dose or setting may have been initialized, but the preset was changed for data collection. Therefore, we would want the table display the latest values for each preset.

[leginonbot]

---

Original Redmine Comment
Author Name: Bridget Carragher (@bcarr-czi)
Original Date: 2019-04-19T01:54:23Z

---

Hmmm.. good point about the atlases. Can we show all atlases from a session? Or should we just show the last one? I am not sure if we shouldn't always start a new session if there is a new atlas?
Also can we show an exemplary high mag image? If there is one - it would be up to the operator to choose one.
I love this automated report and think we can grow it further.
I like the idea of having a picked particles etc. also as Ed does in his manual reports.
Can we caht about the editable text box - it would be good to edit that out into plain text for the pdf. And maybe it should be moved to the end? But let's chat before doing any of this.

[leginonbot]

---

Original Redmine Comment
Author Name: Ed Eng (Ed Eng)
Original Date: 2019-05-23T23:56:39Z

---

Have not fully shifted over to the report.

Currently testing the reports with recent sessions have encountered formatting issues.

1. Would like preset formatting to match the rest of the report
2. Uploaded figures to the file manager, but where are those images and how do we manage the files? Where are they located once uploaded?
3. When trying to create a pdf the added section shows up as grey. See uploaded attachment for 19may22f report.

For an example see: http://emgweb.nysbc.org/betamyamiweb/poster.php?expId=9084
or http://emgweb.nysbc.org/betamyamiweb/poster.php?expId=9038

[leginonbot]

---

Original Redmine Comment
Author Name: Sargis Dallakyan (@dallakyan)
Original Date: 2019-05-28T22:38:36Z

---

Updated @Download PDF@ link to point to the same page with added @&inline=1@ to URL. This will render things inside the editor inline and print the PDF. Added section doesn't show up as grey anymore. This also allowed me to get rid of @save@ button and @Download PDF@ in the PDF. I can look on how to split this into multiple pages, if needed.

The uploaded files are stored under /gpfs/uploads and thumbnail images are stored on emgweb under /srv/www/html/betamyamiweb/thumbs. emgweb has around 200GB space available. Wasn't sure if this would be enough moving forward, that's why I created /gpfs/uploads.

Files can be managed using http://emgweb.nysbc.org/betamyamiweb/filemanager/dialog.php
This is the same UI as you click on image icon in the editor (https://www.responsivefilemanager.com/). Only logged in users with admin privileges can access this for security reasons.

Can't figure out what's different in preset formatting. It shows blue rectangle with title (Imaging Summary) as in the rest of the report.