Merge pull request #1693 from openforis/development

Merge develop to main

config.example.edn

@@ -7,12 +7,16 @@
  :triangulum.server/mode              "dev"
  :triangulum.server/log-dir           "logs"
 
- :triangulum.server/handler           collect-earth-online.routing/authenticated-routing-handler
+ :triangulum.server/handler           triangulum.handler/authenticated-routing-handler
  :triangulum.server/keystore-file     "keystore.pkcs12"
  :triangulum.server/keystore-type     "pkcs12"
  :triangulum.server/keystore-password "foobar"
 
  ;; handler (server)
+ :triangulum.handler/not-found-handler   triangulum.views/not-found-page
+ :triangulum.handler/redirect-handler    collect-earth-online.handlers/redirect-handler
+ :triangulum.handler/route-authenticator collect-earth-online.handlers/route-authenticator
+ :triangulum.handler/routing-tables      [collect-earth-online.routing/routes]
  :triangulum.handler/session-key           "changeme12345678" ; must be 16 characters
  :triangulum.handler/bad-tokens            #{".php"}
  :triangulum.handler/private-request-keys  #{:base64Image :plotFileBase64 :sampleFileBase64}

deps.edn

@@ -7,7 +7,7 @@
         org.clojure/data.json     {:mvn/version "1.0.0"}
         ring/ring                 {:mvn/version "1.8.2"}
         sig-gis/triangulum        {:git/url "https://github.com/sig-gis/triangulum"
-                                   :git/sha "5cffefc2e8a8027a178d7ff1103cb2e38e174bba"}}
+                                   :git/sha "3d41dab63e1bc8ebe046f64db44ae3df986f5bdf"}}
 
  :aliases {:build-db         {:main-opts ["-m" "triangulum.build-db"]}
            :config           {:main-opts ["-m" "triangulum.config"]}

src/clj/collect_earth_online/db/doi.clj

@@ -25,7 +25,7 @@
 (defn get-doi-reference
   [{:keys [params]}]
   (let [project-id (tc/val->int (:projectId params))
-        doi-path   (:doi_path (first (call-sql "select_doi_by_project" project-id)))]
+        doi-path   (:doi_path (last (call-sql "select_doi_by_project" project-id)))]
     (data-response {:doiPath doi-path})))
 
 (defn create-contributors-list
@@ -110,59 +110,68 @@
         (update :survey_questions #(tc/jsonb->clj %))
         (update :aoi_features #(tc/jsonb->clj %))
         (update :created_date #(str %))
+        (update :closed_date (fn [x] (when x (str x))))
         (update :published_date #(str %)))))
 
 (defn upload-deposition-files!
-  [bucket-url project-id zip-file]
+  [doi-id zip-file]
   (let [headers    (req-headers)]
-    (http/put (str bucket-url "/" project-id)
-              {:content-type :multipart/form-data
-               :headers      headers
-               :as           :json
-               :multipart    [{:name "Content/type" :content "application/octet-stream"}
-                              {:name "file" :content (io/file zip-file)}]})))
+    (http/post (str base-url "/deposit/depositions/" doi-id "/files")
+               {:headers      headers
+                :multipart    [{:name "Content/type" :content "application/octet-stream"}
+                               {:name "file" :content (io/file zip-file)}]})))
 
 (defn upload-doi-files!
   [doi-id project-id]
   (let [project-id   project-id
         doi          (first (call-sql "select_doi_by_id" doi-id))
-        bucket       (-> doi :full_data tc/jsonb->clj :links :bucket)
         project-data (json/write-str (get-project-data project-id))
         zip-file     (create-and-zip-files-for-doi project-id project-data)]
     (try
-      (:body (upload-deposition-files! bucket project-id zip-file))
-      (catch Exception _
+      (:body (upload-deposition-files! (:doi_uid doi) zip-file))
+      (catch Exception e
         (throw (ex-info "Failed to upload files."
                         {:details "Error in file upload to zenodo"}))))))
 
 (defn create-doi!
   [{:keys [params session]}]
-  (let [user-id          (:userId session -1)
-        project-id       (:projectId params)
-        project-name     (:projectName params)
-        institution-name (:name (first (call-sql "select_institution_by_id" (-> params :institution) user-id)))
-        description      (:description params)
-        creator          (first (call-sql "get_user_by_id" user-id))
-        contributors     (call-sql "select_assigned_users_by_project" project-id)]
-    (try
-      (->
-       (create-zenodo-deposition! institution-name project-name creator contributors description)
-       :body
-       (insert-doi! project-id user-id)
-       (upload-doi-files! project-id))
-      (data-response {:message "DOI created successfully"})
-      (catch Exception _
-        (data-response {:message "Failed to create DOI."}
-                       {:status 500})))))
+  (let [user-id            (:userId session -1)
+        project-id         (:projectId params)
+        project-name       (:projectName params)
+        institution-name   (:name (first (call-sql "select_institution_by_id" (-> params :institution) user-id)))
+        description        (:description params)
+        creator            (first (call-sql "get_user_by_id" user-id))
+        contributors       (call-sql "select_assigned_users_by_project" project-id)
+        project-published? (:availability (first (call-sql "select_project_by_id" project-id)))
+        doi-published?     (:submitted (last (call-sql "select_doi_by_project" project-id)))]
+    (cond
+      (and (not= "published" project-published?)
+           (not= "closed"    project-published?)) (data-response {:message "In order to create a DOI, the project must be published"}
+                                                                {:status 500})
+      doi-published? (data-response {:message "A DOI for this project has already been published."}
+                                    {:status 500})
+      :else
+      (try
+        (->
+         (create-zenodo-deposition! institution-name project-name creator contributors description)
+         :body
+         (insert-doi! project-id user-id)
+         (upload-doi-files! project-id))
+        (data-response {:message "DOI created successfully"})
+        (catch Exception _
+          (data-response {:message "Failed to create DOI."}
+                         {:status 500}))))))
 
 (defn publish-doi!
   "request zenodo to publish the DOI on DataCite"
   [{:keys [params]}]
   (let [project-id (:projectId params)
-        doi-id     (:doi_uid (first (call-sql "select_doi_by_project" project-id)))]
+        doi-id     (:doi_uid (last (call-sql "select_doi_by_project" project-id)))
+        req        (http/post (str base-url "/deposit/depositions/" doi-id "/actions/publish")
+                              {:as :json
+                               :headers (req-headers)})]
     (try
-      (http/post (str base-url "/deposition/depositions/" doi-id "/actions/publish")
-                 {:headers (req-headers)})
+      (call-sql "update_doi" doi-id (tc/clj->jsonb (:body req)))
       (data-response {})
       (catch Exception _
         (data-response {:message "Failed to publish DOI"}

src/clj/collect_earth_online/db/plots.clj

@@ -256,22 +256,23 @@
 ;;;
 
 (defn add-user-samples [{:keys [params session]}]
-  (let [project-id       (tc/val->int (:projectId params))
-        plot-id          (tc/val->int (:plotId params))
-        session-user-id  (:userId session -1)
-        current-user-id  (tc/val->int (:currentUserId params -1))
-        review-mode?     (and (tc/val->bool (:inReviewMode params))
+  (let [project-id         (tc/val->int (:projectId params))
+        plot-id            (tc/val->int (:plotId params))
+        session-user-id    (:userId session -1)
+        current-user-id    (tc/val->int (:currentUserId params -1))
+        review-mode?       (and (tc/val->bool (:inReviewMode params))
                               (pos? current-user-id)
                               (is-proj-admin? session-user-id project-id nil))
-        confidence       (tc/val->int (:confidence params))
-        collection-start (tc/val->long (:collectionStart params))
-        user-samples     (:userSamples params)
-        user-images      (:userImages params)
-        new-plot-samples (:newPlotSamples params)
-        user-id          (if review-mode? current-user-id session-user-id)
+        confidence         (tc/val->int (:confidence params))
+        confidence-comment (:confidenceComment params)
+        collection-start   (tc/val->long (:collectionStart params))
+        user-samples       (:userSamples params)
+        user-images        (:userImages params)
+        new-plot-samples   (:newPlotSamples params)
+        user-id            (if review-mode? current-user-id session-user-id)
         ;; Samples created in the UI have IDs starting with 1. When the new sample is created
         ;; in Postgres, it gets different ID.  The user sample ID needs to be updated to match.
-        id-translation   (when new-plot-samples
+        id-translation     (when new-plot-samples
                            (call-sql "delete_user_plot_by_plot" plot-id user-id)
                            (call-sql "delete_samples_by_plot" plot-id)
                            (reduce (fn [acc {:keys [id visibleId sampleGeom]}]
@@ -288,6 +289,7 @@
                 plot-id
                 user-id
                 (when (pos? confidence) confidence)
+                (when confidence-comment confidence-comment)
                 (when-not review-mode? (Timestamp. collection-start))
                 (tc/clj->jsonb (set/rename-keys user-samples id-translation))
                 (tc/clj->jsonb (set/rename-keys user-images id-translation)))

src/clj/collect_earth_online/generators/external_file.clj

@@ -277,7 +277,7 @@
     (create-shape-files folder-name "sample" project-id)
     (create-data-file folder-name project-data)
     (sh-wrapper tmp-dir {}
-                (str "7z a " folder-name "/files" ".zip " folder-name "/*"))
+                (str "7z a " folder-name "files" ".zip " folder-name "*"))
     (str folder-name "files.zip")))
 
 (defn zip-shape-files

src/clj/collect_earth_online/handlers.clj

@@ -0,0 +1,33 @@
+(ns collect-earth-online.handlers
+  (:require [collect-earth-online.db.institutions :refer [is-inst-admin?]]
+            [collect-earth-online.db.projects     :refer [can-collect? is-proj-admin?]]
+            [ring.util.codec                      :refer [url-encode]]
+            [ring.util.response                   :refer [redirect]]
+            [triangulum.response                  :refer [no-cross-traffic?]]
+            [triangulum.type-conversion           :refer [val->int]]))
+
+(defn route-authenticator [{:keys [session params headers] :as _request} auth-type]
+  (let [user-id        (:userId session -1)
+        institution-id (val->int (:institutionId params))
+        project-id     (val->int (:projectId params))
+        token-key      (:tokenKey params)]
+    (condp = auth-type
+      :user    (pos? user-id)
+      :super   (= 1 user-id)
+      :collect (can-collect? user-id project-id token-key)
+      :token   (can-collect? -99 project-id token-key)
+      :admin   (cond
+                 (pos? project-id)     (is-proj-admin? user-id project-id token-key)
+                 (pos? institution-id) (is-inst-admin? user-id institution-id))
+      :no-cross (no-cross-traffic? headers)
+      true)))
+
+(defn redirect-handler [{:keys [session query-string uri] :as _request}]
+  (let [full-url (url-encode (str uri (when query-string (str "?" query-string))))]
+    (if (:userId session)
+      (redirect (str "/home?flash_message=You do not have permission to access "
+                     full-url))
+      (redirect (str "/login?returnurl="
+                     full-url
+                     "&flash_message=You must login to see "
+                     full-url)))))

src/clj/collect_earth_online/routing.clj

@@ -1,17 +1,13 @@
 (ns collect-earth-online.routing
-  (:require [triangulum.views                     :refer [render-page not-found-page]]
-            [ring.util.response                   :refer [redirect]]
-            [ring.util.codec                      :refer [url-encode]]
-            [triangulum.type-conversion           :as tc]
-            [triangulum.response                  :refer [forbidden-response no-cross-traffic?]]
-            [collect-earth-online.db.doi          :as doi]
+  (:require [collect-earth-online.db.doi          :as doi]
             [collect-earth-online.db.geodash      :as geodash]
             [collect-earth-online.db.imagery      :as imagery]
             [collect-earth-online.db.institutions :as institutions]
             [collect-earth-online.db.plots        :as plots]
             [collect-earth-online.db.projects     :as projects]
             [collect-earth-online.db.users        :as users]
-            [collect-earth-online.proxy           :as proxy]))
+            [collect-earth-online.proxy           :as proxy]
+            [triangulum.views                     :refer [render-page]]))
 
 (def routes
   {;; Page Routes
@@ -194,41 +190,3 @@
    [:get  "/get-nicfi-tiles"]                {:handler     proxy/get-nicfi-tiles
                                               :auth-type   :no-cross
                                               :auth-action :block}})
-
-(defn- redirect-auth [user-id]
-  (fn [request]
-    (let [{:keys [query-string uri]} request
-          full-url (url-encode (str uri (when query-string (str "?" query-string))))]
-      (if (pos? user-id)
-        (redirect (str "/home?flash_message=You do not have permission to access "
-                       full-url))
-        (redirect (str "/login?returnurl="
-                       full-url
-                       "&flash_message=You must login to see "
-                       full-url))))))
-
-(defn authenticated-routing-handler [{:keys [uri request-method params headers session] :as request}]
-  (let [{:keys [auth-type auth-action handler] :as route} (get routes [request-method uri])
-        user-id        (:userId session -1)
-        institution-id (tc/val->int (:institutionId params))
-        project-id     (tc/val->int (:projectId params))
-        next-handler   (if route
-                         (if (condp = auth-type
-                               :user     (pos? user-id)
-                               :super    (= 1  user-id)
-                               :collect  (projects/can-collect? user-id project-id (:tokenKey params))
-                               :token    (projects/can-collect? -99 project-id (:tokenKey params))
-                               :admin    (cond
-                                           (pos? project-id)
-                                           (projects/is-proj-admin? user-id project-id (:tokenKey params))
-
-                                           (pos? institution-id)
-                                           (institutions/is-inst-admin? user-id institution-id))
-                               :no-cross (no-cross-traffic? headers)
-                               true)
-                           handler
-                           (if (= :redirect auth-action)
-                             (redirect-auth user-id)
-                             forbidden-response))
-                         not-found-page)]
-    (next-handler request)))

src/clj/collect_earth_online/workers.clj

@@ -19,7 +19,7 @@
             file (reverse (file-seq d))]
       (io/delete-file file))))
 
-(defn- start-clean-up-service! []
+(defn start-clean-up-service! []
   (log-str "Starting temp file removal service.")
   (future
     (while true

src/css/custom.css

@@ -541,6 +541,7 @@ a:hover {
 }
 #lPanel ul {
   padding-left: 0;
+  margin-left: 5px;
   list-style: none;
   margin-bottom: 0;
 }
@@ -859,5 +860,7 @@ input:checked + .switch-slider:before {
 }
 
 body {
-    padding-top:60px;
+    margin-left: 10px;
+    margin-top: 60px;
+    overflow-x: hidden;
 }