crbs/cil_php_website

Display data using Elasticsearch and utilize the bootstrap layout

cil_php_website's Issues

Centering the CIL logo in the header

The CIL logo in the header is not centered. Can you make the logo look more natural in the header?
In order to do that, you need to edit

https://github.com/slash-segmentation/CIL_PHP_Website/blob/master/CIL/application/views/templates/cil_header4.php

Browse bar

Adjust the box with the email icon to the same size as the other boxes.

Move the email icon to the center of the box.

Missing onto name - see images/41363

Missing onto name - see images/41363

Add to photobox link broken

The add to photobox link is broken: http://flagella.crbs.ucsd.edu/images/16217

Create wiki page describing installation instructions for website

There needs to be a wiki page written up describing how to install this website on a machine.

Cant hear you

comma messes up the URL in the ontology expansion

See /CIL_RS/index.php/rest/simple_ontology_expansion/mouse_gross_anatomies/Name/TS20,extraembryonic%20component?size=1

Advanced Search - Image Attributes

Add reconstruction, segmentation, and 2D icon as searchable on the advanced search page under Image Attributes

When doing simple the next previous page list at bottom needs some help

On most sites when multiple pages are available for a given search there is usually a line like this with links:

first previous 2 3 4 next last

On this page: http://flagella.crbs.ucsd.edu/images?k=cell&simple_search=Search
Every possible page is given its own link. (see screenshot)

All links in the red box in the screenshot are broken

On this page:

http://flagella.crbs.ucsd.edu/images/11924

Screen shot with broken links in red box (only link that appears to work is the Pubmed one):

Advanced search missing on flagella

Advanced Search page just says "Coming soon"

Fix search page next and previous page links

When doing a search with lots of results
(example: http://flagella.crbs.ucsd.edu/images?k=cell&simple_search=Search)

Way too many next and previous page links appear. As seen in attached screenshot. This should be done in a more simple fashion maybe something like this:

start << 1 | 2 | 3 | 4 | >> end

Links on cell illustration page go back to production

http://flagella.crbs.ucsd.edu/pages/cell_illustration

Blue Navigation Bar

Increase the font to match current page and spread the terms across the bar.

Remove home button from the bar.

Move the Email button to the top of the page next to the Submit button.

Add the separator bar between terms like on the current page.

Add Pivot view to the Navigation Bar.

Downloaded file name is not correct on the ccdb pages

Downloaded file name is not correct on the ccdb pages. The file name is changed to CCDB_18_full_resolution instead of the real file name with extension.

Cannot get results from the adv. search for bateria

/images?k=plasmid&image_search_parms%5Bncbi%5D=Bacteria&advanced_search=Advanced+Search

Search results for "Segment"

The search results for "Segment" are misaligned on the first page.

Advanced search results

Add all of the Image attributes to the top of the search results so users can filter current results.

Do not forget new attributes - reconstruction, segmentation, and 2D icon

Advanced search does not show what it searches for on the result page.

Advanced search does not show what it searches for on the result page:

See http://flagella.crbs.ucsd.edu/images?k=&image_search_parms%5Bbiological_process%5D=&image_search_parms%5Bcell_type%5D=cell+by+organism&image_search_parms%5Bcell_line%5D=&image_search_parms%5Bfoundational_model_anatomy%5D=&image_search_parms%5Bcellular_component%5D=&image_search_parms%5Bmolecular_function%5D=&image_search_parms%5Bncbi%5D=&image_search_parms%5Bitem_type_bim%5D=&image_search_parms%5Bimage_mode_bim%5D=&image_search_parms%5Bvisualization_methods_bim%5D=&image_search_parms%5Bsource_of_contrast_bim%5D=&image_search_parms%5Brelation_to_intact_cell_bim%5D=&image_search_parms%5Bprocessing_history_bim%5D=&image_search_parms%5Bpreparation_bim%5D=&image_search_parms%5Bparameter_imaged_bim%5D=&image_search_parms%5Bhuman_dev_anatomy%5D=&image_search_parms%5Bhuman_disease%5D=&image_search_parms%5Bmouse_gross_anatomy%5D=&image_search_parms%5Bmouse_pathology%5D=&image_search_parms%5Bplant_growth%5D=&image_search_parms%5Bteleost_anatomy%5D=&image_search_parms%5Bxenopus_anatomy%5D=&image_search_parms%5Bzebrafish_anatomy%5D=&advanced_search=Advanced+Search

Headlines

Remove all the headlines.

Add - New website design. Let us know what you think here.

where here is a link to Guest book.

Redesign elements

Move Advanced search to below the Search box flush left to the left edge of the box.

Above the Search box have links to About, Licensing, Notification of Use, Contributors, Interactive Cells, Donate Button, Guest Book, Help, Submit, and the email icon.

We will no longer have a link to In the News but keep the page there in case we decide to bring it back.

Move the Twitter bird, Facebook logo and LinkedIn icon to the top right of the page below the Blue Naviagtion Bar and add,

Tumblr (get icon) - https://cellimagelibrary.tumblr.com
Pinterest (get icon) - https://id.pinterest.com/CILImage/cell-image-library/
Doccheck (get icon) - http://www.doccheck.com/com/profiles/103-cell-image-library/tab/info
Instagram (get icon) - https://www.instagram.com/cell_image_library/

Add the link and Apple App store link below the link icons on the right side of the page below the blue navigation bar.

Center both left and right and up and down and equal space all the logos at the bottom - ASCB, CCDB, NIF, Data Citation Index and Labby Award.

setup unit testing

Any php code on this site should have unit tests verifying correct operation. There also needs to be a wiki page with documentation on how to run unit testing.

Missing chromosome link: /browse/cellcomponent/Chromosome

Missing chromosome link /browse/cellcomponent/Chromosome

Update main readme to include requirements for software

Update readme for this site to document versions of required software and either installation instructions or a link to wiki page with more detailed installation instructions.

Not the results you were expecting and comments links broken

Links in red box broken (see screenshot)

Links on front page for Explore Paramecium redirect to production

The links on front page in red box

: http://flagella.crbs.ucsd.edu/
redirect to production. (see screenshot)

Rename Data Set to Data Sets

To match cell image library main menu rename the main menu item Data Set to Data Sets

Determine optimal conversion parameters for FLV videos to mp4 so they are pretty in html5

To get off of flash we need to convert all FLV videos to mp4 and use html5 to display them in the browser. Before doing conversion it would be good to test a few conversions at different resolutions and display them in html5 container to see how they look

A quick search found that ffmpeg can convert:
http://www.guguncube.com/1103/ffmpeg-convert-adobe-flash-flv-files-to-mp4-files

Advanced Search - Image Attributes - Grouped

Do not wrap the Yes / No check box options for the Grouped aspect in the Image Attributes Section on the Advanced search page. Move the Right hand column more to the right if necessary.

No Submit link on flagella version of CIL

The Submit link to upload data is missing on flagella http://flagella.crbs.ucsd.edu

Guest book link on main page sends you to cellimagelibrary site

The guestbook link on http://flagella.crbs.ucsd.edu/home sends you to production.

Missing image mode - /images/43901

See /images/43901

Hide Thumbnails link under Cell Process does not work

Clicking "Hide Thumbnails" does not appear to work (at least for chrome browser).

Link to page: http://flagella.crbs.ucsd.edu/browse/cellprocess

Screenshot after clicking link:

Help link on main flagella page broken

Help link on top of this page is broken http://flagella.crbs.ucsd.edu/

Home page cleanup

Remove:

Please take this brief survey to help us improve the site. !

Remove from the home page:

The Cell Image Library™ is a freely accessible, easy-to-search, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. The purpose of this database is to advance research, education, and training, with the ultimate goal of improving human health.

Missing lysosome link

/browse/cellcomponent/Lysosome%20and%20Related%20Organelles

Sort by Image Count does not seem to work

Clicking 'Sort by Image Count' does not seem to work on this page:
http://flagella.crbs.ucsd.edu/browse/cellprocess

Pagination URL keeps expanding

Go to http://flagella.crbs.ucsd.edu/images?k=ccdb+maryann&simple_search=Search
and then click page 2 . The URL will expand:

http://flagella.crbs.ucsd.edu/images?k=ccdb+maryann&simple_search=Search&per_page=10&page=&simple_search=Search&per_page=10&page=2

Data sets

Broad Institute images

Clicking a plate takes you to one image in both the old and the new websites. Was that what we always had? or was there a way to visually explore (like Pivot) for each plate?

The old website lists all the chemicals on the image (plate) page - the new website does not. Should it?

New Icons

Get or make new icons for reconstruction, segmentation, and 2D icon

Missing ontoname: 24515

See http://flagella.crbs.ucsd.edu/images/24515

Font color

Make the font for the Advanced Search, Contributors, Help and Submit text black not gray.

Make Featured Image and Explore Paramecium less bold (match current page)

Attribution link label is too long (/images/6519)

Attribution link label is too long (/images/6519)

Laminar Boundries dataset missing under "Data Set" page

The Laminar Boundries dataset missing under "Data Set" page on flagella

http://flagella.crbs.ucsd.edu/pages/datasets

My last name is incorrect

My last name is spelled incorrectly on this page: http://flagella.crbs.ucsd.edu/pages/about and on production as well. The spelling should be Churas

Missing Human Development Anatomy in the CIL content

See http://www.cellimagelibrary.org/images/39006 and
http://flagella.crbs.ucsd.edu/images/39006

Login link on main page on flagella broken

Clicking Login link from http://flagella.crbs.ucsd.edu page redirects to this broken link:

http://flagella.crbs.ucsd.edu/images/column2.html

Make ccdb download links point to iruka

It's currently pointing to the old ccdb server. For example, http://ccdb.ucsd.edu/ccdbdata/e1cb3a1_p/e1cb3a1.pic . It should be pointed to the new repository on iruka.

/images/35451 display image looks fuzzy

The display image on the 35451 page looks fuzzy compared with http://www.cellimagelibrary.org/images/35451

Create wiki page describing release process of this website

There needs to be a wiki page describing a release process. This release process should denote what has changed in this version along with rules for versioning and include the source as a release.

Here is an example of what kind of documentation we need:

https://github.com/drugdata/d3r/wiki/Deploying-D3R