Project overview

The MOLGENIS project provides an integrated database framework in bioinformatics including UI, R, Java and web service interfaces. This project is supported by University Medical Center Groningen, Groningen Bioinformatics Center ​GBIC, European Bioinformatics Institute ​EBI and the Netherlands Bioinformatics Center ​NBIC.

MolgenisNews?

MolgenisDocumentation?

How to use this wiki =

Basic editing is available to registered users

See:

• WikiFormatting
• WikiPageNames
• WikiNewPage
• TracLinks
• WikiMacros
• WikiProcessors
• PageTemplates

There is a also set of installed macros

[[BlogList]]

A macro to display list of posts and extracts outside (or inside) the Blog module - most commonly Wiki pages.

All arguments are optional:

[[BlogList]]

Available named arguments:

• recent= - max. number of posts
• category= - a category
• author= - an author
• period= - time period of the format YYYY/MM
• heading= - a heading for the list
• format= - type of display (see below for details)
• max_size= - max. number of characters to render for each post
• meta= - use =off to hide date, author and categories (default 'on')

Example showing some available named arguments:

[[BlogList(recent=5, max_size=250, period=2007/12, author=osimons, format=float, heading=Some Trac Posts)]]

The arguments for criteria are 'AND'-based, so the above example will render at most 5 posts by 'osimons' in December 2007.

There is no heading unless specified.

Without restriction on recent number of posts, it will use the number currently active in the Blog module as default for 'float' and 'full' rendering, but for rendering of 'inline' list it will render all found as default unless restricted. Additionally for 'float' and 'full' it will truncate content if it is larger than a max_size (if set).

The format= keyword argument supports rendering these formats:

format=inline	Renders an unordered list in the normal text flow (default).
format=float	A floating box out on the side of the page with slightly more detail.
format=full	Full rendering like on period, category and author listings inside blog.

The arguments can appear in any order.

Posts are rendered sorted by newest first for all modes.

[[Cards]]

Show kanban-style stacks of cards.

The arguments are:

• stack: |-separated list of stack names. (required)
• width: Width of the stacks. (Defaults to 400.)
• label: |-separated list of labels shown instead of the stack names. (Defaults to the stack names.)

Example:

    [[Cards(stack=todo|active|done)]]

[[CommitTicketReference]]

Insert a changeset message into the output.

This macro must be called using wiki processor syntax as follows:

{{{
#!CommitTicketReference repository="reponame" revision="rev"
}}}

where the arguments are the following:

• repository: the repository containing the changeset
• revision: the revision of the desired changeset

[[Image]]

Embed an image in wiki-formatted text.

The first argument is the file specification. The file specification may reference attachments in three ways:

• module:id:file, where module can be either wiki or ticket, to refer to the attachment named file of the specified wiki page or ticket.
• id:file: same as above, but id is either a ticket shorthand or a Wiki page name.
• file to refer to a local attachment named 'file'. This only works from within that wiki page or a ticket.

The file specification may also refer to:

• repository files, using the source:file syntax (source:file@rev works also).
• files, using direct URLs: /file for a project-relative, //file for a server-relative, or http://server/file for absolute location. An InterWiki prefix may be used.
• embedded data using the ​rfc2397 data URL scheme, provided the URL is enclosed in quotes.

The remaining arguments are optional and allow configuring the attributes and style of the rendered <img> element:

• digits and unit are interpreted as the size (ex. 120px, 25%) for the image
• right, left, center, top, bottom and middle are interpreted as the alignment for the image (alternatively, the first three can be specified using align=... and the last three using valign=...)
• link=some TracLinks... replaces the link to the image source by the one specified using a TracLinks. If no value is specified, the link is simply removed.
• inline specifies that the content generated be an inline XHTML element. By default, inline content is not generated, therefore images won't be rendered in section headings and other one-line content.
• nolink means without link to image source (deprecated, use link=)
• key=value style are interpreted as HTML attributes or CSS style indications for the image. Valid keys are:
  • align, valign, border, width, height, alt, title, longdesc, class, margin, margin-(left,right,top,bottom), id and usemap
  • border, margin, and margin-* can only be a single number (units are pixels).
  • margin is superseded by center which uses auto margins

Examples:

[[Image(photo.jpg)]]               # simplest
[[Image(photo.jpg, 120px)]]        # with image width size
[[Image(photo.jpg, right)]]        # aligned by keyword
[[Image(photo.jpg, nolink)]]       # without link to source
[[Image(photo.jpg, align=right)]]  # aligned by attribute

You can use an image from a wiki page, ticket or other module.

[[Image(OtherPage:foo.bmp)]]    # from a wiki page
[[Image(base/sub:bar.bmp)]]     # from hierarchical wiki page
[[Image(#3:baz.bmp)]]           # from another ticket
[[Image(ticket:36:boo.jpg)]]    # from another ticket (long form)
[[Image(source:/img/bee.jpg)]]  # from the repository
[[Image(htdocs:foo/bar.png)]]   # from project htdocs dir
[[Image(shared:foo/bar.png)]]   # from shared htdocs dir (since 1.0.2)

Adapted from the Image.py macro created by Shun-ichi Goto <gotoh@…>

[[InterTrac]]

Provide a list of known InterTrac prefixes.

[[InterWiki]]

Provide a description list for the known InterWiki prefixes.

[[KnownMimeTypes]]

List all known mime-types which can be used as WikiProcessors.

Can be given an optional argument which is interpreted as mime-type filter.

[[ListTagged]]

List tagged resources.

Usage:

[[ListTagged(<query>[,exclude=<list>],[[format=<format>],cols=<columns>])]]

format

result list presentation; supported values:

compact	comma-separated inline list of "linked-description"
oldlist (default)	" * linked-id description (tags)" list
table	table... (see corresponding column option too)
short or other value	bulleted list of "linked-description"

cols

columns for 'table' format using a "|"-separated list of column names (order matters); supported columns: realm, id, description, tags

exclude

exclude tagged resources that match a name in the colon-separated list of resource ids, accepts shell-style patterns

See tags documentation for the query syntax.

[[MacroList]]

Display a list of all installed Wiki macros, including documentation if available.

Optionally, the name of a specific macro can be provided as an argument. In that case, only the documentation for that macro will be rendered.

Note that this macro will not be able to display the documentation of macros if the PythonOptimize option is enabled for mod_python!

[[PageOutline]]

Display a structural outline of the current wiki page, each item in the outline being a link to the corresponding heading.

This macro accepts four optional parameters:

• The first is a number or range that allows configuring the minimum and maximum level of headings that should be included in the outline. For example, specifying "1" here will result in only the top-level headings being included in the outline. Specifying "2-3" will make the outline include all headings of level 2 and 3, as a nested list. The default is to include all heading levels.
• The second parameter can be used to specify a custom title (the default is no title).
• The third parameter selects the style of the outline. This can be either inline or pullout (the latter being the default). The inline style renders the outline as normal part of the content, while pullout causes the outline to be rendered in a box that is by default floated to the right side of the other content.
• The fourth parameter specifies whether the outline is numbered or not. It can be either numbered or unnumbered (the former being the default). This parameter only has an effect in inline style.

[[Poll]]

Add a poll. Each argument must be separated by a semi-colon (;) or new-line (if used as a processor). The first argument is the title of the poll, which is also the identifier for each poll.

Usage: [[Poll(<title>; <arg> [; <arg>] ...)]]

Where <arg> conforms to the following:

<arg>	Description
query:<ticket-query>	Add tickets from a query to the poll.
#<n>	Add an individual ticket to the poll.
<text>	A poll question.

eg.

[[RecentChanges]]

List all pages that have recently been modified, ordered by the time they were last modified.

This macro accepts two ordered arguments and a named argument. The named argument can be placed in any position within the argument list.

The first parameter is a prefix string: if provided, only pages with names that start with the prefix are included in the resulting list. If this parameter is omitted, all pages are included in the list.

The second parameter is the maximum number of pages to include in the list.

The group parameter determines how the list is presented:

group=date

The pages are presented in bulleted lists that are grouped by date (default).

group=none

The pages are presented in a single bulleted list.

Tip: if you only want to specify a maximum number of entries and don't want to filter by prefix, specify an empty first parameter, e.g. [[RecentChanges(,10,group=none)]].

[[RepositoryIndex]]

Display the list of available repositories.

Can be given the following named arguments:

format

Select the rendering format:

• compact produces a comma-separated list of repository prefix names (default)
• list produces a description list of repository prefix names
• table produces a table view, similar to the one visible in the Browse View page

glob

Do a glob-style filtering on the repository names (defaults to '*')

order

Order repositories by the given column (one of "name", "date" or "author")

desc

When set to 1, order by descending order

(since 0.12)

[[SubscriberList]]

Display a list of all installed notification subscribers, including documentation if available.

Optionally, the name of a specific subscriber can be provided as an argument. In that case, only the documentation for that subscriber will be rendered.

Note that this macro will not be able to display the documentation of subscribers if the PythonOptimize option is enabled for mod_python!

[[TOC]]

Generate a table of contents for the current page or a set of pages.

If no arguments are given, a table of contents is generated for the current page, with the top-level title stripped:

[[TOC]]

To generate a table of contents for a set of pages, simply pass them as comma separated arguments to the TOC macro, e.g. as in

[[TOC(TracGuide, TracInstall, TracUpgrade, TracIni, TracAdmin, TracBackup,
      TracLogging, TracPermissions, TracWiki, WikiFormatting, TracBrowser,
      TracRoadmap, TracChangeset, TracTickets, TracReports, TracQuery,
      TracTimeline, TracRss, TracNotification)]]

A wildcard * can be used to fetch a sorted list of all pages starting with the preceding pagename stub:

[[TOC(Trac*, WikiFormatting, WikiMacros)]]

The following control arguments change the default behaviour of the TOC macro:

Argument	Description
heading=<x>	Override the default heading of "Table of Contents"
noheading	Suppress display of the heading.
depth=<n>	Display headings of subsequent pages to a maximum depth of <n>.
inline	Display TOC inline rather than as a side-bar.
sectionindex	Only display the page name and title of each page in the wiki section.
titleindex	Only display the page name and title of each page, similar to TitleIndex.
notitle	Supress display of page title.
reverse	Display TOC sorted in reversed order. (Since 11.0.0.4)
from=page	Obtain the list of pages to show from the content (one page name per line) of another wiki page.
nonumbering	Suppress automatic numbering for inline TOC (Since 11.0.0.7)

For titleindex argument, an empty pagelist will evaluate to all pages:

[[TOC(titleindex, notitle, heading=All pages)]]

The sectionindex argument allows a title index to be generated for all pages in a given section of the wiki. A section is defined by wiki page name, using / as a section level delimiter (like directories in a file system). Giving / or * as the page name produces the same result as titleindex (title of all pages). If a page name ends with a /, only children of this page will be processed. Otherwise, the page given in the argument is also included, if it exists. For sectionindex argument, an empty pagelist will evaluate to all page below the same parent as the current page:

[[TOC(sectionindex, notitle, heading=This section pages)]]

The 'from' option allows you to read the lines of content from another wiki page and use that as the pagelist for the table of contents. The page names listed there are processed as if they are named in the TOC macro (start a line with a # to treat it as a comment). If the wiki page TOC/Guide contains

TracGuide
TracInstall
TracReports/Active

then these two calls to TOC are equivalent:

[[TOC(from=TOC/Guide)]]
[[TOC(TracGuide, TracInstall, TracReports/Active)]]

However, updating page TOC/Guide changes the TOC in all places that use from= to refer to it. This can be useful instead of custom macros like [[TracGuideToc]].

[[TagCloud]]

Display a tag cloud.

Show a tag cloud for all tags on resources matching query.

Usage:

[[TagCloud(<query>[,caseless_sort=<bool>][,mincount=<n>])]]

caseless_sort

Whether the tag cloud should be sorted case-sensitive.

mincount

Optional integer threshold to hide tags with smaller count.

See tags documentation for the query syntax.

[[TicketQuery]]

Wiki macro listing tickets that match certain criteria.

This macro accepts a comma-separated list of keyed parameters, in the form "key=value".

If the key is the name of a field, the value must use the syntax of a filter specifier as defined in TracQuery#QueryLanguage. Note that this is not the same as the simplified URL syntax used for query: links starting with a ? character. Commas (,) can be included in field values by escaping them with a backslash (\).

Groups of field constraints to be OR-ed together can be separated by a literal or argument.

In addition to filters, several other named parameters can be used to control how the results are presented. All of them are optional.

The format parameter determines how the list of tickets is presented:

• list -- the default presentation is to list the ticket ID next to the summary, with each ticket on a separate line.
• compact -- the tickets are presented as a comma-separated list of ticket IDs.
• count -- only the count of matching tickets is displayed
• rawcount -- only the count of matching tickets is displayed, not even with a link to the corresponding query (since 1.1.1)
• table -- a view similar to the custom query view (but without the controls)
• progress -- a view similar to the milestone progress bars

The max parameter can be used to limit the number of tickets shown (defaults to 0, i.e. no maximum).

The order parameter sets the field used for ordering tickets (defaults to id).

The desc parameter indicates whether the order of the tickets should be reversed (defaults to false).

The group parameter sets the field used for grouping tickets (defaults to not being set).

The groupdesc parameter indicates whether the natural display order of the groups should be reversed (defaults to false).

The verbose parameter can be set to a true value in order to get the description for the listed tickets. For table format only. deprecated in favor of the rows parameter

The rows parameter can be used to specify which field(s) should be viewed as a row, e.g. rows=description|summary

The col parameter can be used to specify which fields should be viewed as columns. For table format only.

For compatibility with Trac 0.10, if there's a last positional parameter given to the macro, it will be used to specify the format. Also, using "&" as a field separator still works (except for order) but is deprecated.

[[TitleIndex]]

Insert an alphabetic list of all wiki pages into the output.

Accepts a prefix string as parameter: if provided, only pages with names that start with the prefix are included in the resulting list. If this parameter is omitted, all pages are listed. If the prefix is specified, a second argument of value hideprefix can be given as well, in order to remove that prefix from the output.

The prefix string supports the standard relative-path notation when using the macro in a wiki page. A prefix string starting with ./ will be relative to the current page, and parent pages can be specified using ../.

Several named parameters can be specified:

• format=compact: The pages are displayed as comma-separated links.
• format=group: The list of pages will be structured in groups according to common prefix. This format also supports a min=n argument, where n is the minimal number of pages for a group.
• format=hierarchy: The list of pages will be structured according to the page name path hierarchy. This format also supports a min=n argument, where higher n flatten the display hierarchy
• depth=n: limit the depth of the pages to list. If set to 0, only toplevel pages will be shown, if set to 1, only immediate children pages will be shown, etc. If not set, or set to -1, all pages in the hierarchy will be shown.
• include=page1:page*2: include only pages that match an item in the colon-separated list of pages. If the list is empty, or if no include argument is given, include all pages.
• exclude=page1:page*2: exclude pages that match an item in the colon- separated list of pages.

The include and exclude lists accept shell-style patterns.

[[TracAdminHelp]]

Display help for trac-admin commands.

Examples:

[[TracAdminHelp]]               # all commands
[[TracAdminHelp(wiki)]]         # all wiki commands
[[TracAdminHelp(wiki export)]]  # the "wiki export" command
[[TracAdminHelp(upgrade)]]      # the upgrade command

[[TracGuideToc]]

Display a table of content for the Trac guide.

This macro shows a quick and dirty way to make a table-of-contents for the Help/Guide. The table of contents will contain the Trac* and WikiFormatting pages, and can't be customized. See the ​TocMacro for a more customizable table of contents.

[[TracIni]]

Produce documentation for the Trac configuration file.

Typically, this will be used in the TracIni page. The macro accepts two ordered arguments and two named arguments.

The ordered arguments are a configuration section filter, and a configuration option name filter: only the configuration options whose section and name start with the filters are output.

The named arguments can be specified:

section

a glob-style filtering on the section names

option

a glob-style filtering on the option names

[[Workflow]]

Render a workflow graph.

This macro accepts a TracWorkflow configuration and renders the states and transitions as a directed graph. If no parameters are given, the current ticket workflow is rendered. In WikiProcessors mode the width and height arguments can be specified.

(Defaults: width = 800 and height = 600)

Examples:

    [[Workflow()]]

    [[Workflow(go = here -> there; return = there -> here)]]

    {{{
    #!Workflow width=700 height=700
    leave = * -> *
    leave.operations = leave_status
    leave.default = 1

    create = <none> -> new
    create.default = 1

    create_and_assign = <none> -> assigned
    create_and_assign.label = assign
    create_and_assign.permissions = TICKET_MODIFY
    create_and_assign.operations = may_set_owner

    accept = new,assigned,accepted,reopened -> accepted
    accept.permissions = TICKET_MODIFY
    accept.operations = set_owner_to_self

    resolve = new,assigned,accepted,reopened -> closed
    resolve.permissions = TICKET_MODIFY
    resolve.operations = set_resolution

    reassign = new,assigned,accepted,reopened -> assigned
    reassign.permissions = TICKET_MODIFY
    reassign.operations = set_owner

    reopen = closed -> reopened
    reopen.permissions = TICKET_CREATE
    reopen.operations = del_resolution
    }}}

[[access]]

A Trac macro to display or hide parts of wiki pages based on permissions.