Merge pull request #732 from kdaily/fix-internal-links

Fix internal links

Author: Kenneth Daily

README.md

@@ -24,6 +24,7 @@ Internal development can be performed by branching from `gh-pages` to your own f
 Pages are described by categories. These are stored in a Jekyll collection at [_categories](_categories/). The content that describes each category is defined in a YAML header in a file in that directory. The categories avaiable for reference elsewhere are named as the file or as present in the 'name' field of the YAML header.
 
 For example, if you want to create a page with a governance category, you would look in [_categories/governance.md](_categories/governance.md) in the 'name' field and use that value.
+
 ### Creating a page
 
 To create a page using the article layout, start by specifying at the very beginning the title, layout, excerpt, and category in the YAML front matter. The title and excerpt will show up in the article's user guide thumbnail and the category tag will be used to sort the article into its corresponding user guide tab. If no category is specified, it will default into the "How-To" tab. 
@@ -94,6 +95,20 @@ Images can be inserted using either Markdown or HTML, it all depends on your pre
 ### Inserting code 
 The docs may contain a high level overview of a feature, but should link to the [Python docs](https://python-docs.synapse.org/build/html/index.html) and [synapser](https://r-docs.synapse.org/articles/synapser.html) docs, pointing to the relevant anchor, for code examples. This is to ensure code is validated with the client release cycles. 
 
+
+### Inserting relative links
+A page may link to other pages within the documentation site. To do this, use a `link` Liquid tag to properly render the URL:
+
+```
+[link text]({{ site.baseurl }}{% link _articles/getting_started.md %})
+```
+
+If the link uses an anchor to jump to a specific part of the page, it must go outside the `link` tag:
+
+```
+[Annotations]({{ site.baseurl }}{% link _articles/annotation_and_query.md %}#adding-annotations)
+```
+
 ## License
 
 Distributed under the Eclipse Public License, the same as Clojure.

_articles/access_controls.md

@@ -6,7 +6,7 @@ category: governance
 order: 2
 ---
 
-Synapse has two ways to control who can access your content. Sharing Settings determine _who_ can access content, and is akin to individual or group (team) permissions. Conditions for Use determine _how_ data can be used by those users who have been granted access. All content in Synapse has Sharing Settings but not all content has Conditions for Use. See the [Sharing Settings](sharing_settings.md) article for information about those settings - this article covers conditions for use only.
+Synapse has two ways to control who can access your content. Sharing Settings determine _who_ can access content, and is akin to individual or group (team) permissions. Conditions for Use determine _how_ data can be used by those users who have been granted access. All content in Synapse has Sharing Settings but not all content has Conditions for Use. See the [Sharing Settings]({{ site.baseurl }}{% link _articles/sharing_settings.md %}) article for information about those settings - this article covers conditions for use only.
 
 <a name="conditions-for-use"></a>
 

_articles/accounts_certified_users_and_profile_validation.md

@@ -26,7 +26,7 @@ The table below summarizes the user privileges for each level.
 
 ## User Responsibilities
 
-You are solely responsible for your actions on Synapse. You are required to abide by the [Synapse Terms and Conditions of Use](https://s3.amazonaws.com/static.synapse.org/governance/SageBionetworksSynapseTermsandConditionsofUse.pdf?v=4) and all policies and principles described in the [Synapse governance documents](governance.md). We strongly encourage you to familiarize yourself with these documents. Please contact the Synapse Access and Compliance Team (<mailto:act@synapse.org>) if you have any questions.
+You are solely responsible for your actions on Synapse. You are required to abide by the [Synapse Terms and Conditions of Use](https://s3.amazonaws.com/static.synapse.org/governance/SageBionetworksSynapseTermsandConditionsofUse.pdf?v=4) and all policies and principles described in the [Synapse governance documents]({{ site.baseurl }}{% link _articles/governance.md %}). We strongly encourage you to familiarize yourself with these documents. Please contact the Synapse Access and Compliance Team (<mailto:act@synapse.org>) if you have any questions.
 
 {% include important.html content="By using Synapse you consent to all Synapse governance policies and procedures." %}
 
@@ -69,11 +69,11 @@ Go to the settings area of your [Synapse profile homepage](https://www.synapse.o
 
 1. Confirm your user profile is complete including **your full name, current affiliation, and city/country.**
 1. Link to your ORCID profile. **Make sure your profile is public and populate it with at least one piece of information about yourself in addition to your name.**
-1. Physically sign (in ink), initial, and submit the Synapse [Oath](../assets/other/oath.md)
+1. Physically sign (in ink), initial, and submit the Synapse [Oath]({{ site.baseurl }}{% link assets/other/oath.md %})
 1. Submit recent (current within the past month) identity attestation documentation. Acceptable forms of documentation, in English, are:
 
-* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here](../assets/other/signing_official_template.md)) OR
-* A notarized letter attesting to your identity ([template here](../assets/other/notarized_letter_template.md)) OR
+* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here]({{ site.baseurl }}{% link assets/other/signing_official_template.md %})) OR
+* A notarized letter attesting to your identity ([template here]({{ site.baseurl }}{% link assets/other/notarized_letter_template.md %})) OR
 * A copy of your professional license (e.g., a photocopy of your medical license)
 _Please note that a copy of a work or university identification badge is not an accepted form of identity attestation documentation._
 
@@ -83,7 +83,7 @@ You will receive a notification email when your profile has been validated and a
 
 Acceptable forms of documentation, in English, are:
 
-* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here](../assets/other/signing_official_template.md)) OR
-* A notarized letter attesting to your identity ([template here](../assets/other/notarized_letter_template.md)) OR
+* A letter from a signing official on letterhead attesting to your identity. _Please note that you can not serve as your own signing official_ ([template here]({{ site.baseurl }}{% link assets/other/signing_official_template.md %})) OR
+* A notarized letter attesting to your identity ([template here]({{ site.baseurl }}{% link assets/other/notarized_letter_template.md %})) OR
 * A copy of your professional license (e.g., a photocopy of your medical license)
 _Please note that a copy of a work or university identification badge is not an accepted form of identity attestation documentation._

_articles/annotation_and_query.md

@@ -11,7 +11,7 @@ category: metadata-and-annotations
 
  In this case, the annotations you may want to add might look like this:
 
-![Annotation example](../assets/images/annotationsComplete.png)
+![Annotation example]({../assets/images/annotationsComplete.png)
 
 ## Types of Annotations
 
@@ -24,15 +24,15 @@ Annotations can be one of four types:
 
 ## How to Assign Annotations
 
-Annotations may be added when initially uploading a file or at a later date. This can be done using the command line client, the [Python client](https://python-docs.synapse.org/build/html/Views.html#updating-annotations-using-view), the [R client](https://r-docs.synapse.org/articles/views.html#updating-annotations-using-view), or from the web. Using the programmatic clients facilitates batch and automated population of annotations across many files. The web client can be used to bulk update many files using [file views](views.md).
+Annotations may be added when initially uploading a file or at a later date. This can be done using the command line client, the [Python client](https://python-docs.synapse.org/build/html/Views.html#updating-annotations-using-view), the [R client](https://r-docs.synapse.org/articles/views.html#updating-annotations-using-view), or from the web. Using the programmatic clients facilitates batch and automated population of annotations across many files. The web client can be used to bulk update many files using [file views]({{ site.baseurl }}{% link _articles/views.md %}).
 
 ### Adding Annotations
 
 To add annotations on a single entity through the web client, click the **Annotations** button in the upper right corner on a Project, Folder, or File page.
 
 ![Annotation web location](../assets/images/webAnnotation.png)
 
-To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale](managing_custom_metadata_at_scale.md) for a tutorial on how to do this efficiently and effectively leveraging [file views](views.md).
+To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale]({{ site.baseurl }}{% link _articles/managing_custom_metadata_at_scale.md %}) for a tutorial on how to do this efficiently and effectively leveraging [file views]({{ site.baseurl }}{% link _articles/views.md %}).
 
 ##### Command line
 
@@ -65,7 +65,7 @@ Click **File Tools**, **Annotations** and **Edit** to add, delete, or modify ann
 
 ![Annotation editor](../assets/images/annotationsDetail.png)
 
-To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale](managing_custom_metadata_at_scale.md) for a tutorial on how to do this efficiently and effectively leveraging [file views](views.md).
+To add annotations on multiple files, please refer to our Synapse in Practice article [Managing Custom Metadata at Scale]({{ site.baseurl }}{% link _articles/managing_custom_metadata_at_scale.md %}) for a tutorial on how to do this efficiently and effectively leveraging [file views]({{ site.baseurl }}{% link _articles/views.md %}).
 
 ##### Command line
 
@@ -133,7 +133,7 @@ SELECT * FROM syn123456 WHERE "id" = 'syn00012'
 
 ### Finding Files in a Specific Project
 
-To find all files in a specific Project, create a View in the web client. For example, if you'd like to see all files in a Project, navigate to your project and then the **Tables** tab. From there, click **Tables Tools** and **Add File View**. Click **Add container** and **Enter Synapse Id** to create a tabluar file view that contains every file in the project, which you can now query. Importantly, if you want to later query on annotations, you must select **Add All Annotations**. For a more in-depth look at this feature, please read our articles on [File Views](views.md).
+To find all files in a specific Project, create a View in the web client. For example, if you'd like to see all files in a Project, navigate to your project and then the **Tables** tab. From there, click **Tables Tools** and **Add File View**. Click **Add container** and **Enter Synapse Id** to create a tabluar file view that contains every file in the project, which you can now query. Importantly, if you want to later query on annotations, you must select **Add All Annotations**. For a more in-depth look at this feature, please read our articles on [File Views]({{ site.baseurl }}{% link _articles/views.md %}).
 
 ### Listing Files in a Specific Folder
 
@@ -213,4 +213,4 @@ SELECT * FROM syn123 where "chemicalStructure" = '4''-chemical'
 
 # See Also
 
-[Downloading Data](downloading_data.md), [Tables](tables.md)
+[Downloading Data]({{ site.baseurl }}{% link _articles/downloading_data.md %}), [Tables]({{ site.baseurl }}{% link _articles/tables.md %})

_articles/challenge_administration.md

@@ -27,7 +27,7 @@ Maintence of both a **Staging** and **Live** `Project` enables `Wiki` content to
 
 {% include important.html content="All edits and changes should be made on the Staging site." %}
 
-For background on how to create and share `Projects`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project](making_a_project.md).
+For background on how to create and share `Projects`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project]({{ site.baseurl }}{% link _articles/making_a_project.md %}).
 
 ### Synapse Teams
 
@@ -39,7 +39,7 @@ The command `createchallenge` creates three Synapse `Teams`:
 
 * **Challenge pre-registration team** - This `Team` is recommended for when the challenge is under development.  It allows participants to join a mailing list to receive notification of challenge launch news.
 
-Please visit this [page](teams.md) to learn more about `Teams`.
+Please visit this [page]({{ site.baseurl }}{% link _articles/teams.md %}) to learn more about `Teams`.
 
 ### Activating Challenge Configuration
 
@@ -49,21 +49,21 @@ The command `createchallenge` also connects the **challenge participant team** t
 
 The challenge data (e.g. training dataset, scoring data...) are uploaded to the **Live** challenge `Project` when it is ready to be shared with participants.
 
-For background on how to create and share `Project`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project](making_a_project.md).
+For background on how to create and share `Project`, `Files`, `Folders` and `Wiki` pages, please see our article [Making a Project](%{ link _articles/making_a_project.md %}).
 
 ### Adding Conditions for Use
 
 Synapse has the ability to apply access restrictions to sensitive data (e.g. human data), so that legal requirements are met before participants access such data. If human data are being used in the challenge, or if you have any question about the sensitivity of the challenge data, please contact the Synapse **Access and Compliance Team (act@sagebase.org)** for support to ensure that the necessary data access approval procedures are put in place.
 
 There are cases where there are no human data concerns and instead a pop-up agreement needs to be presented before the first data download. Contact the **Access and Compliance Team** to set up this agreement.
 
-Please view the [Access Controls page](access_controls.md) to learn how to add conditions for use on data.
+Please view the [Access Controls page]({{ site.baseurl }}{% link _articles/access_controls.md %}) to learn how to add conditions for use on data.
 
 ### Create an Evaluation Queue for Submissions
 
 Challenge participants can submit Synapse Entities (e.g. `File`, `Folder`, `Project`, `Docker`) to evaluation queues. Multiple Evaluation queues can be created to support challenges with more than one question.
 
-Please visit the [Evaluation Queue article](evaluation_queues.md) to learn more about queue configuration.
+Please visit the [Evaluation Queue article]({{ site.baseurl }}{% link _articles/evaluation_queues.md %}) to learn more about queue configuration.
 
 One of the features of Synapse for DREAM Challenges is the live compilation of submission statistics for all evaluation queues, including total submission count, count per individual/team, count per submission state (scored, invalid) and count per week.  You can see the statistics for various challenges [here](https://www.synapse.org/#!Synapse:syn2504723/wiki/65150).  In order to activate statistics for your evaluation queues, you must be an administrator of the challenge Project. Each queue needs to be configured to generate the statistics. To do this:
 
@@ -90,4 +90,4 @@ Throughout the challenge, participants will continuously submit to the evaluatio
 
 Organizers can create a leaderboard when scores are ready to be revealed to participants. Leaderboards are sorted, paginated, tabular forms that display submission annotations (e.g. scores from the scoring application and other metadata) and update as annotations or scores change. A leaderboard can provide real-time insight into the progress of a challenge.
 
-Learn more about adding leaderboards in the [Evaluation Queue article](evaluation_queues.md).
+Learn more about adding leaderboards in the [Evaluation Queue article]({{ site.baseurl }}{% link _articles/evaluation_queues.md %}).

_articles/challenge_participation.md

@@ -18,30 +18,30 @@ This tutorial will teach you the steps of participating in a challenge.
 
 ## Challenge Registration
 
-If you do not have a Synapse account, please go to our [getting started guide](getting_started.md#becoming-a-certified-user) to become a certified Synapse user.
+If you do not have a Synapse account, please go to our [getting started guide]({{ site.baseurl}}{% link _articles/getting_started.md %}#becoming-a-certified-user) to become a certified Synapse user.
 Participants **must** be registered for the challenge if they want to submit and participate. The registration button can be found on the home page or `How to Participate` page for every challenge. In order to be fully registered for any challenge, you must have a Synapse account. In addition, DREAM Challenges require that you:
 
-(1) become a [certified user](getting_started.md#becoming-a-certified-user);
+(1) become a [certified user]({{ site.baseurl}}{% link _articles/getting_started.md %}#becoming-a-certified-user);
 
 (2) agree to the DREAM Rules of participation, and
 
 (3) agree to the Terms of Use to work with the Challenge data.
 
 ## Join or Create a Team
 
-We encourage you to form a team with other participants for the challenge. You can either join a team or create your own team of collaborators. See instructions on how to form a team [here](teams.md). It is important to note that you **cannot** be on more than one team. Once you have submitted as a team or individual, you will not be able to submit as another team. If you decide to be part of a team, please register your team to the challenge - there will be a place to do this in every challenge wiki.
+We encourage you to form a team with other participants for the challenge. You can either join a team or create your own team of collaborators. See instructions on how to form a team [here]({{ site.baseurl }}{% link _articles/teams.md %}). It is important to note that you **cannot** be on more than one team. Once you have submitted as a team or individual, you will not be able to submit as another team. If you decide to be part of a team, please register your team to the challenge - there will be a place to do this in every challenge wiki.
 
 ## Accessing Challenge Data
 
 The data stored on the challenge Synapse site can be accessed using the Synapse website or programmatically using the Synapse R or Python clients. Instructions on using Synapse are provided in the [Synapse User Guide](./). File descriptions are provided on the Data Description page in each challenge wiki.
 
 ## Run your Algorithms and Submit to the Challenge
 
-You can submit to a challenge queue by using the R, Python or web client. All submissions must be first uploaded to Synapse. Follow these [instructions](getting_started.md#project-and-data-management-on-synapse) to learn how to upload to a project. Most challenge queues will be labeled by `challengename-subchallenge#` as a challenge may have different questions that it may want you to answer.  Learn more about submitting to [evaluation queues](evaluation_queues.md)
+You can submit to a challenge queue by using the R, Python or web client. All submissions must be first uploaded to Synapse. Follow these [instructions]({{ site.baseurl }}{% link _articles/getting_started.md %}) to learn how to upload to a project. Most challenge queues will be labeled by `challengename-subchallenge#` as a challenge may have different questions that it may want you to answer.  Learn more about submitting to [evaluation queues]({{ site.baseurl }}{% link _articles/evaluation_queues.md %})
 
 
 ## Share Ideas and Ask Questions
 
 Every challenge has a discussion forum for participants (the `Discussion` tab on the Challenge Project page). The forum is a space for participants to ask any questions and raise ideas.
 
-Instructions on how to use the discussion forum can be found [here](discussion.md)
+Instructions on how to use the discussion forum can be found [here]({{ site.baseurl }}{% link _articles/discussion.md %})