URN: redirect to the right URL

- Register a new URN with the server name organisation as base URL.
- Fixes URN creation.
- Adds the patch DNB method to already registered URN.
- Adds the get DNB method to get URN information.
- Marks an URN pid when a document is deleted.
- Fixes the query to retrieve all the unregistered URNs.
- Adds a new optional parameter to specify the data when a test document
  is created.
- Closes: #849.
- Closes: #811.
- Avoids npm server crash in development.
- Adds options to the script server.
- Adds files permissions.
- Fixes unit tests with a .env file.

Co-Authored-by: Johnny Mariéthoz <Johnny.Mariethoz@rero.ch>

pyproject.toml

@@ -75,6 +75,7 @@ python-levenshtein = "<0.20.0"
 jsonschema = "<4.0.0"
 pydocstyle = ">=6.1.1,<6.2"
 requests-mock = "^1.11.0"
+pysftp = "^0.2.9"
 
 [tool.poetry.dev-dependencies]
 Flask-Debugtoolbar = ">=0.10.1"

scripts/server

@@ -20,14 +20,16 @@ source $(dirname "$0")/functions
 
 set -e
 PORT=5000
+CELERY_LOG_LEVEL="DEBUG"
+worker=true
 
 # Poetry is a mandatory condition to launch this program!
 if [[ -z "${VIRTUAL_ENV}" ]]; then
   message "Launch this script via poetry command: poetry run ${PROGRAM}" "error"
   exit 1
 fi
 
-if ! options=$(getopt -o p: port: -- "$@")
+if ! options=$(getopt -o nlp: -l no-worker,loglevel,port: -- "$@")
 then
   # something went wrong, getopt will put out an error message for us
   exit 1
@@ -37,8 +39,13 @@ while [ $# -gt 0 ]
 do
   case $1 in
     -p|--port) PORT=$2; shift;;
+    -l|--loglevel)
+      CELERY_LOG_LEVEL=$2
+      shift ;;
+    -n|--no-worker)
+      worker=false ;;
     (--) shift; break;;
-    (-*) error_msg+exit "$0: Unrecognized option $1";;
+    (-*) message "$0: Unrecognized option $1" "error"; exit 1;;
   esac
   shift
 done
@@ -48,12 +55,20 @@ title "Start web server and celery"
 
 script_path=$(dirname "$0")
 
-export FLASK_ENV=development
+if [[ -z "${FLASK_DEBUG}" ]]; then
+  export FLASK_DEBUG=True
+fi
+if [[ -z "${FLASK_ENV}" ]]; then
+  export FLASK_ENV="development"
+fi
+
+# Start Worker and Beat
+if $worker; then
+  section "Start celery worker" "info"
+  celery --app sonar.celery worker --loglevel ${CELERY_LOG_LEVEL} --beat & PID_CELERY=$!
+  message "Done" "success"
+fi
 
-# Start Worker and Server
-section "Start celery worker" "info"
-celery --app sonar.celery worker --loglevel INFO --beat & pid_celery=$!
-message "Done" "success"
 
 # Start web server
 section "Start web server" "info"

sonar/config.py

@@ -59,7 +59,6 @@ def _(x):
     """Identity function used to trigger string extraction."""
     return x
 
-
 # Application default theme, used in several modules (previewer, admin, ...)
 APP_THEME = ['bootstrap3']
 

sonar/config_sonar.py

@@ -17,11 +17,7 @@
 
 """Specific configuration SONAR."""
 
-SONAR_APP_SERVER_NAME = 'sonar.rero.ch'
-
-SONAR_APP_BASE_URL = 'https://localhost:5000'
-
-SONAR_APP_API_URL = 'https://localhost:5000/api/'
+SONAR_APP_SERVER_NAME = 'localhost:5000'
 
 SONAR_APP_ANGULAR_URL = 'https://localhost:5000/manage/'
 """Link to angular integrated app root."""

sonar/modules/documents/api.py

@@ -133,21 +133,17 @@ def guess_controlled_affiliations(cls, data):
                         'controlledAffiliation'] = controlled_affiliations
 
     @classmethod
-    def get_record_by_identifier(cls, identifiers, types=None):
+    def get_record_by_identifier(cls, identifiers):
         """Get a record by its identifier.
 
         :param list identifiers: List of identifiers
-        :param list types: List of types
         """
-        if types is None:
-            types = ['bf:Local', 'bf:Doi']
-
         search = DocumentSearch()
 
-        # Search identifiers.
+        # Search only for DOI or local indentifiers.
         search_identifiers = [
             identifier for identifier in identifiers
-            if identifier['type'] in types
+            if identifier['type'] in ['bf:Local', 'bf:Doi']
         ]
 
         # No identifiers to analyze