ALS-7300: Prepare for Analysis Page in BDC (#185)

src/lib/assets/configuration.json

@@ -55,8 +55,8 @@
   "apiPage": {
     "cards": [
       {
-        "header": "Example Analyses with PIC-SURE page",
-        "body": "Detailed step-by-step example code that demonstrates how to use PIC-SURE for analysis.",
+        "header": "Setting Up the PIC-SURE API",
+        "body": "Step-by-step instructions to get started using the PIC-SURE API",
         "link": "/analyze/example"
       }
     ]
@@ -79,11 +79,11 @@
         "btnText": "Start Exploring"
       },
       {
-        "title": "Analyze",
-        "description": "Access data and kickstart your research",
+        "title": "Prepare for Analysis",
+        "description": "Use the PIC-SURE API to prepare data for analysis",
         "icon": "fa-solid fa-chart-line",
         "url": "/analyze",
-        "btnText": "Go to Analyze"
+        "btnText": "Prepare for Analysis"
       }
     ],
     "stats": ["Variables", "Participants", "Data Sources"]

src/lib/configuration.ts

@@ -75,7 +75,7 @@ export const routes: Route[] = [
   },
   {
     path: '/analyze',
-    text: 'Analyze',
+    text: 'Prepare for Analysis',
     privilege: [PicsurePrivileges.QUERY, BDCPrivileges.AUTHORIZED_ACCESS],
   },
   {

src/routes/(picsure)/(authorized)/analyze/+page.svelte

@@ -11,11 +11,26 @@
   <title>{branding.applicationName} | API</title>
 </svelte:head>
 
-<Content title="Analyze">
+<Content title="Prepare for Analysis with the PIC-SURE API">
   <section class="flex flex-col gap-8">
     <p class="mt-4">
-      To start your analysis, use the following code to connect to PIC-SURE. Note that you will need
-      your personal access token below to complete the connection.
+      The PIC-SURE Application Programming Interface (API) can be used in an analysis environment of
+      your choice. This API is available in both Python and R coding languages.
+    </p>
+    <p>
+      To connect to the PIC-SURE Application Programming Interface (API), you will need your
+      personal access token. Copy your token and save as a text file called “token.txt” in the
+      working directory of your chosen analysis workspace, such as BioData Catalyst Powered by Seven
+      Bridges or BioData Catalyst Powered by Terra.
+    </p>
+    <div class="flex justify-center">
+      <UserToken />
+    </div>
+    <p>
+      To start your analysis, copy and execute the following code in an analysis environment, such
+      as BioData Catalyst Powered by Seven Bridges or BioData Catalyst Powered by Terra, to connect
+      to the PIC-SURE API. Note that you will need your personal access token to complete the
+      connection.
     </p>
     <TabGroup class="card p-4">
       <Tab bind:group={tabSet} name="python" value={0}>Python</Tab>
@@ -26,48 +41,46 @@
             language="python"
             lineNumbers={true}
             buttonCopied="Copied!"
-            code={`# Requires python 3.7 or later
+            code={`# Requires python 3.6 or later
 import sys
 import pandas as pd
 import matplotlib.pyplot as plt
-!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-adapter-hpds.git
+# BDC Powered by Terra users uncomment the following line to specify package install location
+# sys.path.insert(0, r"/home/jupyter/.local/lib/python3.7/site-packages")
 !{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-client.git
-
-import PicSureHpdsLib
+!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-python-adapter-hpds.git
+!{sys.executable} -m pip install --upgrade --force-reinstall git+https://github.com/hms-dbmi/pic-sure-biodatacatalyst-python-adapter-hpds.git
 import PicSureClient
-
+import PicSureBdcAdapter
+# Set up connection to PIC-SURE API
+PICSURE_network_URL = "https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure"
 token_file = "token.txt"
+
 with open(token_file, "r") as f:
-my_token = f.read()
+    my_token = f.read()
 
-connection = PicSureClient.Client.connect(url = PICSURE_network_URL, token = my_token)`}
+bdc = PicSureBdcAdapter.Adapter(PICSURE_network_URL, my_token)`}
           ></CodeBlock>
         {:else if tabSet === 1}
           <CodeBlock
             language="r"
             lineNumbers={true}
             code={`# Requires R 3.4 or later
-install.packages("devtools")
-
+### Uncomment this code if you are not using the PIC-SURE environment in *BDC-Seven Bridges*, or if you do not have all the necessary dependencies installed.
+#install.packages("devtools")
+Sys.setenv(TAR = "/bin/tar")
+options(unzip = "internal")
 devtools::install_github("hms-dbmi/pic-sure-r-adapter-hpds", ref="main", force=T, quiet=FALSE)
 library(dplyr)
-
-PICSURE_network_URL = "https://nhanes.hms.harvard.edu/picsure"
+PICSURE_network_URL = "https://picsure.biodatacatalyst.nhlbi.nih.gov/picsure"
 token_file <- "token.txt"
 token <- scan(token_file, what = "character")
 session <- picsure::bdc.initializeSession(PICSURE_network_URL, token)
-session <- picsure::bdc.setResource(session = session)`}
+session <- picsure::bdc.setResource(session = session,  resourceName = "AUTH")`}
           ></CodeBlock>
         {/if}
       </svelte:fragment>
     </TabGroup>
-    <p>
-      Copy your personal access token and save as a text file called “token.txt” in the same working
-      directory to execute the code above.
-    </p>
-    <div class="flex justify-center">
-      <UserToken />
-    </div>
   </section>
   <section id="info-cards" class="w-full flex flex-wrap flex-row justify-center mt-6">
     {#each branding.apiPage.cards as card}

src/routes/(picsure)/(authorized)/analyze/example/+page.svelte

@@ -26,18 +26,30 @@
 
       <h4 class="font-medium mt-8">1. Set up your analysis workspace</h4>
       <p>
-        First, you will need to set up your analysis workspace. This can be done locally or in a
-        cloud computing environment. Examples of how to programmatically access the PIC-SURE API
-        with Python or R are publicly available. These include Jupyter notebooks and RStudio files,
-        which you can access on the <a
+        First, you will need to set up your analysis workspace. This can be done in one of the
+        BioData Catalyst cloud computing environments, Seven Bridges or Terra. Examples of how to
+        programmatically access the PIC-SURE API with Python or R are publicly available. These
+        include Jupyter notebooks and RStudio files, which you can access on the
+        <a
           class="anchor"
-          href="https://github.com/hms-dbmi/Access-to-Data-using-PIC-SURE-API/"
+          href="https://github.com/hms-dbmi/Access-to-Data-using-PIC-SURE-API/tree/master/NHLBI_BioData_Catalyst"
           target="_blank">GitHub repository</a
         >
       </p>
       <p>
-        The PIC-SURE team recommends starting with the PIC-SURE_101 example code. You can clone this
-        GitHub repository to your analysis workspace or set up a new file.
+        The PIC-SURE team recommends starting with the PIC-SURE_101 example code. You can access
+        these files in the
+        <a
+          class="anchor"
+          href="https://platform.sb.biodatacatalyst.nhlbi.nih.gov/u/biodatacatalyst/data-export-from-the-pic-sure-ui"
+          target="_blank">Data Export from the PIC-SURE UI Seven Bridges Public Project</a
+        >
+        or using one of the
+        <a
+          class="anchor"
+          href="https://terra.biodatacatalyst.nhlbi.nih.gov/#workspaces?tab=public&filter=pic-sure"
+          target="_blank">PIC-SURE Workspaces on Terra</a
+        >
       </p>
 
       <h4 class="font-medium mt-8">2. Get your Personal Access Token</h4>