Editing GO Site

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Warning: Please make sure that you have read the most recent version of this document before contacting Seth or Moni.


General notes

  • In the interest of keeping the interface usable and prevent the most common types of mistakes, we have removed the WYSIWYG editor in preference for the usual Drupal/html editing. A little HTML knowledge will take you a long way. If this causes problems, please let us know.
  • The user login page is at: http://geneontology.org/user/login ; this may change in the future--if this link does not work, check back here
  • All internal links should be relative. Examples below.
    • On the other hand, to link to an info page such as the 'Contact' tab, type:
      More information is available on the <a href="/form/contact-go">Tools Page</a>.
    • To link to the book containing the GO evidence code guide, you may type the following:
      Refer to the <a href="/book/guide-go-evidence-codes">GO evidence code guide</a> for the list of valid evidence codes.
  • Editors cannot currently change menus, if you need a menu change please contact a Manager (currently Chris, Seth, or Moni).
  • Editors (you) have broad powers in editing and creating content, however are limited in deleting content; if you need something deleted, please contact a Manager (currently Chris, Seth, or Moni).
  • To view a book as a single page, click on the Printer-friendly version link.
  • Save your work. Remember to always save your work.

How to add content

First note that all content on a Drupal website is stored and treated as "nodes". A node is any posting, such as an info page, book page, or an article. However, different types of nodes have different properties and abilities. Sections further down will address some of the differences in editing and display.

After login there will be a menu visible in the left column. It contains links to add new content, currently: article, info page, book page, highlighted term, and external project. There is also a link to list all available current content at find content.

Info pages

Info pages are just general purpose pages for unstructured chunks of information--image an About page. Info pages can be added to books, but this is not generally recommended.

  1. Click Add info page from navigation.
  2. Enter a Title for the page. It will be displayed at the top. Please 'Capitalize Each Word' in the title. Keep in mind that the title will also form the final URL.
  3. Carefully choose the intended audience from the User Story menu. You may have multiple user stories.
  4. Choose the appropriate Tags to categorize this content. Is this page a guide document? Or is it describing the structure of the ontology? You may have multiple tags.
  5. The editing box (Body) can be resized from the bottom right corner.
    1. If you are creating a new page, you can just type the text, using HTML as needed. Allowed tags are listed.
    2. Alternatively, you can directly copy and paste the text from the raw HTML found in the corresponding file from the list of old site documents. If you choose to follow the latter method, please be aware that you need to further edit the text to remove unnecessary titles, and in many cases to introduce breaks. Please compare with the 'old' site for accuracy of content and sequence.
  6. If you wish control the text that appears in teasers or content lists, you may edit what appears by opening the Edit summary link.
  7. To add images to your document, click on the image link and either select a previously uploaded image or upload a new image.
  8. Preview your work using the button at the bottom of the page.
  9. Save your work. Remember to always save your work.

Book pages

A book is a set of pages tied together in a hierarchy, like chapters. Books can be used for guides, manuals, FAQs, etc. It can also be used as a shadow taxonomy for pages, but this is not usually recommended.

  1. Click Add book page from navigation.
  2. Enter a Title for the page. It will be displayed at the top. Please 'Capitalize Each Word' in the title. Keep in mind that the title will also form the final URL.
  3. Carefully choose the intended audience from the User Story menu. You may have multiple user stories.
  4. Choose the appropriate Tags to categorize this content. Is this page a guide document? Or is it describing the structure of the ontology? You may have multiple tags.
  5. The editing box (Body) can be resized from the bottom right corner.
    1. If you are creating a new page, you can just type the text, using HTML as needed. Allowed tags are listed.
    2. Alternatively, you can directly copy and paste the text from the raw HTML found in the corresponding file from the list of old site documents. If you choose to follow the latter method, please be aware that you need to further edit the text to remove unnecessary titles, and in many cases to introduce breaks. Please compare with the 'old' site for accuracy of content and sequence.
  6. If you wish control the text that appears in teasers or content lists, you may edit what appears by opening the Edit summary link.
  7. To add images to your document, click on the image link and either select a previously uploaded image or upload a new image. The pop-up window offers you options to Upload/Thumbnails/Insert File. Click on Upload, then Browse and you'll see all the images from the old website. Select the one you need, upload it, then insert file.
  8. To finish creating a new book using this newly created page as the 'front page', scroll down to the bottom of the page and click on Book outline. A drop-down menu under the word Book will appear on the right. Choose the <create a new book> option from the menu. A short fragment of text will appear under the menu, warning you that This will be the top-level page in this book; that is ok. You may now save your work.
  9. To add into a book hierarchy:
    1. As explained above, if you save at this point, the content you just prepared will be the 'front page' of the book. You may also click on the Book outline tab at the bottom and select a different book where you want to add this page (and its parent, if applicable).
  10. Preview your work using the button at the bottom of the page.
  11. Save your work. Remember to always save your work.

To add additional pages to a book, you must have saved the book at least once. Then, you may click on the Add child page link at the bottom of a book page, and follow directions above.

Articles

Articles (article pages) are designed for time-sensitive content such as news, press releases, newsletters, announcements, or thoughts.

  1. Click Add article page from navigation.
  2. Enter a Title for the page. It will be displayed at the top. For the title, please 'Capitalize Each Word' as you would in the title of a book. Keep in mind that the title will also form the final URL (Capitalize the first letter in each word).
  3. Carefully choose the tags to associate with the article from the menu. You may have multiple tags.
  4. The editing box (Body) can be resized from the bottom right corner. If you are creating a new page, you can just type the text, using HTML as needed. Allowed tags are listed below the edit area.
  5. If you wish control the text that appears in teasers or content lists, you may edit what appears by opening the Edit summary link.
  6. To add images to your the body of your article click on the Insert image link under the edit area. This will allow you to upload an image and add the link at point.
  7. You may also associate an image with the article as a whole: select the image and click on the Image Upload.
  8. Preview your work using the button at the bottom of the page.
  9. Save your work. Remember to always save your work.

Note: This type of node will automatically be posted to Twitter every time' unless you specify otherwise. To prevent pushing out to Twitter, click on Post to twitter.com and uncheck the box before saving.

External projects

An external project is description or placeholder for a GO-related project. It should mainly be treated as a forwarding stub, unless said project has not yet gotten to the point where it has its own pages.

  1. TODO
  2. Save your work. Remember to always save your work.

Highlighted terms

Highlighted, or otherwise special, GO term for public consumption.

  1. TODO
  2. Save your work. Remember to always save your work.

Note: This type of node will automatically be posted to Twitter every time' unless you specify otherwise. To prevent pushing out to Twitter, click on Post to twitter.com and uncheck the box before saving.

How to edit content

All non-book content

This is rather easier than content generation.

  1. Log in
  2. Navigate to the page that you want to edit, either directly or through Find content
  3. Click on the Revisions tab
  4. Make your desired changes, just as if you were creating the content
  5. Save your work. Remember to always save your work.

Bulk book edits

We are not (yet) supporting bulk book edits for Editors. We may change this depending on feedback.

Books can be edited page by page by following the non-book editing instructions above.

Books can be edited either by editing individual nodes (tedious) or using the method outlined below.

  1. Login
  2. Click Find content in navigation
  3. Click the "Books" tab
  4. Select the edit order and title link for the book that you wanted to edit
  5. On this page you may change order and nesting by dragging and dropping items; you may also rename the individual "chapter" titles
  6. Save your work. Remember to always save your work.

Versions and reversions

All nodes are currently setup to create new revisions after saving when editing, so go ahead and try that change. To roll back to a previous revision:

  1. Login
  2. Navigate to said page
  3. Click on the Revisions tab
  4. View the revisions by clicking on the links under Revision
  5. Revert by clicking the revert link under Operations
  6. Save your work. Remember to always save your work.

Inserting images

All images from the 'old' GO site have been uploaded and are available in a public folder in the new Drupal site.

To insert an image:

  1. Use the 'Insert Image' link at the bottom of the editing window.
  2. A pop-up window will show you all available directories. All images from the old site are stored in the 'public' directory. (see image labeled GOC_Drupal-image-selection-window.png)
  3. Double click on your image of choice to insert it in the page.
  4. A new line of text similar to this will appear on the editing window: <img src="/sites/default/files/public/foo.gif" width="180" height="60" alt="foo.gif" />
  5. You may now preview or save your work.
  6. Save your work. Remember to always save your work.

Dealing with highlighted text / boxed text

  1. Please convert highlighted/boxed text into bold text using the HTML tags <strong>Bold Text Here</strong>.
  2. Please remember: no highlights and no background color.
  3. Save your work. Remember to always save your work.

Style guide

Headers and TOC

Headers for content should start at h2 and go down from there. If you've already started at h3 don't worry--those will eventually fixed in the churn.

Tables of contents should not be produced by hand. They can be automatically added to most pages with the [toc] filter tag added to the top of the page content. The current setting for the TOC are to only list headers at h2 and h3.

Tables

Tables should use the classes: table, table-striped, table-bordered, and table-hover. A typical table should be started like:

<table class="table table-striped table-bordered table-hover">

Logos

Logos in projects will be cropped over 220x165. If you're having trouble getting getting your logo into an appropriate format, contact Seth or Moni for some help.

There's something I want! / It's not working!

  • We're still testing the new site and its workflows (thank you!), so not all of the pieces will fit perfectly yet. If there is something that you'd like (a new tag, a larger icon), please contact Seth or Moni to see if they can help you out.
  • If something seems to be broken, it might not just be you. Please contact Seth or Moni before frustration sets in so we can try and work out what's going on (or manage your expectations).
  • Keep in mind that these instructions and the current state of the site might fall out of sync. If that's the case, contact Seth or Moni to see if they can fix or update things.