Wiki

synapseclient.wiki

Wiki

A Wiki page requires a title, markdown and an owner object and can also include images.

Creating a Wiki

import synapseclient
from synapseclient import Wiki

## Initialize a Synapse object & authenticate
syn = synapseclient.Synapse()
syn.login()

entity = syn.get('syn123456')

content = """
# My Wiki Page

Here is a description of my **fantastic** project!

An attached image:
${image?fileName=logo.png&align=none}
"""

wiki = Wiki(title='My Wiki Page',
            owner=entity,
            markdown=content,
            attachments=['/path/to/logo.png'])

wiki = syn.store(wiki)

Embedding images

Note that in the above example, we've attached a logo graphic and embedded it in the web page.

Figures that are more than just decoration can be stored as Synapse entities allowing versioning and provenance information to be recorded. This is a better choice for figures with data behind them.

Updating a Wiki

import synapseclient

## Initialize a Synapse object & authenticate
syn = synapseclient.Synapse()
syn.login()

entity = syn.get('syn123456')
wiki = syn.getWiki(entity)

wiki.markdown = """
# My Wiki Page

Here is a description of my **fantastic** project! Let's
*emphasize* the important stuff.

An embedded image that is also a Synapse entity:
${image?synapseId=syn1824434&align=None&scale=66}

Now we can track it's provenance and keep multiple versions.
"""

wiki = syn.store(wiki)

Classes

Wiki

Bases: DictObject

Represents a wiki page in Synapse with content specified in markdown.

PARAMETER	DESCRIPTION
title	Title of the Wiki
owner	Parent Entity that the Wiki will belong to
markdown	Content of the Wiki (cannot be defined if markdownFile is defined)
markdownFile	Path to file which contains the Content of Wiki (cannot be defined if markdown is defined)
attachments	List of paths to files to attach
fileHandles	List of file handle IDs representing files to be attached
parentWikiId	(optional) For sub-pages, specify parent wiki page

Source code in synapseclient/wiki.py

class Wiki(DictObject):
    """
    Represents a wiki page in Synapse with content specified in markdown.

    Arguments:
        title: Title of the Wiki
        owner: Parent Entity that the Wiki will belong to
        markdown: Content of the Wiki (cannot be defined if markdownFile is defined)
        markdownFile: Path to file which contains the Content of Wiki (cannot be defined if markdown is defined)
        attachments: List of paths to files to attach
        fileHandles: List of file handle IDs representing files to be attached
        parentWikiId: (optional) For sub-pages, specify parent wiki page
    """

    __PROPERTIES = (
        "title",
        "markdown",
        "attachmentFileHandleIds",
        "id",
        "etag",
        "createdBy",
        "createdOn",
        "modifiedBy",
        "modifiedOn",
        "parentWikiId",
    )

    def __init__(self, **kwargs):
        # Verify that the parameters are correct
        if "owner" not in kwargs:
            raise ValueError("Wiki constructor must have an owner specified")

        # Initialize the file handle list to be an empty list
        if "attachmentFileHandleIds" not in kwargs:
            kwargs["attachmentFileHandleIds"] = []

        # update the markdown
        self.update_markdown(
            kwargs.pop("markdown", None), kwargs.pop("markdownFile", None)
        )

        # Move the 'fileHandles' into the proper (wordier) bucket
        if "fileHandles" in kwargs:
            for handle in kwargs["fileHandles"]:
                kwargs["attachmentFileHandleIds"].append(handle)
            del kwargs["fileHandles"]

        super(Wiki, self).__init__(kwargs)
        self.ownerId = id_of(self.owner)
        del self["owner"]

    def json(self):
        """Returns the JSON representation of the Wiki object."""
        return json.dumps({k: v for k, v in self.items() if k in self.__PROPERTIES})

    def getURI(self):
        """For internal use."""

        return "/entity/%s/wiki/%s" % (self.ownerId, self.id)

    def postURI(self):
        """For internal use."""

        return "/entity/%s/wiki" % self.ownerId

    def putURI(self):
        """For internal use."""

        return "/entity/%s/wiki/%s" % (self.ownerId, self.id)

    def deleteURI(self):
        """For internal use."""

        return "/entity/%s/wiki/%s" % (self.ownerId, self.id)

    def update_markdown(self, markdown=None, markdown_file=None):
        """
        Updates the wiki's markdown. Specify only one of markdown or markdown_file

        Arguments:
            markdown: text that will become the markdown
            markdown_file: path to a file. Its contents will be the markdown
        """
        if markdown and markdown_file:
            raise ValueError("Please use only one argument: markdown or markdownFile")

        if markdown_file:
            # pop the 'markdownFile' kwargs because we don't actually need it in the dictionary to upload to synapse
            markdown_path = os.path.expandvars(os.path.expanduser(markdown_file))
            if not os.path.isfile(markdown_path):
                raise ValueError(markdown_file + "is not a valid file")
            with open(markdown_path, "r") as opened_markdown_file:
                markdown = opened_markdown_file.read()

        self["markdown"] = markdown

Functions

json

json()

Returns the JSON representation of the Wiki object.

Source code in synapseclient/wiki.py

def json(self):
    """Returns the JSON representation of the Wiki object."""
    return json.dumps({k: v for k, v in self.items() if k in self.__PROPERTIES})

getURI

getURI()

For internal use.

Source code in synapseclient/wiki.py

def getURI(self):
    """For internal use."""

    return "/entity/%s/wiki/%s" % (self.ownerId, self.id)

postURI

postURI()

For internal use.

Source code in synapseclient/wiki.py

def postURI(self):
    """For internal use."""

    return "/entity/%s/wiki" % self.ownerId

putURI

putURI()

For internal use.

Source code in synapseclient/wiki.py

def putURI(self):
    """For internal use."""

    return "/entity/%s/wiki/%s" % (self.ownerId, self.id)

deleteURI

deleteURI()

For internal use.

Source code in synapseclient/wiki.py

def deleteURI(self):
    """For internal use."""

    return "/entity/%s/wiki/%s" % (self.ownerId, self.id)

update_markdown

update_markdown(markdown=None, markdown_file=None)

Updates the wiki's markdown. Specify only one of markdown or markdown_file

PARAMETER	DESCRIPTION
markdown	text that will become the markdown DEFAULT: None
markdown_file	path to a file. Its contents will be the markdown DEFAULT: None

Source code in synapseclient/wiki.py

def update_markdown(self, markdown=None, markdown_file=None):
    """
    Updates the wiki's markdown. Specify only one of markdown or markdown_file

    Arguments:
        markdown: text that will become the markdown
        markdown_file: path to a file. Its contents will be the markdown
    """
    if markdown and markdown_file:
        raise ValueError("Please use only one argument: markdown or markdownFile")

    if markdown_file:
        # pop the 'markdownFile' kwargs because we don't actually need it in the dictionary to upload to synapse
        markdown_path = os.path.expandvars(os.path.expanduser(markdown_file))
        if not os.path.isfile(markdown_path):
            raise ValueError(markdown_file + "is not a valid file")
        with open(markdown_path, "r") as opened_markdown_file:
            markdown = opened_markdown_file.read()

    self["markdown"] = markdown

WikiAttachment

Bases: DictObject

Represents a wiki page attachment.

Source code in synapseclient/wiki.py

class WikiAttachment(DictObject):
    """Represents a wiki page attachment."""

    __PROPERTIES = ("contentType", "fileName", "contentMd5", "contentSize")

    def __init__(self, **kwargs):
        super(WikiAttachment, self).__init__(**kwargs)

Functions