Merge pull request #26 from PathwayCommons/iss25_static-site

maxkfranz · web-flow · commit e78e66666539 · 2022-11-08T17:35:45.000-05:00
Preparation to serve site
diff --git a/.gitignore b/.gitignore
@@ -80,7 +80,6 @@ typings/
 
 # Nuxt.js build / generate output
 .nuxt
-dist
 
 # Gatsby files
 .cache/
diff --git a/dist/bundle.css b/dist/bundle.css
@@ -0,0 +1 @@
+../src/dashboard/build/bundle.css
diff --git a/dist/bundle.css.map b/dist/bundle.css.map
diff --git a/dist/bundle.js b/dist/bundle.js
@@ -0,0 +1 @@
+../src/dashboard/build/bundle.js
diff --git a/dist/bundle.js.map b/dist/bundle.js.map
diff --git a/dist/img b/dist/img
@@ -0,0 +1 @@
+../src/dashboard/img/
diff --git a/dist/index.html b/dist/index.html
@@ -0,0 +1 @@
+../src/dashboard/index.html
diff --git a/example-data/2022-10.json b/example-data/2022-10.json
diff --git a/package.json b/package.json
@@ -8,15 +8,16 @@
     "hyper-recent": "hyper-recent.js"
   },
   "scripts": {
-    "start": "echo Nothing to start yet",
+    "start": "http-server -p 3000 --proxy http://localhost:3000? dist",
+    "build:data": "cd ./scripts && ./search.sh && ./recommendations.sh",
     "build:css": "esbuild --bundle src/dashboard/index.css --outfile=src/dashboard/build/bundle.css --loader:.jpg=dataurl",
     "watch:css": "esbuild --bundle src/dashboard/index.css --outfile=src/dashboard/build/bundle.css --loader:.jpg=dataurl --watch --sourcemap",
     "build:js": "esbuild src/dashboard/index.js --bundle --outfile=src/dashboard/build/bundle.js",
     "watch:js": "esbuild src/dashboard/index.js --bundle --outfile=src/dashboard/build/bundle.js --watch --sourcemap",
-    "build": "run-s build:css build:js",
+    "build": "run-s build:data build:css build:js",
     "watch": "run-p watch:css watch:js watch:reload watch:http",
     "watch:reload": "livereload src/dashboard",
-    "watch:http": "http-server -o -p 3000 --proxy http://localhost:3000? src/dashboard",
+    "watch:http": "http-server -o -p 3000 --proxy http://localhost:3000? dist",
     "test": "mocha",
     "coverage": "nyc mocha",
     "fix": "eslint ./src --fix",
diff --git a/scripts/recommendations.sh b/scripts/recommendations.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
-PAPER_ID="PMID:32165850"
-CATEGORY_ID="alzheimers-therapeutics"
+PAPER_IDS=("PMID:33933186" "PMID:33318676")
+CATEGORY_IDS=("alzheimers-diagnosis" "alzheimers-neuroinflammation")
 
 DATA_DIRECTORY="../example-data"
 MAX_PAPERS=50
@@ -17,63 +17,70 @@ PAPER_RECOMMENDATIONS_API_PATH=recommendations/
 PAPER_RECOMMENDATIONS_PATH=papers/forpaper/
 PAPER_RECOMMENDATIONS_LIMIT=500
 PAPER_RECOMMENDATIONS_FIELDS=title,year,externalIds,venue,authors,abstract
-RECOMMENDATION_URL="${API_BASE_URL}${PAPER_RECOMMENDATIONS_API_PATH}${API_VERSION_PATH}${PAPER_RECOMMENDATIONS_PATH}${PAPER_ID}?limit=${PAPER_RECOMMENDATIONS_LIMIT}&fields=${PAPER_RECOMMENDATIONS_FIELDS}"
 
-echo "Fetching from Semantic Scholar ${RECOMMENDATIONS_API_PATH}"
-echo "Paper: ${PAPER_ID}"
+for i in ${!CATEGORY_IDS[@]}; do
+  CATEGORY_ID=${CATEGORY_IDS[$i]}
+  PAPER_ID=${PAPER_IDS[$i]}
+  RECOMMENDATION_URL="${API_BASE_URL}${PAPER_RECOMMENDATIONS_API_PATH}${API_VERSION_PATH}${PAPER_RECOMMENDATIONS_PATH}${PAPER_ID}?limit=${PAPER_RECOMMENDATIONS_LIMIT}&fields=${PAPER_RECOMMENDATIONS_FIELDS}"
 
-json=$(curl -s -X GET ${RECOMMENDATION_URL})
-recommendedPapers=$(echo ${json} | jq '.recommendedPapers')
+  echo "Fetching from Semantic Scholar ${RECOMMENDATIONS_API_PATH}"
+  echo "Paper: ${PAPER_ID}"
+  echo "CATEGORY_ID: ${CATEGORY_ID}"
 
-numPapersRaw=$(echo ${recommendedPapers} | jq 'length')
-echo "numPapers: ${numPapersRaw}"
+  json=$(curl -s -X GET ${RECOMMENDATION_URL})
+  recommendedPapers=$(echo ${json} | jq '.recommendedPapers')
 
-selectedPapers=$(
-  echo ${recommendedPapers} | jq '[ .[] |
-  select((.venue == "bioRxiv" or (.venue == "medRxiv")) and (.year == 2022)) |
-  .paperId
-  ] |
-  .[0:'${MAX_PAPERS}']'
-)
+  numPapersRaw=$(echo ${recommendedPapers} | jq 'length')
+  echo "numPapers (Total): ${numPapersRaw}"
 
-numPapers=$(echo ${selectedPapers} | jq 'length')
-echo "numPapers: ${numPapers}"
+  selectedPapers=$(
+    echo ${recommendedPapers} | jq '[ .[] |
+    select((.venue == "bioRxiv" or (.venue == "medRxiv")) and (.year == 2022)) |
+    .paperId
+    ] |
+    .[0:'${MAX_PAPERS}']'
+  )
 
-# echo ${selectedPapers} | jq > ${DATA_DIRECTORY}/${CATEGORY_ID}.json
+  numPapers=$(echo ${selectedPapers} | jq 'length')
+  echo "numPapers (Filtered): ${numPapers}"
 
-### Get the paper details
-# RECOMMENDATION_URL="${API_BASE_URL}${ACADEMIC_GRAPH_API_PATH}${API_VERSION_PATH}${ACADEMIC_GRAPH_PAPER_PATH}.?fields=${ACADEMIC_GRAPH_PAPER_FIELDS}"
-DELAY=1
-selectedPapersArr=( $(echo ${selectedPapers} | jq '.[]') )
-COUNTER=0
-NUM_ITEMS=${#selectedPapersArr[@]}
-echo "numitems ${NUM_ITEMS}"
-echo '[' > ${DATA_DIRECTORY}/${CATEGORY_ID}.json
-for i in "${selectedPapersArr[@]}"
-do
-  let COUNTER++
-  id=$(echo ${i} | tr -d '"')
-  ACADEMIC_GRAPH_PAPER_URL="${API_BASE_URL}${ACADEMIC_GRAPH_API_PATH}${API_VERSION_PATH}${ACADEMIC_GRAPH_PAPER_PATH}${id}?fields=${ACADEMIC_GRAPH_PAPER_FIELDS}"
-  json=$(curl -s -X GET ${ACADEMIC_GRAPH_PAPER_URL})
-  record=$(
-    echo ${json} | jq '. |
-    {
-      paperId: .paperId,
-      title: .title,
-      journal: .venue,
-      date: .publicationDate,
-      doi: .externalIds.DOI,
-      brief: .tldr.text,
-      authors: .authors | [.[] | .name] | join("; ")
-    }'
-  )
-  printf "%s" "${record}" >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
-  if [ "${COUNTER}" == "${NUM_ITEMS}" ]; then
-    printf "%s\n" "" >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
-  else
-    printf "%s\n" "," >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
-  fi
+  # echo ${selectedPapers} | jq > ${DATA_DIRECTORY}/${CATEGORY_ID}.json
 
-  sleep ${DELAY}
+  ### Get the paper details
+  # RECOMMENDATION_URL="${API_BASE_URL}${ACADEMIC_GRAPH_API_PATH}${API_VERSION_PATH}${ACADEMIC_GRAPH_PAPER_PATH}.?fields=${ACADEMIC_GRAPH_PAPER_FIELDS}"
+  DELAY=1
+  selectedPapersArr=( $(echo ${selectedPapers} | jq '.[]') )
+  COUNTER=0
+  NUM_ITEMS=${#selectedPapersArr[@]}
+  echo "numitems ${NUM_ITEMS}"
+  echo '[' > ${DATA_DIRECTORY}/${CATEGORY_ID}.json
+  for i in "${selectedPapersArr[@]}"
+  do
+    let COUNTER++
+    id=$(echo ${i} | tr -d '"')
+    ACADEMIC_GRAPH_PAPER_URL="${API_BASE_URL}${ACADEMIC_GRAPH_API_PATH}${API_VERSION_PATH}${ACADEMIC_GRAPH_PAPER_PATH}${id}?fields=${ACADEMIC_GRAPH_PAPER_FIELDS}"
+    json=$(curl -s -X GET ${ACADEMIC_GRAPH_PAPER_URL})
+    record=$(
+      echo ${json} | jq '. |
+      {
+        paperId: .paperId,
+        title: .title,
+        journal: .venue,
+        date: .publicationDate,
+        doi: .externalIds.DOI,
+        brief: .tldr.text,
+        authors: .authors | [.[] | .name] | join("; ")
+      }'
+    )
+    printf "%s" "${record}" >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
+    if [ "${COUNTER}" == "${NUM_ITEMS}" ]; then
+      printf "%s\n" "" >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
+    else
+      printf "%s\n" "," >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
+    fi
+
+    sleep ${DELAY}
+  done
+  echo ']' >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
 done
-echo ']' >> ${DATA_DIRECTORY}/${CATEGORY_ID}.json
+
diff --git a/scripts/search.sh b/scripts/search.sh
@@ -5,27 +5,27 @@ DATA_DIRECTORY="../example-data"
 
 MEDRXIV_SOURCE="medrxiv"
 BIORXIV_SOURCE="biorxiv"
-DATE_PREFIX="2022-10"
-START_DATE="${DATE_PREFIX}-01"
-END_DATE="${DATE_PREFIX}-31"
+
+START_DATE=$(date -v -1m +%Y-%m-%d)
+END_DATE=$(date +%Y-%m-%d)
 
 echo "Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}"
-biorxivPapers=$(node ../src/cli.js download --output="${DATA_DIRECTORY}/${DATE_PREFIX}_${BIORXIV_SOURCE}.json" --source=${BIORXIV_SOURCE} ${START_DATE} ${END_DATE})
+biorxivPapers=$(node ../src/cli.js download --output="${DATA_DIRECTORY}/${END_DATE}_${BIORXIV_SOURCE}.json" --source=${BIORXIV_SOURCE} ${START_DATE} ${END_DATE})
 numPapersRawBiorxiv=$(echo ${biorxivPapers} | jq 'length')
 echo "numPapersRawBiorxiv: ${numPapersRawBiorxiv}"
 
 echo "Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}"
-medrxivPapers=$(node ../src/cli.js download --output="${DATA_DIRECTORY}/${DATE_PREFIX}_${MEDRXIV_SOURCE}.json" --source=${MEDRXIV_SOURCE} ${START_DATE} ${END_DATE})
+medrxivPapers=$(node ../src/cli.js download --output="${DATA_DIRECTORY}/${END_DATE}_${MEDRXIV_SOURCE}.json" --source=${MEDRXIV_SOURCE} ${START_DATE} ${END_DATE})
 numPapersRawMedrxiv=$(echo ${medrxivPapers} | jq 'length')
 echo "numPapersRawMedrxiv: ${numPapersRawMedrxiv}"
 
 echo "Combining results..."
-combined=$(jq -s add ${DATA_DIRECTORY}/${DATE_PREFIX}_*.json)
-rm "${DATA_DIRECTORY}/${DATE_PREFIX}_${BIORXIV_SOURCE}.json"
-rm "${DATA_DIRECTORY}/${DATE_PREFIX}_${MEDRXIV_SOURCE}.json"
+combined=$(jq --slurp '[.[][]]' ${DATA_DIRECTORY}/${END_DATE}_*.json)
+# rm "${DATA_DIRECTORY}/${END_DATE}_${BIORXIV_SOURCE}.json"
+# rm "${DATA_DIRECTORY}/${END_DATE}_${MEDRXIV_SOURCE}.json"
 
-DATA_FILE="${DATA_DIRECTORY}/2022-10.json"
-echo ${combined} | jq >> ${DATA_FILE}
+DATA_FILE="${DATA_DIRECTORY}/${END_DATE}.json"
+echo ${combined} | jq > ${DATA_FILE}
 
 
 QUERY="alzheimer"
@@ -48,5 +48,5 @@ collection=$(
     }]'
   )
 
-echo ${collection} | jq >> ${OUTPUT_FILE}
-
+echo ${collection} | jq > ${OUTPUT_FILE}
+# rm "${DATA_FILE}"
diff --git a/src/dashboard/categories.js b/src/dashboard/categories.js
@@ -1,12 +1,12 @@
 import alzheimersDisease from '../../example-data/alzheimers-disease.json';
 import alzheimersDiagnosis from '../../example-data/alzheimers-diagnosis.json';
 import alzheimersNeuroinflammation from '../../example-data/alzheimers-neuroinflammation.json';
-import alzheimersTherapeutics from '../../example-data/alzheimers-therapeutics.json';
+// import alzheimersTherapeutics from '../../example-data/alzheimers-therapeutics.json';
 
 const ALZHEIMERS_DISEASE_ID = 'alzheimers-disease';
 const ALZHEIMERS_DIAGNOSIS_ID = 'alzheimers-diagnosis';
 const ALZHEIMERS_NEUROINFLAMMATION_ID = 'alzheimers-neuroinflammation';
-const ALZHEIMERS_THERAPEUTICS = 'alzheimers-therapeutics';
+// const ALZHEIMERS_THERAPEUTICS = 'alzheimers-therapeutics';
 
 const toDate = o => {
   o.date = new Date(o.date);
@@ -28,12 +28,13 @@ export const categories = [
     id: ALZHEIMERS_NEUROINFLAMMATION_ID,
     name: 'Alzheimer\'s Disease: Neuroinflammation',
     description: 'Relationships between neuroinflammation and amyloid and tau pathologies and its effect on disease trajectory.'
-  },
-  {
-    id: ALZHEIMERS_THERAPEUTICS,
-    name: 'Alzheimer\'s Disease: Therapeutics',
-    description: 'Nonpharmacological and pharmacological management of the cognitive and behavioral symptoms of AD.'
   }
+  // ,
+  // {
+  //   id: ALZHEIMERS_THERAPEUTICS,
+  //   name: 'Alzheimer\'s Disease: Therapeutics',
+  //   description: 'Nonpharmacological and pharmacological management of the cognitive and behavioral symptoms of AD.'
+  // }
 ];
 
 export const getPapers = ({ id, limit = 20 }) => {
@@ -49,9 +50,9 @@ export const getPapers = ({ id, limit = 20 }) => {
     case ALZHEIMERS_NEUROINFLAMMATION_ID:
       papers = alzheimersNeuroinflammation;
       break;
-    case ALZHEIMERS_THERAPEUTICS:
-      papers = alzheimersTherapeutics;
-      break;
+    // case ALZHEIMERS_THERAPEUTICS:
+    //   papers = alzheimersTherapeutics;
+    //   break;
     default:
       console.error(`Unable to load ${id}.`);
   }
diff --git a/src/dashboard/index.html b/src/dashboard/index.html
@@ -3,7 +3,7 @@
   <head>
     <title>Hyper-recent Biology Papers</title>
 
-    <link rel="stylesheet" href="build/bundle.css" />
+    <link rel="stylesheet" href="bundle.css" />
 
     <script>
       if (location.hostname === "localhost" || location.hostname === "127.0.0.1") {
@@ -16,6 +16,6 @@
   <body>
     <div id="root"></div>
 
-    <script src="build/bundle.js"></script>
+    <script src="bundle.js"></script>
   </body>
 </html>
