Added multiple file download API

apps/api/R/workflows.R

@@ -49,16 +49,31 @@ getWorkflows <- function(req, model_id=NA, site_id=NA, offset=0, limit=50, res){
     result <- list(workflows = qry_res)
     result$count <- nrow(qry_res)
     if(has_next){
-      result$next_page <- paste0(
-        req$rook.url_scheme, "://",
-        req$HTTP_HOST,
-        "/api/workflows",
-        req$PATH_INFO,
-        substr(req$QUERY_STRING, 0, stringr::str_locate(req$QUERY_STRING, "offset=")[[2]]),
-        (as.numeric(limit) + as.numeric(offset)),
-        "&limit=", 
-        limit
-      )
+      if(grepl("offset=", req$QUERY_STRING, fixed = TRUE)){
+        result$next_page <- paste0(
+          req$rook.url_scheme, "://",
+          req$HTTP_HOST,
+          "/api/workflows",
+          req$PATH_INFO,
+          substr(req$QUERY_STRING, 0, stringr::str_locate(req$QUERY_STRING, "offset=")[[2]]),
+          (as.numeric(limit) + as.numeric(offset)),
+          "&limit=", 
+          limit
+        )
+      }
+      else {
+        result$next_page <- paste0(
+          req$rook.url_scheme, "://",
+          req$HTTP_HOST,
+          "/api/workflows",
+          req$PATH_INFO,
+          substr(req$QUERY_STRING, 0, stringr::str_locate(req$QUERY_STRING, "limit=")[[2]] - 6),
+          "offset=",
+          (as.numeric(limit) + as.numeric(offset)),
+          "&limit=", 
+          limit
+        )
+      }
     }
     if(has_prev) {
       result$prev_page <- paste0(
@@ -200,7 +215,7 @@ getWorkflowStatus <- function(req, id, res){
 #* @get /<id>/file/<filename>
 getWorkflowFile <- function(req, id, filename, res){
   Workflow <- tbl(global_db_pool, "workflows") %>%
-    select(id, user_id) %>%
+    select(id, user_id) %>% 
     filter(id == !!id)
 
   qry_res <- Workflow %>% collect()
@@ -229,3 +244,82 @@ getWorkflowFile <- function(req, id, filename, res){
     return(bin)
   }
 }
+
+
+#################################################################################################
+#' Get the list of files in a workflow specified by the id
+#' @param id Workflow id (character)
+#' @return List of files
+#' @author Nihar Sanda
+#* @serializer contentType list(type="application/octet-stream")
+#* @get /<id>/files
+
+getWorkflowFileDetails <- function(req, id, res){
+  Workflow <- tbl(global_db_pool, "workflows") %>%
+    select(id, user_id) %>%
+    filter(id == !!id)
+
+  qry_res <- Workflow %>% collect()
+
+  if (nrow(qry_res) == 0) {
+    res$status <- 404
+    return(list(error="Workflow with specified ID was not found"))
+  }
+  else {
+    file_names <- list()
+    file_names <- list.files(paste0(Sys.getenv("DATA_DIR", "/data/"), "workflows/PEcAn_", id))
+
+    return(list(workflow_id = id))
+  }
+}
+
+#################################################################################################
+#' Get the zip of specified files of the workflow specified by the id
+#' @param id Workflow id (character)
+#' @return Details of requested workflow
+#' @author Nihar Sanda
+#* @serializer contentType list(type="application/octet-stream")
+#* @post /<id>/file-multiple/
+
+getWorkflowFilesAsZip <- function(req, id, filenames, res){
+  if(req$HTTP_CONTENT_TYPE == "application/json") {
+    filenames_req <- req$postBody
+  }
+
+  filenamesList <- jsonlite::fromJSON(filenames_req)
+  filenames <- filenamesList$files
+
+  Workflow <- tbl(global_db_pool, "workflows") %>%
+    select(id, user_id) %>%
+    filter(id == !!id)
+
+  qry_res <- Workflow %>% collect()
+
+  if (nrow(qry_res) == 0) {
+    res$status <- 404
+    return()
+  }
+  else {
+    full_files <- vector(mode = "character", length = length(filenames))
+    for (i in 1:length(filenames)) {
+
+      # Check if the requested file exists on the host
+      filepath <- paste0(Sys.getenv("DATA_DIR", "/data/"), "workflows/PEcAn_", id, "/", filenames[i])
+      if(! file.exists(filepath)){
+        res$status <- 404
+        return()
+      }
+
+      if(Sys.getenv("AUTH_REQ") == TRUE){
+        if(qry_res$user_id != req$user$userid) {
+          res$status <- 403
+          return()
+        } 
+      }
+
+      full_files[i] <- filepath
+    }
+    zip_file <- zip::zipr("output.zip", full_files)
+    return(zip_file)
+  }
+}

apps/api/pecanapi-spec.yml

@@ -41,6 +41,8 @@ tags:
     description: Everything about PEcAn PFTs (Plant Functional Types)
   - name: inputs
     description: Everything about PEcAn inputs
+  - name: posteriors
+    description: Everything about PEcAn posteriors
 
 #####################################################################################################################
 ##################################################### API Endpoints #################################################
@@ -779,6 +781,40 @@ paths:
           description: Authentication required
         '403':
           description: Access forbidden
+
+  /api/workflows/{id}/file-multiple/:
+    post:
+      tags:
+        - workflows
+      summary: Download multiple files
+      parameters:
+        - in: path
+          name: id
+          description: ID of the PEcAn Workflow
+          required: true
+          schema:
+            type: string
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/WorkflowFiles_POST'
+
+
+      responses:
+        '200':
+          description: Download the zip file consisting of the desired files
+          content:
+            application/octet-stream:
+              schema:
+                type: string
+                format: binary    
+        '401':
+          description: Authentication required
+        '415':
+          description: Unsupported request content type
+
 
   /api/runs/:
     get:
@@ -992,6 +1028,123 @@ paths:
           description: Access forbidden
         '404':
           description: Run data not found
+
+  /api/posteriors/:
+    get:
+      tags:
+        - posteriors
+      summary: Search for the posteriors
+      parameters:
+        - in: query
+          name: pft_id
+          description: If provided, returns all posteriors for the provided model_id
+          required: false
+          schema:
+            type: string
+        - in: query
+          name: host_id
+          description: If provided, returns all posteriors for the provided host_id
+          required: false
+          schema:
+            type: string
+        - in: query
+          name: offset
+          description: The number of posteriors to skip before starting to collect the result set.
+          schema:
+            type: integer
+            minimum: 0
+            default: 0
+          required: false
+        - in: query
+          name: limit
+          description: The number of posteriors to return.
+          schema:
+            type: integer
+            default: 50
+            enum:
+              - 10
+              - 20
+              - 50
+              - 100
+              - 500
+          required: false
+      responses:
+        '200':
+          description: List of posteriors
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  inputs:
+                    type: array
+                    items: 
+                      type: object
+                      properties:
+                        id:
+                          type: string
+                        file_name:
+                          type: string
+                        file_path:
+                          type: string
+                        pft_name:
+                          type: string
+                        tag:
+                          type: string
+                        hostname:
+                          type: string
+                        start_date:
+                          type: string
+                        end_date:
+                          type: string
+                  count:
+                    type: integer
+                  next_page:
+                    type: string
+                  prev_page:
+                    type: string
+
+        '401':
+          description: Authentication required
+        '403':
+          description: Access forbidden
+        '404':
+          description: Workflows not found
+
+  /api/posteriors/{posterior_id}:
+    get:
+      tags:
+        - posteriors
+      summary: Download a desired PEcAn posterior file
+      parameters:
+        - in: path
+          name: posterior_id
+          description: ID of the PEcAn Posterior to be downloaded
+          required: true
+          schema:
+            type: string
+        - in: query
+          name: filename
+          description: Optional filename specified if the id points to a folder instead of file
+          required: false
+          schema:
+            type: string
+      responses:
+        '200':
+          description: Contents of the desired input file  
+          content:
+            application/octet-stream:
+              schema:
+                type: string
+                format: binary
+        '400':
+          description: Bad request. Input ID points to directory & filename is not specified
+        '401':
+          description: Authentication required
+        '403':
+          description: Access forbidden
+
+
 #####################################################################################################################
 ###################################################### Components ###################################################
 #####################################################################################################################
@@ -1275,6 +1428,20 @@ components:
             dbfiles:
               type: string
               example: pecan/dbfiles
+
+    WorkflowFiles_POST:
+      type: object
+
+      properties:
+        files:
+          type: array
+          items:
+            type: string
+          example: [
+          "pecan.xml",
+          "workflow.R"
+          ]
+
   securitySchemes:
     basicAuth:
       type: http