fix deployment link and relative URLs

Author: alistairewj

jekyll-site/_config.yml

@@ -1,7 +1,7 @@
 # Site settings
 title: "MIMIC Database"
 description: "A large, publicly available critical care database"
-baseurl: "" # the subpath of your site, e.g. /blog
+baseurl: "/mimic-website" # the subpath of your site, e.g. /blog
 url: "https://mimic.mit.edu" # the base hostname & protocol for your site
 repository: "MIT-LCP/mimic-website"
 

jekyll-site/_docs/gettingstarted/cloud/bigquery.md

@@ -40,7 +40,7 @@ The query should return some data, and your browser window should be similar to
 
 At this point you are ready to use MIMIC on BigQuery!
 
-A tutorial on using BigQuery to query MIMIC-III is available [here](/docs/iii/tutorials/intro-to-mimic-iii-bq).
+A tutorial on using BigQuery to query MIMIC-III is available [here]({{ "/docs/iii/tutorials/intro-to-mimic-iii-bq" | relative_url }}).
 
 Note that we have a number of pre-generated "views" of the data. These are available in the `mimiciv_derived` dataset which you are free to query. All code used to generate these views has been made openly available on the [MIMIC-IV code repository](https://github.com/MIT-LCP/mimic-iv/).
 

jekyll-site/_docs/gettingstarted/cloud/gcs.md

@@ -9,7 +9,7 @@ description: "Access the MIMIC datasets on Google Cloud Storage (GCS)."
 
 # Google Cloud Storage
 
-The MIMIC databases are hosted on Google Cloud Storage (GCS). Access to the bucket, if available, can be requested via the PhysioNet project page. See [this page for more detail on this process](/docs/gettingstarted).
+The MIMIC databases are hosted on Google Cloud Storage (GCS). Access to the bucket, if available, can be requested via the PhysioNet project page. See [this page for more detail on this process]({{ "/docs/gettingstarted" | relative_url }}).
 
 Datasets available on GCS include:
 

jekyll-site/_docs/gettingstarted/cloud/index.md

@@ -33,4 +33,4 @@ There are three steps to accessing data on the cloud:
 3. Log-in to the appropriate service and navigate to the resource
 
 These steps assume you are already credentialed and have signed the data use agreement for MIMIC-IV.
-If you have not, read this page for instructions on gaining access to [MIMIC](/docs/gettingstarted).
+If you have not, read this page for instructions on gaining access to [MIMIC]({{ "/docs/gettingstarted" | relative_url }}).

jekyll-site/_docs/gettingstarted/cloud/link.md

@@ -45,4 +45,4 @@ For AWS, add your AWS canonical ID. This is *not your e-mail*. It is a numeric i
 
 ## Linked account
 
-Once you have successfully linked a cloud account to your PhysioNet profile, the next step is to request access to [MIMIC](/docs/gettingstarted/cloud/request) for your cloud account.
+Once you have successfully linked a cloud account to your PhysioNet profile, the next step is to request access to [MIMIC]({{ "/docs/gettingstarted/cloud/request" | relative_url }}) for your cloud account.

jekyll-site/_docs/gettingstarted/cloud/request.md

@@ -16,7 +16,7 @@ For MIMIC-III, go to the [MIMIC-III PhysioNet project page](https://physionet.or
 For MIMIC-IV, go to the [MIMIC-IV PhysioNet project page](https://physionet.org/content/mimiciv).
 
 Once there, scroll to the bottom to the "Files" section.
-*If* the page shows a restricted-access warning, you need to get access to [MIMIC](/docs/gettingstarted).
+*If* the page shows a restricted-access warning, you need to get access to [MIMIC]({{ "/docs/gettingstarted" | relative_url }}).
 Otherwise, you should see the following:
 
 ![Methods for accessing MIMIC-IV](/img/cloud/mimiciv_files.png)
@@ -47,7 +47,7 @@ You will receive an e-mail detailing instructions for how to access MIMIC on Big
 Once you have been granted access to a cloud resource, the next step is to navigate to that resource in the cloud.
 
 * For the GCP Storage Bucket, click the link e-mailed to you.
-* For BigQuery, see the [BigQuery page](../bigquery). You may also be interested in the [querying tutorial on BigQuery] for [MIMIC-III](/docs/iii/tutorials/intro-to-mimic-iii-bq//) or [MIMIC-IV](/docs/iv/tutorials/bigquery/).
+* For BigQuery, see the [BigQuery page](../bigquery). You may also be interested in the [querying tutorial on BigQuery] for [MIMIC-III]({{ "/docs/iii/tutorials/intro-to-mimic-iii-bq/" | relative_url }}) or [MIMIC-IV]({{ "/docs/iv/tutorials/bigquery/" | relative_url }}).
 * AWS access is currently unavailable for MIMIC-IV, but planned.
 
-Once you have access to MIMIC, we highly recommend you read the respective database introduction: [MIMIC-III](/docs/iii), [MIMIC-IV](/docs/iv/).
+Once you have access to MIMIC, we highly recommend you read the respective database introduction: [MIMIC-III]({{ "/docs/iii" | relative_url }}), [MIMIC-IV]({{ "/docs/iv/" | relative_url }}).

jekyll-site/_docs/gettingstarted/index.md

@@ -39,4 +39,4 @@ If you are a student (including graduate students) or a postdoc, you must provid
 
 We highly recommend accessing the data through a cloud service.
 In order to use the cloud service, you must associate your PhysioNet account with your cloud account.
-The [cloud access page](./cloud) provides instructions on how to do this.
+The [cloud access page]({{ "/docs/gettingstarted/cloud" | relative_url }}) provides instructions on how to do this.

jekyll-site/_docs/gettingstarted/local/index.md

@@ -11,7 +11,7 @@ description: "Set up MIMIC locally on your own database server."
 
 ## PhysioNet  
 
-Once your [application to access MIMIC](/docs/gettingstarted/) has been approved, you will be granted access to the 'MIMIC-III Clinical Database' project page on PhysioNet:  
+Once your [application to access MIMIC]({{ "/docs/gettingstarted/" | relative_url }}) has been approved, you will be granted access to the 'MIMIC-III Clinical Database' project page on PhysioNet:  
 https://physionet.org/content/mimiciii/
 
 ## Data and build scripts

jekyll-site/_docs/gettingstarted/local/install-mimic-locally-ubuntu.md

@@ -9,7 +9,7 @@ description: "Step-by-step guide for installing MIMIC-III locally on Unix/Mac sy
 
 # Installing MIMIC-III in a local Postgres database
 
-Prerequisites: *This tutorial assumes that you have already completed the [steps required to gain access](/docs/gettingstarted) to the MIMIC dataset on PhysioNet.*
+Prerequisites: *This tutorial assumes that you have already completed the [steps required to gain access]({{ "/docs/gettingstarted" | relative_url }}) to the MIMIC dataset on PhysioNet.*
 
 Note that this install was written and tested using Mac OS X and Ubuntu 15.04. If you feel there are key details missing, please [raise an issue](https://github.com/MIT-LCP/mimic-website/issues) with your suggested improvements - we would love to incorporate them!
 
@@ -24,7 +24,7 @@ These steps are roughly equivalent, though you may learn more about the database
 
 Before proceeding with this tutorial you will need to:
 
-1. Download the MIMIC-III Clinical Database (see [here](/docs/gettingstarted/) for details on gaining access).
+1. Download the MIMIC-III Clinical Database (see [here]({{ "/docs/gettingstarted/" | relative_url }}) for details on gaining access).
 2. Place the MIMIC-III Clinical Database as either .csv or .csv.gz files somewhere on your local computer.
 3. Download the PostgreSQL scripts from [here](https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iii/buildmimic/postgres) - only the files which end in `.sql` are required.
 
@@ -40,7 +40,7 @@ On Mac OSX with the [Homebrew package manager](http://brew.sh/), simply type ```
 
 ### 2. Download the CSV data files
 
-Assuming that you have completed the [steps required to gain access](/docs/gettingstarted) to the MIMIC dataset, you should be able to access the CSV data files on PhysioNet at: https://physionet.org/content/mimiciii/.
+Assuming that you have completed the [steps required to gain access]({{ "/docs/gettingstarted" | relative_url }}) to the MIMIC dataset, you should be able to access the CSV data files on PhysioNet at: https://physionet.org/content/mimiciii/.
 
 Download these files to a local folder and decompress them if desired (it is possible to load the data directly into a database from compressed data files). The program `gzip` can be used to decompress the data (e.g. ```gzip -d *.gz```).
 

jekyll-site/_docs/gettingstarted/local/install-mimic-locally-windows.md

@@ -15,7 +15,7 @@ These are relatively brief instructions provided to ease installation of Postgre
 
 Before proceeding with this guide you will need to:
 
-1. Download the MIMIC-III Clinical Database (see [here](/docs/gettingstarted) for details on gaining access).
+1. Download the MIMIC-III Clinical Database (see [here]({{ "/docs/gettingstarted" | relative_url }}) for details on gaining access).
 2. Extract the MIMIC-III Clinical Database as .csv files somewhere on your local computer.
 3. Download the PostgreSQL scripts from [here](https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iii/buildmimic/postgres) - only the files which end in `.sql` are required.