Merge pull request #170 from camicroscope/develop

For 3.12.0
camicroscope · May 2, 2024 · 23eab1a · 23eab1a
2 parents 72ec488 + 7209034
commit 23eab1a
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Showing 6 changed files with 108 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -59,7 +59,7 @@ An item with no filter value is returned in all cases, and is thus also public.
 ## Local Development Environment
 In order to quickly setup a development environment, make use of the `setup_script.sh` script. This will setup the project, initialize and seed the database configurations, import routes and initialize environment config files and generate the keys required.
 
-First clone the <a href = "https://github.com/camicroscope/Caracal/tree/backup-dev">Caracal (backup-dev branch)</a>, <a href = "https://github.com/camicroscope/caMicroscope">caMicroscope</a> and the <a href = "https://github.com/camicroscope/Distro">Distro</a> repositories and make sure that all of them are in the same parent directory.
+First clone <a href = "https://github.com/camicroscope/Caracal">Caracal</a>, <a href = "https://github.com/camicroscope/caMicroscope">caMicroscope</a> and the <a href = "https://github.com/camicroscope/Distro">Distro</a> repositories and make sure that all of them are in the same parent directory.
 
 Run the script with  `./setup_script` or `bash ./setup_script.sh`
 

diff --git a/caracal.js b/caracal.js
@@ -75,11 +75,13 @@ var HANDLERS = {
   },
   "monitorCheck": monitor.check,
   "mongoFind": dataHandlers.General.find,
+  "mongoPaginatedFind": dataHandlers.General.paginatedFind,
   "mongoFindWithRegex": dataHandlers.General.findWithRegex,
   "mongoAdd": dataHandlers.General.add,
   "mongoUpdate": dataHandlers.General.update,
   "mongoDelete": dataHandlers.General.delete,
   "mongoDistinct": dataHandlers.General.distinct,
+  "mongoCount": dataHandlers.General.count,
   "filterHandler": auth.filterHandler,
   "permissionHandler": permissionHandler,
   "editHandler": auth.editHandler,

diff --git a/handlers/dataHandlers.js b/handlers/dataHandlers.js
@@ -13,6 +13,26 @@ General.find = function(db, collection) {
   };
 };
 
+General.paginatedFind = function(db, collection) {
+  return function(req, res, next) {
+    var query = req.query;
+    mongoDB.paginatedFind(db, collection, query).then((x) => {
+      req.data = x;
+      next();
+    }).catch((e) => next(e));
+  };
+};
+
+General.count = function(db, collection) {
+  return function(req, res, next) {
+    var query = req.query;
+    mongoDB.count(db, collection, query).then((x) => {
+      req.data = x;
+      next();
+    }).catch((e) => next(e));
+  };
+};
+
 General.findWithRegex = function(db, collection) {
   return function(req, res, next) {
     var query = req.query;

diff --git a/handlers/pathdbIipHandler.js b/handlers/pathdbIipHandler.js
@@ -28,7 +28,10 @@ iipCheck = function(req, res, next) {
         console.log(x);
         // get path
         if (x && x['field_iip_path'] && x['field_iip_path'].length && x['field_iip_path'][0]['value']) {
-          req.newFilepath = x['field_iip_path'][0]['value'];
+          newFilepath = x['field_iip_path'][0]['value'];
+          newFilepath = encodeURIComponent(newFilepath);
+          newFilepath = newFilepath.replaceAll("%2F", "/");
+          req.newFilepath = newFilepath;
           console.log(req.newFilepath);
           next();
         } else {

diff --git a/service/database/index.js b/service/database/index.js
@@ -42,6 +42,72 @@ class Mongo {
         }
     }
 
+        /**
+     * Runs the MongoDB find() method to fetch documents with pagination.
+     *
+     * @async
+     * @param {string} database Name of the database
+     * @param {string} collectionName Name of the collection to run operation on
+     * @param {document} query Specifies selection filter using query operators.
+     * To return all documents in a collection, omit this parameter or pass an empty document ({}).
+     * @param {boolean} [transform=false] check to transform the IDs to ObjectID in response
+     *
+     * {@link https://docs.mongodb.com/manual/reference/method/db.collection.find/ Read MongoDB Reference}
+     */
+        static async paginatedFind(database, collectionName, query, transform = true) {
+            try {
+                query = transformIdToObjectId(query);
+
+                const collection = getConnection(database).collection(collectionName);
+                let { _page = 0, _pageSize = 1000, ...filterQuery } = query;
+                const _skip = _page * _pageSize;
+                _pageSize = parseInt(_pageSize, 10);
+                const data = await collection.find(filterQuery).skip(_skip).limit(_pageSize).toArray();
+
+                /** allow caller method to toggle response transformation */
+                if (transform) {
+                    data.forEach((x) => {
+                        x["_id"] = {
+                            $oid: x["_id"],
+                        };
+                    });
+                }
+
+                return data;
+            } catch (e) {
+                console.error(e);
+                throw e;
+            }
+        }
+
+    /**
+     * Runs the MongoDB count() method to count documents.
+     *
+     * @async
+     * @param {string} database Name of the database
+     * @param {string} collectionName Name of the collection to run operation on
+     * @param {document} query Specifies selection filter using query operators.
+     * To return all documents in a collection, omit this parameter or pass an empty document ({}).
+     * @param {boolean} [transform=false] check to transform the IDs to ObjectID in response
+     *
+     * {@link https://docs.mongodb.com/manual/reference/method/db.collection.count/ Read MongoDB Reference}
+     */
+        static async count(database, collectionName, query, transform = true) {
+            try {
+                query = transformIdToObjectId(query);
+
+                const collection = getConnection(database).collection(collectionName);
+                const count = await collection.count(query);
+
+                let data =[{"count": count}];
+
+                return data;
+            } catch (e) {
+                console.error(e);
+                throw e;
+            }
+        }
+
     /**
      * Runs a distinct find operation based on given query
      *
@@ -201,10 +267,12 @@ class Mongo {
 module.exports = {
     add: Mongo.add,
     find: Mongo.find,
+    paginatedFind: Mongo.paginatedFind,
     update: Mongo.update,
     delete: Mongo.delete,
     aggregate: Mongo.aggregate,
     distinct: Mongo.distinct,
     createIndex: Mongo.createIndex,
-    createCollection: Mongo.createCollection
+    createCollection: Mongo.createCollection,
+    count: Mongo.count,
 };
diff --git a/setup_script.sh b/setup_script.sh
@@ -24,9 +24,12 @@ fi
 ###
 ## check if the system has required services installed
 ###
-if ! command -v "mongo" &>/dev/null; then
-    echo "mongo could not be found on path. Please ensure that mongo is installed and is on PATH"
-    exit
+if command -v "mongo" &>/dev/null; then
+    MONGO="mongo"
+elif command -v "mongosh" &>/dev/null; then
+    MONGO="mongosh"
+else
+    echo "mongo or mongo could not be found on path. Please ensure that mongo is installed and is on PATH"
 fi
 
 if ! command -v "node" &>/dev/null; then
@@ -109,7 +112,7 @@ echo "Copying files complete!"
 ###
 ## try connecting to mongodb instance
 ###
-until mongo --host "${HOST}" --eval "print(\"Connected!\")" >/dev/null; do
+until $MONGO --host "${HOST}" --eval "print(\"Connected!\")" >/dev/null; do
     sleep 2
 done
 echo "[ database ] : connection established"
@@ -118,8 +121,8 @@ echo "[ database ] : connection established"
 ## check if database exists
 ###
 QUERY="db.getMongo().getDBNames().indexOf(\"${DB_NAME}\")"
-COMMAND="mongo ${HOST} --eval '${QUERY}' --quiet"
-if [ $(mongo ${HOST} --eval ${QUERY} --quiet) -lt 0 ]; then
+COMMAND="${MONGO} ${HOST} --eval '${QUERY}' --quiet"
+if [ $(${MONGO} ${HOST} --eval ${QUERY} --quiet) -lt 0 ]; then
     echo "[ database ] : does not exist"
     exit 1
 else
@@ -149,11 +152,11 @@ case $yn in
 
     echo "[ resource ] : clearing old configurations"
     echo "[ resource ] : seeding collections"
-    mongo --quiet --host $HOST $DB_NAME .seeder.collection.js
+    $MONGO --quiet --host $HOST $DB_NAME .seeder.collection.js
     echo "[ resource ] : seeding indexes"
-    mongo --quiet --host $HOST $DB_NAME .seeder.idx.js
+    $MONGO --quiet --host $HOST $DB_NAME .seeder.idx.js
     echo "[ resource ] : seeding configurations"
-    mongo --quiet --host $HOST $DB_NAME .seeder.default.js
+    $MONGO --quiet --host $HOST $DB_NAME .seeder.default.js
 
     ###
     ## ask the user if they want to remove the seeding files