© 2016 Center for Expanded Data Annotation and Retrieval
CEDAR is supported by the National Institutes of Health through an NIH Big Data to Knowledge program grant.
(Grant Number 1U54AI117925-01)
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About CEDAR User Guide


Welcome to the CEDAR User Guide. This document contains technical information about operation and artifacts of the CEDAR Workbench. The documents are added as time allows to describe the most central aspects of the CEDAR system. The CEDAR User Guide targets typical users and uses of the CEDAR system. Should you just need some basic information about getting started, the following resources may be helpful:

We invite your feedback if you would like to see additions or changes to this User's Guide.




Accounts and Logging In [Ready]

This first chapter in the CEDAR manual provides a basic understanding to the reader regarding how to create a user account on the CEDAR Workbench, how to access the account, and how to access the different resources in the CEDAR Workbench.


    Creating a CEDAR Account

    The first step to create metadata templates and metadata with the CEDAR workbench is to create a CEDAR workbench user account. To do this, visit https://cedar.metadatacenter.org and click on the “Register” link below the Password line. Enter your first name, last name, a functional email address, and a password as shown in the screenshot below. After clicking on register, check your email address for a link to validate your user account. After validation you can easily log in to the CEDAR workbench as indicated in the next section.



    Logging in with CEDAR

    To log in, go to https://cedar.metadatacenter.org, and enter the account name and your password as shown in the screenshot below. If you have forgotten your password, you can use the “Forgot Password?” link just below the Password line. Once you have logged in, you will see the CEDAR Workspace as shown in the next section.

    alt text



    Visibility of your CEDAR Account

    All of the CEDAR account names are visible to other CEDAR users, by navigating to the /All/Users folder. (Only 100 users are loaded at a time; scroll to the bottom of the page to load more names.)

    In fact, because sometimes you may want to share or describe the location of your directory, we encourage you to make sure your user name is unique, and if you have two accounts, to give them different user names. If you want to change an existing user name on an account, please contact us at user-support@metadatacenter.org.

    If the shared resources include any folders, everything within those folders (recursively) will be shared with the same permissions.

    If you share content that you have created in your workspace, anyone who can see your shared resources will also see name of the folder hierarchy within which they live. (They will not be able to navigate into unshared parts of that hierarchy.)

    Finally, when you create or update assets, the unique identifier that CEDAR creates for your account is saved in the metadata of the asset. Eventually we may publish a service that provides your account name—and any other profile information you have explicitly shared—to someone who visits the unique identifier. To avoid this, keeping all your work private will prevent anyone from discovering your unique identifier.







Finding Resources [Preliminary]

This second chapter in the CEDAR manual provides a basic understanding on how to find different resources (i.e., any of template, element, field, instance, folder) in the CEDAR Workbench: those resources that are created by me, those resources that are shared with me, and those resources that are shared with everybody. The reader will also get a brief overview on how to filter and sort the retrieved results and formulate advanced queries.


    Simple Searching

    The CEDAR Workbench organizes resources in three different sets, depending on the ownership and sharing: 1) resources created by the logged-in user and are listed under the “Workspace” tab, 2) resources shared with the logged-in user, and 3) public resources that are shared with every user.

    Searching for a resource in a particular set is vey simple. Just click on the given set (e.g., “Shared with everybody”) and input the search string as free text (e.g., “Antibody”) using the Search bar provided in the navigation header of the CEDAR Workbench. All the resources in a given set that have the string “Antibody” listed in their labels, version, or description are showcased to the logged-in user.

    TIP: Since most fields that are Common Data Elements (CDEs) have versions that end in ‘0.0’, that can be a quick way to find CDEs that match your needs.

    This process is indicated in the Figure below. In later sections, we will demonstrate how to organize and constrain these search results, and perform advanced searches.



    Organizing the Results

    The user has an option to view the search resources either as a grid of different resource tiles (As shown in the Figure below) or as a list of different resources. The user can switch between these views using the icon highlighed in the blue-colored rectangle in the Figure.

    Moreover, the user can also sort the different resources based on their title, the resource creation date, and the resource modification date. To sort the resources, the user has to click the sort icon highlighted in the red-colored rectangle, and select their desired option.

    In the next section, we will discuss how the user can constrain the search results by filtering on the different resource types.



    Constraining the Results by Type

    By default, when the user searches for resources (e.g., all resources that mention “Antibody”), all resources are presented to the user irrelevant of their type (i.e., field, element, template, or metadata instance). As the user (i.e., template publisher or the metadata creator) starts creating several of these resources, or has shared access to several of these resources, the total number of resources retrieved for a given search query becomes very large for intuitive navigation.

    While we paginate the search results, the user can further constrain the search results by filtering them according to the type of the resources. To set a type filter, simply click on the desirable icons indicated in the left side-bar of the CEDAR workbench (as highlighted in the Figure below). These icons are listed as Template, Element, Field, and Metadata, from left to right. The corresponding type represented by the icon can also be displayed by hovering over the icon. On selection, the icon is ‘whitened-out’ (i.e. displayed in white) and the resources for the corresponding type are NOT displayed in the search results (e.g., Field resources are not shown in the search results in the Figure below). To revert back (i.e., to show the Field resources), the user simply has to click on the corresponding icon again.



    Advanced Searching - Patterns

    We’re sorry, this resource has not yet been developed. You are welcome to contribute to its development at the link below.



    Advanced Searching - Search Fields

    This section contains some examples of the query syntax that can be used to find CEDAR artifacts by field name and/or value.

    Finding template instances by field name and/or field value

    Suppose the following template instance:

    Examples of queries that will retrieve the instance above:

    • Search by field name and value:

      title:statistics

      publisher:"City of New York"

      "publishing institution":"City of New York" (note that ‘Publishing Institution’ has been defined in the template as the preferred label of the field ‘Publisher’)

    • Search by field name (any value):

      publisher:*, or publisher:

    • Search by field value (any name):

      *:"New York", or :"New York"

    • Boolean queries:

      title:Statistics OR title:Math (the OR is optional)

      title:(Statistics OR Math)

      title:Math OR (title:Statistics AND publisher:"New York")

      Dataset OR disease:CRC

    • Wildcard queries:

      • One or more characters: title:stat*

      • Single character: title:stat?stics

    • URLs:

      url:https://catalog.data.gov/dataset/demographic-statistics-by-zip-code-acfc9

    • Ontology terms:

      • Search by term label: topic:statistics

      • Search by term URI: topic:http://edamontology.org/topic_2269

      • Search by term label and URI: topic:http://edamontology.org/topic_2269 AND topic:data

    Finding templates, elements, and fields, by field name

    Suppose the template for the previous instance:

    Here are some examples of queries that can be used to find the template above:

    title:*, or simply title:

    Publish*:

    "Contact Email":

    to?ic:







Desktop and Navigation [Pending]


    Moving and Copying Content

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    Navigating Using the Browser - Buttons and Links

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    Navigating via the User Interface

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    The CEDAR Workbench Desktop

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Filling Out (Creating) Metadata [Pending]


    Creating the Metadata Form

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    Saving and Validating

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    Special Case Submitting Your Metadata

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Sharing Your Content [Pending]


    Creating Groups



    How Permissions Work

    Introduction

    You may have some questions about CEDAR’s access privileges, like these:

    1. How can I keep my files private (or make them public)?
    2. How can someone collaborate with me on a lot of different files?
    3. Why can’t I save this metadata where the template is?
    4. How can I tell whether other people can see my file?
    5. I just logged in for the first time, why can’t see some of the shared files?

    In this tutorial we’ll talk about how CEDAR permissions work, and help you answer questions like these.

    (You can see answers to the questions at the end of this page.)

    Permission types

    You want to access individual resources in CEDAR, or keep someone else from accessing them. So what you need to know, for a given node, is whether a particular user:

    • can read,
    • can write,
    • can publish,
    • can create a draft version of,
    • can change the permissions (sharing) of, or
    • can change the owner of the node.

    The operations above are evaluated on-the-fly in CEDAR. They are not attached to nodes in the system, but are computed from different graph relationships (like folder hierarchies) and properties when they are needed.

    A basic concept that may help you interpret CEDAR permissions is that you only need one permission on a resource to perform that operation.

    Permission rules

    For simplicity, we refer to the object in each question as a resource (templates, elements, fields, and metadata instances are all resources), but this section also applies to folders.

    We should not that for practical reasons, the administrator of the CEDAR system has permission to do all of the actions represented by the 6 permission types above.

    Now let’s start with a few easy-to-answer questions.

    Who can change the owner of a resource?

    Only the owner of a resource can change the owner of a resource. Each resource has only one owner.

    Who can change a resource’s permissions?

    The resource’s permissions are changed via the Share menu for the resource.

    To change a resource’s permissions, the following must be true:

    • The user has write access to the resource. (This means they can update the resource. And who can do that? See below.)

    Who can read a resource?

    For a user to be able to read a resource, at least one of the following must be true:

    • The user owns the resource, or a folder that contains the resource
    • The user, or any group of which the user is a member, can read or write the resource or any folder containing it (except the root folder ‘/’ and users folder ‘/Users’).

    For example, because any user can read the ‘/Shared’ folder, any user can also read any content at any level under the ‘/Shared’ folder. (Unfortunately, this means we can’t give users write permission in this folder, because then they can overwrite any other shared content. We’ll create an exception rule to handle this soon.)

    Who can update a resource?

    These rules are similar to reading. For a user to be able to update a resource, at least one of the following must be true:

    • The user owns the resource, or a folder that contains the resource
    • The user, or any group of which the user is a member, can write the resource or any folder containing it

    The creation rules are just like the updating rules, except simpler, since the user can’t own or write a resource that doesn’t exist. (To create a resource, use the ‘New +’ icon at the upper left of your workspace.) So one of the following must be true:

    • The user must own any containing folder (that is, any single folder higher in the hierarchy than the new resource).
    • The user must be able to write any containing folder (that is, any single folder higher in the hierarchy than the new resource). Note that no user can write or create resources directly in the ‘/’, ‘/Users’, or ‘/Shared’ folder.

    Copying a folder or resource into a target folder, or moving a resource into a target folder, requires the same permission as creating a resource in the target folder.

    Who can create a draft version of a published resource?

    A draft version of a resource is a resource that can be overwritten, by editing and saving it. All resources in CEDAR start out as a draft, and must be explicitly published (see next item) before this question applies.

    For a user to create a draft from a published resource, the following must be true:

    • The user owns the published resource that serves as the original content for the draft.
    • The resource is a type that supports versioning (field, element or template).
    • The resource is the most recently published in the version history of this resource

    The last rule means you can not create a draft from some earlier published version of the resource.

    Who can publish a resource?

    Publishing a resource is like ‘releasing’ source code or defining a version of a document: a published resource can never be modified. The only types of resource that can be published are templates, elements, and fields, and they must start out in draft state. (The act of publication replaces the ‘draft’ version.)

    For a user to publish a resource, the following must all be true:

    • The user owns the resource that is to be published.
    • The resource is in draft state (all resources start in draft state, and if a draft exists, it is always the most recent resource in a version history)
    • The resource is of a versioned type (field, element or template).

    Answers

    Now we can answer our original questions.

    1. How can I keep my files private (or make them public)? Your resources will stay private if they are in your own CEDAR user folder, and you have not shared any of their parent folders with anyone else.

    To make your files public, simply share them, or one of their parent folders, with the individuals or groups who should get access. The ‘everybody’ group can be used to share the content with all CEDAR users.

    1. How can someone collaborate with me on a lot of different files? Just share the folder containing all of your collaborative files with them. Sharing write privileges on the folder will let them modify all the contained files. (If you want to have a shared folder for your project under /Users/Shared/, just ask us to create it for you. Be aware the contents are readable by all CEDAR users.)

    2. Why can’t I save this metadata where the template is? Often templates are in a read-only folder, so that the template can not be changed. CEDAR will automatically save created metadata to your home folder, and then you can move it to any other folder that for which you have write permissions.

    3. How can I tell which other people can see my file? Unfortunately there is no simple way to evaluate this, without examining the sharing permissions on the resource, and on every folder above it.

    4. I just logged in for the first time, why can’t I see some of the shared files? All CEDAR permissions must be materialized in Elasticsearch, in order to be used directly for search queries. When you first log in, your materializations must be created, which can take some time. In a similar way, a change in the permission of any given node is not propagated instantly into the Elasticsearch index. Depending on the size of the affected subtree (if the node is a folder), materializing this permission can take several seconds.



    Types of Sharing - Reading and Writing







Viewing Resource Information [Pending]


    Viewing

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    Viewing Resource as Raw JSON

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    Viewing Resource Content

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    Viewing Resource Metadata

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