This box searches only this space. The box at the upper right searches the entire CyVerse wiki.


For overview information, see the CyVerse website.

Getting Started with CyVerse

GETTING STARTED WITH CYVERSE

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Adding a new section to your Dashboard

To add a new section:

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This feature is currently broken. Sorry.

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Under Activity Stream, click Gadget URL.

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About the CyVerse wiki

CyVerse uses Confluence Wiki. This is a general how-to guide for using and working in the CyVerse wiki.

Tip

This is not meant to be an all-inclusive guide to using the Wiki. If you need more in-depth information, check their Help info at https://confluence.atlassian.com/doc/confluence-documentation-home-135922.html. It's helpful.

If you don't find something here about the wiki that you wish was here or want to know about that would also be pertinent to other CyVerse users, email Kathleen.

If you can't access a space others on your team are using (the page just doesn't appear in your list on that space), ask a Special Assistant to help you.

Logging in to the wiki

To view many pages and to create or edit a page (permissions set by the space admin), you need to be logged in.

  1. Go to https://wiki.cyverse.org/wiki/.
  2. Enter your CyVerse username and password.

If you don't remember your username or password, or you can't get in (and you know you're using the right username and password), see Resetting Your Password on the website.

Using your personal space

Each CyVerse user gets his or her own personal space. By default, all content in it is open to the public so everyone can view it. You can restrict visibility and editing permissions for the entire space and any pages you save to your personal space.

  1. Click CyVerse Wiki on the menu bar to view your dashboard.
  2. Under Site Spaces, click View All.
  3. In the Space Directory on the left, click Personal Spaces.
  4. Find your name in the list.
  5. Add your space to your list of Favorite Spaces by clicking the star to the right.
  6. To change the visibility setting of the space (since you're the admin of your space, you can do this):
    1. Click Spaces on the menu bar and then click your name.
    2. Click Browse and then click Space Admin.
    3. Under Security on the left, click Permissions.
    4. Change the permissions for Individual Users and Anonymous Users (users who aren't logged in to the wiki) as needed.
    5. Click Save All.
  7. To change the visibility of a page in your space:
    1. View the page (but do not open for edit).
    2. Click Tools > Restrictions.
    3. Verify Viewing is selected.
    4. To limit viewing of the page to only you, click Me, or select the users or groups who can view the page.
    5. Click Save.
    6. You may also want to put a panel, possibly hidden if you want (instructions for both below), to indicate that the page is visible only to X users.
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Customizing your dashboard

You are the ruler of your dashboard so you can lay it out however you want. Some useful things are adding your most commonly used or important spaces to your list of Favorite Spaces (see below), defining how many updates are listed in each section, and much more.

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userkkennedy

Using Favourite spaces and pages

You can have a list of favorite spaces and favorite pages. This is a useful way to view only the updates you want to see. (Yes, Kathleen knows Favourite is not how we spell it in the U.S., but this is how it is in Confluence!)

Favourite Spaces: Adding a favorite space and viewing your Favourite Spaces list

  1. To add a favorite space:
    1. From your Dashboard, find the space to favorite in the Site Spaces list.
    2. Click the star to the right of the space name.
  2. To remove a page from your Favourite Spaces list, click the star to the right of the space name.
  3. To view updates in only your list of Favourite spaces:
    1. Click CyVerse Wiki at the top left to return to your Dashboard.
    2. Click Spaces in the left column, if not already selected:
      Image Modified
      You also can click the Favourite Spaces tab in the right column. The setting remains until you change it.

Favourite Pages: Adding a favorite page and viewing your Favourite Pages list

Have a page you refer to often and tired of trying to find it? Make it a favorite and it will show up on your Dashboard.

  1. To add a favorite page:
    1. Click to view the page to favorite (don't open it for Edit).
    2. Click Tools on the right and then click Favourite.
  2. To view your favorite pages:
    1. Click CyVerse Wiki at the top left to return to your Dashboard.
    2. Click Pages on the left:
      Image Modified
  3. To remove a page from your Favourite Pages list, click the star to the right of the page name.

Watching a page or space

If there's a page or space you'd like to receive emails about updates (for example, edited content or new comments), you can put a watch on it.

  1. View (but don't open for edit) the page you want to watch.
  2. Click Watch at the top right of the page.
  3. Click either of both or .

About space permissions and page restrictions

Permissions are set at the space level by the space admin.

Restrictions are set at the page level. If the space administrator gave you the rights to add a page, you can edit the page and set restrictions for what users can see and do on your page. The administrator of the space maintains all rights to all pages in the space.

If Edit isn't displayed at the top right, you don't have edit permissions. If you need them, contact the space administrator.

To find out the name of a space administrator, go to Spaces > Space Directory and click Image Modified on the right of the space name.

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For content writers and editors

To create or edit a page, you must have permissions from the space administrator. If you're the space admin, you have full rights.

Basically, if Edit isn't displayed at the top right of the page, you don't have edit permissions. If you want them, contact the space administrator.

Setting space permissions and page restrictions

Space permissions and page restrictions on the Confluence wiki are the way in which you control who sees and edits pages in your space. Confluence doesn't make it all that intuitive, so here's a quick overview.

Permissions are set at the space level by the space admin. Restrictions are set at the page level; your ability to define restrictions depends on the permissions the space admin has given you.

Here's the tricky part: If you want someone to be able to edit a page on your space, the space administration has to give the user or group Add permissions on the space level. Add permission also means they can create a page on your space, which can be not the greatest thing, but it's not a common occurrence.

Groups in Confluence, populated from LDAP groups, set the level of permission or restriction. Within the group you can drill down to specific settings for the space as well as for the page:

  • iplant-everyone: All authenticated and logged-in CyVerse account holders. This is the default setting.
  • staff: For CyVerse staff only. This does not include students (which does not have its own group), so if you want to allow a student access to the space, you'll need to add the student in the Individual Users section. Just make sure you remove the rights when the student is no longer with CyVerse.

There are other groups as well, such as sciteam, core-services, eot, and more. To search for a group or user, click the search button, and enter the first 3-4 letters of the group name or user name to find. If you don't find it, enter an asterisk, click Search, and then browse through the list.

Setting space permissions (space admin only)

  1. In your space, click Browse > Space Admin.
  2. Log in as Admin, using your regular username and password.
  3. Click Permissions on the left:
  4. Click Edit Permissions to add or edit permissions.
    Note: To allow a user to edit a page, you must click Add. This also gives the user the rights to create a page in the space but that's the way Confluence set it up.
    In the above example, the core-services and staff groups have the permission to add (and thus edit) pages in the space, but the iplant-everyone group can only view pages.
  5. Log in with your CyVerse username and password.
  6. Set the permissions for the group (Note: You can restrict pages for any group or user on the page itself; see the following section):
    • To give the group viewing permissions by default, click View in the row.
    • To allow users to add comments by default, click Comments > Add.
  7. Click Save All.

Setting page restrictions

You can define the rights a user or group has to a page or group of pages in your space. Even if you gave a group permission to edit (by giving the Add space permissions), you can restrict or further define access to a page in the space.

  1. View the page to which you want to add restrictions.
  2. Click Tools (on the right)and then click Restrictions:
    • To restrict viewing of the page, click Restrict viewing, and then click either Me (so only you can see the page), Person, or Group.
      If you selected Person or Group, select the person or group (search by entering the first few letters of a name or group), click Restrict, and then click Save.
    • To restrict editing of the page, click Restrict editing, and then click either Me (so only you can edit the page), Person, or Group.
      If you selected Person or Group,select the person or group (search by entering the first few letters of a name or group), click Restrict, and then click Save.

You may want to check with the user or a user in the group for whom you gave edit permissions to make sure the Edit option is now available.

Want to use the same settings on more than one page?

Pages inherit their settings from their parent page. If you have a group of pages that you want to use the same settings on, create the new page as a child of the page with the settings to use.

CreatePage

Creating a new page

  1. Click Create at the top. (If it's not visible, you don't have permissions. Ask the space administrator or Mary Margaret to help.)
  2. Click Blank page and then click the Create button.

Page titles

We've all been confused by finding a lot of pages with the exact same title. This is not helpful when people are trying to find the content they need.

Note: If you find a lot of pages with the same or similar title, the space name under the title will guide you to the right page:

  • Use a unique and easily distinguishable title

Examples:
GOOD: Getting Started with Atmosphere, or Atmosphere Getting Started
NOT GOOD: Getting Started

  • Be clear, concise, and specific

Write a title that clearly states what it's about.

Examples:
GOOD: Docker Overview
NOT GOOD: Home

  • Use title case

Examples:
GOOD: Good Titles Use Title Case
NOT  GOOD: Good titles use title case

  • Don't start with an article (The, Of, For)

"The" (or any other article) adds nothing to the meaning of the page and clutters up the title in search results.

Editing a page

  1. Click to view the page to edit.
  2. Click Edit at the top right.

    If Edit isn't displayed, you don't have permission to edit it. Contact the space administrator or ask Mary Margaret to help. If it's a space Kathleen writes for (Getting Started, Atmosphere, BisQue, Data Store, DE, etc.), ask Kathleen.

  3. Edit the page:
  • To create columns, or to add, remove, or move a section, click and select the layout or section to use.
  • To add a heading (helpful if you want to add a Table of Contents (TOC) to the page for quick access by those reading the page), click the style selector at the top right (usually shows Paragraph), and select the heading level. Paragraph is default text and isn't added to the TOC.

If you do use a TOC, be sure to nest your content sections so Heading 1 is first, then the next heading under that section would be Heading 2, so the TOC shows the proper structure.

Editing in the source editor

The default editing mode is WYSIWYG. It works pretty well most of the time but sometimes things get stuck. You can get around it by editing in the source editor:

  1. Click  (Open in source editor) at the top right.
  2. Edit the code as needed.
  3. Click Apply.

Editing an existing section in Wiki markup (Markdown)

You can still enter text using the same old markup we used before, but it's immediately converted to the new editor, which strips out the markup code. The bigger problem is you can't dig into the code to correct problems when they arise.

If you just want to edit a small section that's giving you heartburn, here's a workaround:

  1. Click in a new line below the problem section and enter (curly bracket).
  2. Start entering "wik" to bring up the Wiki markup without migration macro, and then press Enter to select it. (You can also get to it from Insert > Other Macros.)
  3. Copy the problem section and paste it into the wiki-markup panel.
  4. Reformat it using markup. (Yes, it's kind a pain but it works.)
  5. Click Preview. It's formatted without showing the markup.
  6. Click Save. It's saved in markup for future editing.
  7. Delete the original section.

You can easily add new text in the wiki-markup panels too, and if you'd rather use Markdown, that's an option too. Help Tips are provided to the right of the screen while in Wiki Markup mode along with a link to a full notation guide. Read more about it here.

Moving a page in the space list (admin only)

By default, new pages go at the bottom of the space list on the left. It's fairly easy to move a page in the same space that you administrate. Moving a page to a different space is a different topic altogether and not within the scope of this page.

  1. In the space, click Browse at the top and then click Pages.
  2. Expand the tree list and find the page to move.
  3. Drag the page to the location.

Adding links

Adding external links

  1. Click where you want to add the link.
  2. Enter the link text that will be displayed.
  3. Click  on the toolbar.
  4. Select the insert method:
    • To search for the target page on the wiki:
      1. Verify Search is selected on the left.
      2. Either enter some or all of the page name in the search field to search the entire wiki, or click the second drop-down arrow and select the space name to narrow down to a specific space.
      3. Click Search.
      4. Select the target page.
      5. Click Insert.
    • To add a link to a page on the web, click Web link, paste the URL to the page, enter the link text, and click Insert.

LinkWikiPage

Adding links to a CyVerse wiki page

When you need to link to a page on our wiki—say, in an Ask question, paper, or in JIRA—you can use the tiny link, available within the wiki page.

  1. As a logged-in user, click to view the page to which you want to link.
  2. Press k (or go to Tools > Link to this Page).
  3. Copy the Tiny Link field.
  4. Paste in the link field, as outlined in the previous section.

Adding attachments

  1. Click Insert and then click Attachment.
  2. Browse to the location of the file to attach and click Insert.

Adding images

  1. Click in the position where you want the image.
  2. Click Insert and then click Image.
  3. Browse to the location of the image and click Open.
  4. Click to select the image in the list and then click Insert.
  5. Click to resize, add a border, or resize (or drag and resize it as needed).

Previewing and saving the page

Preview mode lets you can see how a page will look when you save it. It's not a big deal to Save it (which publishes it too) but here's how you can preview it before you do.

  1. Click the Preview button at the bottom.
  2. Edit some more, or click Save.

Other bells and whistles

There are some useful things you can add to your pages that help you manage the page, highlight content, and more. Here are a few. If you really want to delve in, ask Kathleen or google "Confluence Wiki" and whatever it is you want to do. Sometimes we don't have the right plugin, so you may be out of luck, but there are a lot of things you can use to make your pages more interesting and navigable by your readers.

This page will grow with time, but here's something to get you started.

Reusing content on multiple pages (Inclusions pages)

It's tedious to have to write or edit the same section over and over, and then more than likely you'll forget all the pages you put it on, which means content is out of sync across pages. The solution is using an Inclusions page. Write it once and plug the macro tag into all of the pages you want it to show up. When changes are required, all you have to do is update the Inclusions page in one place and it propagates to all of the pages you've included it in. For example, the following sentence is a separate Inclusions page I created because I use it so much:

 

The code I used for it is as simple as this after inserting the Include Page macro: docs:_login_/DE

Step 1 (one-time only): Create the _InclusionsLibrary page per space.

  1. Log in to the Wiki.
  2. Create the page:
    1. Click Create at the top and choose your space.
    2. Click Blank page > Create.
  3. In the title field, enter _InclusionsLibrary (prefaced with an underscore, as will be all Inclusions pages in your space). This will be the main page for all your Include pages and you'll save all your Inclusions pages under this page.
  4. Save the page.
  5. Move the page so it doesn't show up in the navigation pane:
    1. Click Browse > Pages.
    2. Drag the _InclusionsLibrary page ABOVE the home page for the space.

Step 2: Create the Include page.

Content on this page will be displayed exactly as shown when you insert it into other pages.

  1. In your space, click Create > Blank page > Create.
  2. Enter the title for the Inclusions page, prefacing with an underscore to denote an Include page.
  3. In the body, enter the text you want to reuse.
  4. Click Preview to see how it will look.
  5. When done, click Save.

Step 3: Insert the Include page content where you want it on your wiki page.

  1. Open the page for edit you want to add the Include page content to.
  2. Click where you want to add the content.
  3. Enter a curly brace ( { ).

  4. Type Include and then click Include Page.

  5. In the field, enter the name of the Include page. It will show up as Not Found but it's okay, it will be there if you did it correctly.

  6. Click Preview to see how it will look. If it's not showing up properly, go back to the Include page and edit and save it, and then refresh your page.

  7. When done, click Save.

Highlighting important content

There are several different ways you can highlight important information on your page.

For all of the following, open the page for edit, click Insert > Other macros, and then select one of the following, then enter the note that will be contained in the note:

  • Info boxes

Insert > Other macros > Info

This is an Info box. Similar usage to a Note but less colorful.

  • Notes

Insert > Other macros > Note

This is a Note. Useful for side information or something you want to highlight but that isn't critical information.
  • Info boxes

This is an info box.

Use it for information you want to call attention to that is not critical in nature.

  • Warnings

Insert > Other macros > warning

This is a warning.

Use warnings for something that may cause a dire consequence (like data loss)–and put it before the step or section so the user doesn't perform the action then see that doing so was going to cause something bad to happen.

  • Expanding sections

Expanding sections are a good way to include content that may not be necessary but could be useful. Also good for screen shots when the graphic is useful but not necessary, or for examples of code that can be copied but only needed by those who want to copy the code. Use your discretion.

  1. Click Insert > Other macros > Expand.
  2. Click the header and then click Edit to change the clickable text.
  3. Click in the section and add the text that will show when the section is expanded or insert an image (Insert > Image). In the example below, I changed "Expand to..." to "Here's an example of how you might use an Expand section." Just make sure it's something explanatory enough so users know to click to view more info or skip if they don't need to see it.
  4. When done, click Preview to see how it looks.
Here's an example of how you might use an Expand section.

Here's some text that would be useful but isn't really necessary. The user can click to view it, or skip to the next step quickly and easily.

Note that I changed the title of the Expand header.

You also can add a graphic:

  • Panels

This adds a colored panel with a content section. Good for a section you really want to call attention to since you can customize the colors of the font and background color for the title and body.

  1. On the page where you want the panel, enter {panel and then click Panel to select the macro (or click Insert > Other macros > Panel).
  2. Edit the panel header:
    1. Click the Panel header and then click Edit.
      Note: All of the following settings are things Kathleen uses—feel free to use your own or mine.
    2. Panel Title: Enter a descriptive note to indicate the general group that can still view the page. This is what shows as the title of the panel when viewed on the page.
    3. Border Style: solid.
    4. Border Colour: red.
    5. Border Pixel Width: 3px.
    6. Background Color, LightBlue.
    7. Title Background Colour, MediumTurquoise.
  3. Click Close.
  4. Click in the panel and add the text that will show under the panel header.
  5. Click Preview to see how it will look. Edit as needed.

    LightBlueMagentaThis is the panel headersolidred3px

    Here's an example of a panel (with a Magenta header because Kathleen likes magenta).

Adding an anchor and then linking to the anchor in the same or different page

Anchors should be placed above the section you want to show when the user clicks the link, because they open below the anchor.

  1. To create the anchor:
    1. In a row above the section to display when clicked, enter {anc and then click anchor.
    2. Enter the anchor name with no spaces. It's not case-sensitive, so use something that's descriptive enough to remember.
    3. Save the page.
    4. If the link will go on a different page, copy the URL to the page.
  2. In the page where you want the link to the anchor:
    1. Click in the spot, and click .
    2. Click Advanced.
    3. In the Link field, paste the URL you just copied and then immediately after the link, enter # and the anchor name.
      If the link is on the same page, just enter # and the anchor name.
    4. In the Link Text field, enter the text that will be linked.
    5. Click Insert.

Removing a Wiki page from view (best alternative for archiving a page)

Although only the space admin can archive a page, restricting the ability to view the page effectively archives the page by removing it from view to most users. An advantage is that it also removes the page from search results while keeping the page's contents available for historical purposes–always a good idea.

This is the way Kathleen does it for viewing; use it or change it as needed.

  1. Change the visibility of the page so it shows only to selected users:
    1. As a logged-in user, view the page but do not open for edit.
    2. Click Tools and then click Restrictions.
    3. Verify Restrict viewing is selected.
    4. Click Person and select the usernames of the CyVerse users who should still see the page. Make sure you include the team lead or manager.
    5. Click Close.
  2. Create a Show If section that shows the content only to the users to whom you just restricted viewing visibility:
    1. Open the page for edit.
    2. At the very top of the content, enter {show if and then click Show If to select the macro (or click Insert > Other macros > Show if).
    3. In the Users field, enter the user names or the group name in the User Groups field. Make sure you include your name in the Users list, if you're restricting to specific users.
    4. Click Insert.

  3. Create a panel within the Show If panel and then add the note (see the previous section). This makes it obvious what you did to the page.
  4. Click Preview to see how it will look. Edit as needed.
  5. Click Save.
  6. Log out of the wiki and go back to the page to see if you can view it.

You also can just create a panel independent of a Show If section to highlight something more important.

 

INLINEStaffLightBlueMagentaViewable only by Staffsolidred3px

Here's an example of a panel that is visible to all staff (I chose Magenta for the title color because I like magenta):

Only Staff can see this section and panel.