Style search results page

[jonrkarr]

Below are notes about what needs to be improved and specific CSS changes that address most of these issues. I'm also attaching a screenshot of what the page looks like with these changes.

• Color scheme
  • Use consisent color scheme. This is a helpful tool https://paletton.com/#uid=33z0u0kvc++jb+qpd+XPj+VZCGN
  • Background of navigation bar
  • Logo, icons, text in navigation bar
  • Search results
  • box
• Navigation bar
  • Use new logo in navigation bar
  • Reduce height of logo so there is margin between the logo and the top and bottom of the navigation bar
  • Add help, about links to navigation bar with help, about icons
• Page content
  • Use consistent padding on top, left, bottom, right
• Integrate search bar into navigation bar or remove
• Table of contents
  • Move to left of search results
  • Change to unordered list
  • Remove underlining on hover
  • Change link colors to black
  • Make position "sticky" (see CSS notes below)
• Search results
  • Move to right of search results
  • Visually distinguish each result section
  • Shorten field names (KEGG ID --> KEGG)
  • Add hyperlinks for each field (e.g., to KEGG, YMDB, ECMDB)
  • Remove undefined ids (e.g., YMDB ID: undefined)
  • Replace (-> with → or other arrow)
  • Add pagination
  • Space the results more compactly
• Add spinner or other element to indicate that the user should wait for the search results to load
• HTML metadata
  • Change title to Datanator: Molecular data for integrative research or similar
  • Replace favicon with new logo
  • Set additional metadata. Here's an example:

    <meta name="description" content="Web application for simulating kinetic models of biological processes and visually analyzing their results" />
    <meta name="keywords" content="biomodel, biochemical, molecular, cell, simulate, visualize, reproducible, standards, CellML, SBML, SED-ML, Vega" />
    <meta name="language" content="EN">
    <meta name="copyright" content="Center for Reproducible Biomedical Modeling" />
    <meta name="author" content="Center for Reproducible Biomedical Modeling, info@reproduciblebiomodels.org" />
    <meta name="reply-to" content="info@reproduciblebiomodels.org" />
    <meta name="url" content="https://www.biosimulations.org">
    <meta name="identifier-URL" content="https://www.biosimulations.org">

• Organization
  • Place all styling into style sheet; do not insert style into HTML
  • Pick meaningful css class names for each HTML DOM element
  • Avoid nesting css classes with itself (e.g., google results within google results). The inner and outer containers should have different names.
• Use margin rather than <br/> to space DOM elements. Only use <br/> within paragraphs of text.

/* top navigation bar */
.bp3-navbar.bp3-dark {
    background: #1890ff;
    box-shadow: 0 2px 3px #00000066;
}

.logo-holder {
    height: 46px;
    margin-top: 2px;
    margin-bottom: 2px;
}

.bp3-dark .bp3-button:not([class*=bp3-intent-]) .bp3-icon {
    color: #fff;
}

/* page content */
.general {
    margin: 0 auto;
    margin-top: 50px;
    padding-top: 2rem;
    padding-bottom: 2rem;
    max-width: 1200px;
    display: flex;
    justify-content: space-between;
}
.general > .MuiGrid-root {
    max-width: 15%;
    flex-basis: 15%;
    margin-right: 2rem;    
}

/* search input box */
.ConcSearch {
    display: none !important;
}

/* contents */
.contents {
    color: #333;
    padding: 0.5rem;
    margin: 0 !important;
    border-radius: 4px;
    border: 1px solid #ffc306;
    background: #fffcf2; /* 95% lighten of primary color */
    box-shadow: 3px 3px 5px #00000066;
    position: sticky;
    top: calc(50px + 2rem);
}
.contents h3 {
    margin: 0;
    margin-top: -0.25rem;
    margin-bottom: 0.5rem;
    height: auto;
    padding: 0;
    line-height: 100%;
}
.contents ol {
    list-style-type: circle;
    padding: 0;
    margin: 0;
    margin-left: 1.1rem;
}
.contents a {
    margin-left: -0.125rem;
}
.contents a {
    color: #333;    
}
.contents a:hover {
    text-decoration: none;
}

/* search results */
.general > .google.results {
    width: 100%;
}

.google.results > .MuiGrid-root {
    width: 100%;
    max-width: unset;
    flex-basis: unset;
}
.google.results > .MuiGrid-root > div {
    width: 100%;
    border: 1px solid #1890ff;
    border-radius: 4px;
    background: #f3f9ff;
    box-shadow: 3px 3px 5px #00000066;
}
.google.results > .MuiGrid-root > div:not(:first-child) {
    margin-top: 2rem;
}

.google.results .MuiTypography-h6 {
    color: #fff;
    background: #1890ff;    
    font-weight: bold;
    padding-left: 0.5rem;
    padding-right: 0.5rem;
}

.google.results .MuiList-root {
    width: 100%;
    padding: 1rem;
}

.google.results li {
    padding: 0;
    margin: 0;
}
.google.results li:not(:first-child) {
    margin-top: 1.0rem;
}
.google.results li .MuiListItemText-multiline {
    margin: 0;
}

.google.results li a {
    color: #000;
    font-weight: bold;
    font-size: 1rem;    
}

/* general styling */
br {
    display: none;
}

[jonrkarr]

The page is looking better. However, I can't comment on most of the page because I don't see any results.

• Logo
  • I saved the logo in SVG format. This can be edited with Inkscape or any text editor.
  • Stick with the color palette above. In particular, use the orange color FFC306 and a lighter shade (FFCF36 or FFDA66)
• Table of contents
  • This shouldn't be shown until the results load. The page looks odd with the spinner next to the TOC.
• Spinner
  • This should be vertically and horizontally centered within the content portion of the page.
• Search bar
  • Should be hidden and only revealed when a search icon (e.g., magnifying glass is clicked).
  • The meaning of the two boxes is still not clear. " in " needs to be inserted in between the two boxes
  • The background color is too dark. Use a lighter shade than 1892FF (e.g., 70BBFD)

[yosefdroth]

I made those changes. How is the search results page now?

Example link - http://datanator.info/general/?q=glucose&organism=Escherichia%20coli

[jonrkarr]

Some of the changes have not been made. It is important to address each point of an issue. I have created new issues for items which have not been addressed. See #29 #30. The comments in #24 about vertical spacing probably also apply.

[jonrkarr]

Unfortunately, I don't see any results. The server is unavailable. Error 503. I do see that the spinner is centered. That looks nice.

Can you save the page in HTML (Save as --> "Webpage, complete") and attach to the issue?

I think the URL for search results should be renamed (general --> search). See #38.

http://datanator.info/search/?q=glucose&organism=Escherichia%20coli

[yosefdroth]

Datanator_ Molecular data for integrative research.zip

[jonrkarr]

Remaining issues to address

• Change order of sections

  1. Metabolites
  2. Proteins
  3. Reactions

• Protein section

  • Can we display UniProt ids?

• Reaction section

  • Can we EC numbers?
  • Can we display the names associated with the EC numbers?

• Style

  • Align vertical position of first section with TOC
  • Remove "style="margin-top: 10px"
  • Same as comments in #24
  • Increase vertical spacing between sections
  • Remove "style="margin-top: 10px"
  • Same as comments in #24
  • Polish style of "Load More"
    • Rename "Load More (10+)" to "Load More" or "Load 10 More"
    • Can we indicate the total number of results? E.g. "Load 10 More of XX"
    • Make full width, set background color to light orange, set bottom radius to 3px, set color to gray

      .google.results button  {
      width: 100%;
      background-color: #ffe69b !important;
      color: rgb(0, 0, 0, 0.54);
      border-bottom-left-radius: 3px;
      border-bottom-right-radius: 3px;
      }

[jonrkarr]

Reordered sections

[jonrkarr]

Also display search query

[jonrkarr]

Also display number of search results

[jonrkarr]

CSS styling done.

Notes about additional content that is needed are now covered by #77, #78, #79, and #80.