Docs: Project and Sample (#623)

* Add more to docs

* Add import metadata

* Add consistency to docs, reformat

* add PR comment changes

* Fix rebase

* rephrase note in import

* Add membership comment to viewing histories

* Add missed file change for previous commit

docs-site/docs/user/organization/members/group-and-project-members.md

@@ -79,15 +79,16 @@ To add a user to a group:
 6. Select an optional **Access expiration**
 7. Click the **Add member to group** button
 
-## Edit member for a group or project
+## Edit members for a group or project
 
 Prerequisite:
 
 You must have at least a **Maintainer** role, or you must be the owner of the group
 
-1. From the left sidebar, select **Projects** or **Groups**, and find your project or group for which you would like to update a member
-2. From the left sidebar, select **Members**
-3. Find the member that you would like to update
+1. From the left sidebar, select **Projects** or **Groups**
+2. Select the project or group
+3. From the left sidebar, select **Members**
+4. Find the member that you would like to update
 
 To update a member's role:
 
@@ -107,13 +108,14 @@ You must have at least a **Maintainer** role, or the project must be under your
 
 To add a direct user to a project:
 
-1. From the left sidebar, select **Projects**, and find your project
-2. From the left sidebar, select **Members**
-3. Click the **Add Member** button
-4. Select the user you want to add to the project
-5. Select an access level (role)
-6. Select an optional **Access expiration**
-7. Click the **Add member to project** button
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Members**
+4. Click the **Add Member** button
+5. Select the user you want to add to the project
+6. Select an access level (role)
+7. Select an optional **Access expiration**
+8. Click the **Add member to project** button
 
 ## Which roles you can assign
 
@@ -137,10 +139,11 @@ Prerequisites:
 
 To remove a member from a project:
 
-1. From the left sidebar, select **Projects**, and find your project
-2. From the left sidebar, select **Members**
-3. On the right hand side of the row for the member you want to remove, click the `ellipsis` and select **Remove** from the dropdown.
-4. Confirm that you would like to remove the member from the project in the popup by clicking the **OK** button
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Members**
+4. On the right hand side of the row for the member you want to remove, click **Remove**.
+5. Confirm that you would like to remove the member from the project in the popup by clicking the **OK** button
 
 ## Remove a member from a group
 
@@ -157,7 +160,8 @@ Prerequisites:
 
 To remove a member from a group:
 
-1. From the left sidebar, select **Groups**, and find your group
-2. From the left sidebar, select **Members**
-3. On the right hand side of the row for the member you want to remove, click the `ellipsis` and select **Remove** from the dropdown.
-4. Confirm that you would like to remove the member from the group in the popup by clicking the **OK** button
+1. From the left sidebar, select **Groups**
+2. Select the group
+3. From the left sidebar, select **Members**
+4. On the right hand side of the row for the member you want to remove, click **Remove**.
+5. Confirm that you would like to remove the member from the group in the popup by clicking the **OK** button

docs-site/docs/user/project/projects/manage-projects.md

@@ -75,7 +75,17 @@ To update the URL of the project:
 3. Select **Change project URL**
 
 ## View Project History
-<!-- TODO: Add steps to view project history -->
+
+Prerequisite:
+- You must have at least the Maintainer role for the project.
+- You must be a direct or inherited member of the project's ancestry. Shared groups and their members cannot see the history.
+
+To view a project's history:
+
+1. Select the project that you want to edit and then on the left sidebar
+2. Select **History**
+
+A new project version is created each time the project's information is changed. Clicking a version within the project's history will display what changes were made to the project.
 
 ## Transfer Project
 

docs-site/docs/user/project/projects/projects-intro.md

@@ -3,4 +3,12 @@ id: introduction
 ---
 
 # Projects
-<!-- TODO: Add projects intro/description -->
+
+Projects are used to organize and manage samples. They can belong to either a group (or subgroup) or a user.
+
+Access to projects can be granted either through direct user invitation or inviting a group, allowing its members to access the project.
+
+Through a project, automated analysis of samples can be set up. Follow these steps to learn how.
+<!-- TODO: link steps to automated WE set up when available -->
+
+Learn how to work with projects under [Manage Projects](manage-projects).

docs-site/docs/user/project/samples/manage-samples.md

@@ -14,8 +14,9 @@ Prerequisite:
 
 To view samples that the project contains:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
 
 ## Create Sample
 
@@ -26,12 +27,13 @@ Prerequisites:
 
 To create a new sample in a project:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select **New Sample**
-4. Enter the name of the sample in the **Name** field
-5. Enter an optional description for the sample in the **Description** field
-6. Select **Create sample**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select **New Sample**
+5. Enter the name of the sample in the **Name** field
+6. Enter an optional description for the sample in the **Description** field
+7. Select **Create sample**
 
 ## Update Sample
 
@@ -42,13 +44,14 @@ Prerequisites:
 
 To update sample details:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select the sample that you would like to edit
-4. Select **Edit this sample**
-5. Enter the name of the sample in the **Name** field
-6. Enter an optional description for the sample in the **Description** field
-7. Select **Update sample**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. Select **Edit this sample**
+6. Enter the name of the sample in the **Name** field
+7. Enter an optional description for the sample in the **Description** field
+8. Select **Update sample**
 
 ## Transfer Samples
 
@@ -64,11 +67,12 @@ Otherwise:
 
 To transfer samples into another project:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select the checkboxes for the samples that you would like to transfer
-4. Select **Transfer samples**
-5. From the transfer samples pop-up, select the project to which you would like to transfer the samples to, and select **Submit**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the checkboxes for the samples that you would like to transfer
+5. Select **Transfer samples**
+6. From the transfer samples pop-up, select the project to which you would like to transfer the samples to, and select **Submit**
 
 ## Clone Samples
 
@@ -80,11 +84,12 @@ Prerequisites:
 
 To clone samples into another project:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select the checkboxes for the samples that you would like to clone
-4. Select **Clone samples**
-5. From the clone samples pop-up, select the project to which you would like to clone the samples to, and select **Submit**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the checkboxes for the samples that you would like to clone
+5. Select **Clone samples**
+6. From the clone samples pop-up, select the project to which you would like to clone the samples to, and select **Submit**
 
 ## Delete Sample
 
@@ -95,11 +100,24 @@ Prerequisites:
 
 To remove a sample:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select the sample that you would like to remove
-4. Select **Remove**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. Select **Remove**
 
 ## View Sample History
 
-<!-- TODO: Add steps for sample history -->
+Prerequisite:
+- You must have at least the Maintainer role for the sample's project.
+- You must be a direct or inherited member of the project's ancestry. Shared groups and their members cannot see the history.
+
+To view a sample's history:
+
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. Click the **History** tab
+
+A new sample version is created each time the sample's information is changed. Clicking a version within the sample's history will display what changes were made to the sample.

docs-site/docs/user/project/samples/sample-files.md

@@ -12,9 +12,11 @@ Prerequisites:
 
 - You must have access to the project either through membership, or through a namespace share
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. The table lists all the single-end and paired-end files which have been uploaded to the sample
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. The table lists all the single-end and paired-end files which have been uploaded to the sample
 
 ## Upload Files to Samples
 
@@ -25,31 +27,40 @@ Prerequisites:
 
 To upload files to a sample:
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select **Upload Files**
-4. From the dialog, select **Choose files**
-5. Select the files you would like to upload. Multi file selection is enabled
-6. Select **Upload**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. Select **Upload Files**
+6. From the dialog, select **Choose files**
+7. Select the files you would like to upload. Multi file selection is enabled
+8. Select **Upload**
 
 ## Concatenate Sample files
 
 Prerequisites:
 
 - You must have access to the project either through membership, or through a namespace share
-- You must have an **Maintainer** role
+- You must have a **Maintainer** role
 - Files of the same type (single-end or paired-end) and compression can be concatenated together
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. Select the checkboxes for the files you would like to concatenate, and select **Concatenate files**
-4. In the dialog, the files to be concatenated are listed.
-5. Enter the **Filename**. This will be the base name of the concatenated files.
-6. Select the checkbox **Delete originals** if you would like to remove the original files after concatenation
-7. Select **Concatenate**
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. Select the checkboxes for the files you would like to concatenate, and select **Concatenate files**
+6. In the dialog, the files to be concatenated are listed.
+7. Enter the **Filename**. This will be the base name of the concatenated files.
+8. Select the checkbox **Delete originals** if you would like to remove the original files after concatenation
+9. Select **Concatenate**
 
 ## Download Sample files
-<!-- TODO: Add steps to download sample files -->
+
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. Click the filename you'd like to download
 
 ## Delete Sample files
 
@@ -58,7 +69,9 @@ Prerequisites:
 - You must have access to the project either through membership, or through a namespace share
 - You must have an **Owner** role
 
-1. From the left sidebar, select **Projects**, select the project
-2. From the left sidebar, select **Samples**
-3. To delete multiple files, select the checkboxes for the files you would like to delete, then click **Delete Files**
-4. To delete individual single end and paired-end reads, select **Delete** for the files you would like to delete.
+1. From the left sidebar, select **Projects**
+2. Select the project
+3. From the left sidebar, select **Samples**
+4. Select the sample
+5. To delete multiple files, select the checkboxes for the files you would like to delete, then click **Delete Files**
+6. To delete individual single end and paired-end reads, select **Delete** for the files you would like to delete.