Merge remote-tracking branch 'refs/remotes/origin/dev' into dev

pepkit · Jul 25, 2024 · d55b28a · d55b28a
2 parents f5141ef + 6f08e1b
commit d55b28a
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Showing 3 changed files with 54 additions and 14 deletions.
diff --git a/web/src/components/schemas/schema-list-card.tsx b/web/src/components/schemas/schema-list-card.tsx
@@ -8,7 +8,7 @@ type Props = {
 
 export const SchemaListCard = (props: Props) => {
   const { schema } = props;
-  const { namespace, name, description, last_update_date } = schema;
+  const { namespace, name, description, last_update_date, submission_date } = schema;
   return (
     <div className="border border-dark p-2 shadow-sm rounded mt-3">
       <div className="d-flex flex-column gap-1">
@@ -22,8 +22,12 @@ export const SchemaListCard = (props: Props) => {
         </div>
         <p className="text-muted mb-0">{description || 'No description'}</p>
         <p className="fst-italic mb-0 text-sm">
-          <i className="bi bi-clock me-1"></i>
-          {dateStringToDateTime(last_update_date)}
+          <span className="mx-1">
+            <i className="bi bi-clock me-1"> Updated: {dateStringToDateTime(last_update_date)}</i>{' '}
+          </span>
+          <span className="mx-1">
+            <i className="bi bi-clock me-1"> Created: {dateStringToDateTime(submission_date)}</i>
+          </span>
         </p>
       </div>
     </div>

diff --git a/web/src/pages/Home.tsx b/web/src/pages/Home.tsx
@@ -136,8 +136,8 @@ export function Home() {
               <h2 className="fw-bold">Web server and API</h2>
               <p className="text-balance pe-4">
                 The PEPhub web server and API are designed to provide a user-friendly interface for exploring and
-                working with biologically ortiented sample metadata. The web server allows users to search for metadata,
-                view detailed information about these metadata, and create new metadata.
+                working with biologically oriented sample metadata. The web server allows users to search for metadata,
+                view detailed information about these metadata, and create projects.
               </p>
             </Col>
             <Col sm={6} md={6} className="d-flex flex-column align-items-center justify-content-center h-100">
@@ -190,11 +190,11 @@ export function Home() {
               <p className="text-balance pe-4">
                 PEPhub provides a Python an R client for interacting with the PEPhub API. The client allows users to
                 download and work with project metadata programmatically, without the need to interact with the native
-                API. <code>peppy</code> is available on PyPI with other useful tools for genomic metadata manipulation.
+                API. <code>PEPHubClient</code> is available on PyPI with other useful tools for metadata manipulation.
                 Peppy:{' '}
-                <a href="https://pypi.org/project/peppy/" className="bi bi-box-fill">
+                <a href="https://pypi.org/project/pephubclient/" className="bi bi-box-fill">
                   {' '}
-                  PyPI peppy
+                  PyPI pephubclient
                 </a>
                 .
               </p>

diff --git a/web/src/utils/const.ts b/web/src/utils/const.ts
@@ -95,8 +95,10 @@ export const CLIENT_PYTHON_CODE_MD = `
 import peppy
 
 project = peppy.Project.from_pephub('databio/example')
+# where 'databio/example' is the project registry path
 
-print(project)
+for sample in proj.samples:
+  print(sample)
 \`\`\`
 `;
 
@@ -105,21 +107,50 @@ import peppy
 
 project = peppy.Project.from_pephub('databio/example')
 
-print(project)
+for sample in proj.samples:
+  print(sample)
 `;
 
 export const CLIENT_R_CODE_MD = `
 \`\`\`r
+library(pepr)
 
-# PEPHub client is not yet available in R
-# R package is under development
+pep <- pullProject('databio/example:default')
+
+for (sample in sampleTable(pep)) {
+  print(sample)
+} 
 
 \`\`\`
 `;
 
 export const CLIENT_R_CODE_RAW = `
-# PEPHub client is not yet available in R
-# R package is under development
+library(pepr)
+
+pep <- pullProject('databio/example:default')
+
+for (sample in sampleTable(pep)) {
+  print(sample)
+} 
+`;
+
+export const CLIENT_CLI_CODE_MD = `
+\`\`\`bash
+
+phc login
+
+phc pull databio/example:default --zip
+\`\`\`
+`;
+
+export const CLIENT_CLI_CODE_RAW = `
+library(pepr)
+
+pep <- pullProject('databio/example:default')
+
+for (sample in sampleTable(pep)) {
+  print(sample)
+} 
 `;
 
 export const PEPHUBCLIENT_SNIPPETS = [
@@ -133,4 +164,9 @@ export const PEPHUBCLIENT_SNIPPETS = [
     code: CLIENT_R_CODE_MD,
     raw: CLIENT_R_CODE_RAW,
   },
+  {
+    language: 'CLI',
+    code: CLIENT_CLI_CODE_MD,
+    raw: CLIENT_CLI_CODE_RAW,
+  },
 ];