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This page provides tutorials and illustrations on how to use the CSpec Editor UI and its features.
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This page provides tutorials and illustrations on how to use the CSpec Editor UI and its features.
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[[_TOC_]]
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## Introduction to CSpec Editor
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ClinGen Criteria Specification Editor is an application which is designed primarily to allow users with appropriate access and permissions to do the following:
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1. **Create new** criteria specification document
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2. **Edit** previously existing specification documents
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3. **Reopen**, **submit** specification documents for approval and **release** approved criteria specification documents
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The Editor in general will also allow to
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1. Track the specification approval process and versioning of these documents
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2. Transfer content to external applications _via_ ClinGen Data Exchange
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The beta version of the Editor is available here [https://cspec.genome.network/cspec/ed/svi](https://cspec.genome.network/cspec/ed/svi)
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The beta version of the Editor is available here <https://cspec.genome.network/cspec/ed/svi>
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## User Management
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All users must be logged in to the cspec editor to gain access to the documents that are affiliated to their vceps. One can access the login form here - <https://cspec.genome.network/cspec/ed/svi>. Type in your credentials in the form shown below:
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<img src="uploads/7ff89af5710e66b78d5362f2fb6e42d1/login.png" width="500" height="200">
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All users must be logged in to the cspec editor to gain access to the documents that are affiliated to their vceps. One can access the login form here - <https://cspec.genome.network/cspec/ed/svi>. Type in your credentials in the form shown below: 
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### First time users
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### First time users
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First time users must register to gain access to our system. Please use your email registered in the Group and Personnel Management System to register. One can access the Registration form by clicking the _Register_ button shown in the login form - <https://cspec.genome.network/cspec/ed/svi>. That link will lead you to the form as shown below:
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<kbd>
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<img src="uploads/1d87f36975dd8774a6e5cb08bf1a5394/register.png" width="450" height="400">
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</kbd>
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<kbd></kbd>
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### Requesting Access
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- Log in to the Editor - https://cspec.genome.network/cspec/ed/svi once you are [registered](#First-time-users).
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The CSpec Editor ideally should match the vcep membership with GPM as soon as a registered user logs in. However, GPM integration to the CSpec and autoregistration feature will be available ONLY for the future releases of the Editor.
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First time users with no affiliation will see a message as shown below:
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- Log in to the Editor - <https://cspec.genome.network/cspec/ed/svi> once you are [registered](#First-time-users). The CSpec Editor ideally should match the vcep membership with GPM as soon as a registered user logs in. However, GPM integration to the CSpec and autoregistration feature will be available ONLY for the future releases of the Editor. First time users with no affiliation will see a message as shown below: 
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- Users can request access to a VCEP by using the _Request Access_ feature at the top right hand side (below your account name) as shown below:
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<kbd>
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<img src="uploads/c68e18234f0e5081ec802d5fe43ece2c/rAccess.png" width="100" height="70">
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</kbd>
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<kbd></kbd>
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#### Request Access As a VCEP Coordinator/Member or SVI approver
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A user can request for a specific role (defined within the scope of CSpec Editor) to gain access to a specific VCEP.
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<kbd>
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<img src="uploads/04d52244091491fc6840d7d92a7356f2/requestAccesscoordinator.png" width="350" height="150">
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</kbd>
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A user can request for a specific role (defined within the scope of CSpec Editor) to gain access to a specific VCEP.
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<kbd></kbd>
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1. Choose the VCEP of interest
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2. Choose the Role from the three available options:
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a) **VCEP Coordinator** - VCEP Coordinator can create, edit, submit and release Criteria Specification documents. A VCEP coordinator can add a registered user as a coordinator or a member to their respective VCEPs. b) **VCEP Member** - VCEP member can create, edit Criteria Specification documents. c) **SVI approver** - Approves/reviews submitted specifications. Choose _All VCEPs_ if you are requesting for this role.
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2. Choose the Role from the three available options: a) **VCEP Coordinator** - VCEP Coordinator can create, edit, submit and release Criteria Specification documents. A VCEP coordinator can add a registered user as a coordinator or a member to their respective VCEPs. b) **VCEP Member** - VCEP member can create, edit Criteria Specification documents. c) **SVI approver** - Approves/reviews submitted specifications. Choose _All VCEPs_ if you are requesting for this role.
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## Entry Page
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Entry page shows a tabular view of all the specifications that a user has access to. The specification documents are grouped with respect to the VCEPs. Given below is an example of an entry page view for a test user who is a coordintor for multiple VCEPs.
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The table is:
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Entry page shows a tabular view of all the specifications that a user has access to. The specification documents are grouped with respect to the VCEPs. Given below is an example of an entry page view for a test user who is a coordintor for multiple VCEPs.  The table is:
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- By default sorted alphabetically by the VCEP name
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- Each column is sortable individually.
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- Pagination can be adjusted using the page controls on the top left hand side.
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- Search field allows filtering specification document by gene, disease, status, etc.
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## Creating a new specification document
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Click the _Create New_ item in the Tools menu at the top right hand side of the Entry page as shown below:
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Submit the create new form. The form _Submit_ button will be disabled until all the required fields are selected or filled in:
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<kbd>
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<img src="uploads/efc5180b9ce9b8fcd3b86fe9d3942954/createNew.png" width="350" height="300">
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</kbd>
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Click the _Create New_ item in the Tools menu at the top right hand side of the Entry page as shown below:  Submit the create new form. The form _Submit_ button will be disabled until all the required fields are selected or filled in:
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<kbd></kbd>
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Once a new document has been successfully created the success message will guide you to the new document like so:
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Once a new document has been successfully created the success message will guide you to the new document like so:
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<kbd>
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<img src="uploads/a31925b5413f8b1ef63c8c8ba0198c53/success.png" width="200" height="70">
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</kbd>
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<kbd></kbd>
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## Detailed view of a specification document
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One can access the specification document page by clicking the pencil icon at the end of each row in the entry table.
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Sections of a specification document are:
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One can access the specification document page by clicking the pencil icon at the end of each row in the entry table. Sections of a specification document are:
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### General Metadata
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Metadata about the specification include the title, version, current status, etc,.
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A specification document goes through a series of stages, right from when a new document is created. These stage transitions are displayed at this section as breadcrumbs and an example is shown below.
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Metadata about the specification include the title, version, current status, etc,. A specification document goes through a series of stages, right from when a new document is created. These stage transitions are displayed at this section as breadcrumbs and an example is shown below. 
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### Changing the status of the document
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One can change the status of the document using the tool option at the top right hand side and this feature is designed to respond based on the permissions a user has.
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<kbd>
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</kbd>
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For instance a _VCEP coordinator_ can submit the document in _Classification Rules In Prep_ stage for approval (_Classification Rules Submitted_).
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<kbd>
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</kbd>
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Once submitted, a coordinator can no longer make edits to that document. To make further edits the submission has to be either a) withdrawn - choosing the option _Withdraw Classification Rules Submitted_ or b) must be formally approved by the SVI approver. Similarly, an _SVI approver_ can approve OR review ( document returned without approval ) the submitted document to move the status of a document to the next stage, _Pilot Rules In Prep_ or _Classification Rules In Prep_ respectively.
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### Change (update) the disease information
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A VCEP coordinator can change the following properties which are defined as the scope of the document in either of the _Prep_ stages (Classification Rules In Prep, Pilot Rules In Prep)
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Use the Edit Scope tool as shown here.
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One can change the status of the document using the tool option at the top right hand side and this feature is designed to respond based on the permissions a user has. <kbd> </kbd>For instance a _VCEP coordinator_ can submit the document in _Classification Rules In Prep_ stage for approval (_Classification Rules Submitted_). <kbd> </kbd>Once submitted, a coordinator can no longer make edits to that document. To make further edits the submission has to be either a) withdrawn - choosing the option _Withdraw Classification Rules Submitted_ or b) must be formally approved by the SVI approver. Similarly, an _SVI approver_ can approve OR review ( document returned without approval ) the submitted document to move the status of a document to the next stage, _Pilot Rules In Prep_ or _Classification Rules In Prep_ respectively.
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### Change (update) the disease information
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A VCEP coordinator can change the following properties which are defined as the scope of the document in either of the _Prep_ stages (Classification Rules In Prep, Pilot Rules In Prep). Use the Edit Scope tool as shown here.
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Fill the _Edit Scope_ form and hit _Submit_ to make the following changes:
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1. Transcript
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2. Add new diseases
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3. Remove previously existing diseases
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4. Update the mode of inheritance
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4. Update the mode of inheritance
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### Criteria & Strength Specifications
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A VCEP coordinator or a member can edit the _Criteria & Strength Specifications_ table. Details can be found [here](/Criteria-And-Strength-Specifications)
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## Reopen a previously released/existing specification document
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A _Released_ specification document must be reopened in order to make further edits. The document then must be versioned and submitted for approval. To reopen the document use the tool option on the top right hand side of the specification document. Once reopened the document status will be _Pilot Rules In Prep_
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<kbd>
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</kbd>
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### Re-submit the reopened document.
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A _Released_ specification document must be reopened in order to make further edits. The document then must be versioned and submitted for approval. To reopen the document use the tool option on the top right hand side of the specification document. Once reopened the document status will be _Pilot Rules In Prep_ <kbd></kbd>
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### Re-submit the reopened document.
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Once a reopened document has been edited, it must be submitted for approval by submitting the document. Click the tool option, as shown below at the top right hand side of the document to _submit_ your document.
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Once a reopened document has been edited, it must be submitted for approval by submitting the document. Click the tool option, as shown below at the top right hand side of the document to _submit_ your document. 
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This tool will launch a modal as show below. Please mark the following:
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1. Correct version (minor or major with respect to the changes made)
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2. Release notes
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3. Click the submit button which will place the document in _Pilot Rules Submitted_
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#### Change the version of a submitted document
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Once submitted one can alter the version of the document by using the overwrite version feature. Withdraw the submission or if a submitted document is returned without approval this feature will be enabled. Use the tool option to see this feature. By default this is set to _No_.
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If the _Yes_ button is clicked for the _Change version?_ field an additional input field will appear. Fill in the new version here which will overwrite the running version of the document.
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Make sure to add all the three places in your version, that is it must be of the form - _1.0.0_
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Submit your document once you have the correct version entered as shown in the example below:
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Once submitted one can alter the version of the document by using the overwrite version feature. Withdraw the submission or if a submitted document is returned without approval this feature will be enabled. Use the tool option to see this feature. By default this is set to _No_.  If the _Yes_ button is clicked for the _Change version?_ field an additional input field will appear. Fill in the new version here which will overwrite the running version of the document. Make sure to add all the three places in your version, that is it must be of the form - _1.0.0_  Submit your document once you have the correct version entered as shown in the example below: 
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## Release an approved document
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Releasing a document will publish all the content of the approved document to
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Releasing a document will publish all the content of the approved document to
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1. The CSpec Registry
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2. The Data Exchange Kafka service, thereby making it available for VCI and other applications.
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2. The Data Exchange Kafka service, thereby making it available for VCI and other applications.
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Follow the steps below to release a document. To release a document, the submitted document must be **approved** and placed in _Approved For Release_ state as shown below. Review the content and make all the required changes before a document is released.
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1. Change the status of the document by clicking the top right hand side tool option.
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2. This will launch a release option and submit the form.
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\ No newline at end of file |
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2. This will launch a release option and submit the form.  |
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\ No newline at end of file |
