From a650ae0792fe6f1a5934f23693e76046cd73ff0d Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Tue, 28 Jun 2022 17:52:52 +0200
Subject: [PATCH] Deposit files works for invenio
---
.invenio/.gitignore | 4 +-
.invenio/api_authentication/configuration.py | 2 +-
.invenio/api_container/configuration.py | 2 +-
.invenio/api_database/configuration.py | 2 +-
.invenio/api_document/configuration.py | 2 +-
.invenio/api_identifier/configuration.py | 2 +-
.../api_query/api/table_data_endpoint_api.py | 4 +-
.invenio/api_query/configuration.py | 2 +-
.invenio/api_table/configuration.py | 2 +-
.invenio/{analyze.ipynb => deposit.ipynb} | 10 +-
.invenio/dev.py | 89 ++---
.invenio/feature_extract.ipynb | 367 ++++++++++++++++++
.invenio/requirements.txt | 3 +-
.../at/tuwien/endpoints/DocumentEndpoint.java | 28 +-
.../at/tuwien/endpoints/FileEndpoint.java | 19 +-
.../src/main/resources/application-docker.yml | 1 +
.../src/main/resources/application.yml | 4 +-
.../src/test/java/at/tuwien/BaseUnitTest.java | 47 ++-
.../endpoint/DocumentEndpointUnitTest.java | 39 ++
.../DocumentServiceIntegrationTest.java | 8 +-
.../service/FileServiceIntegrationTest.java | 40 +-
.../src/test/resources/images/mock.png | Bin 0 -> 11666 bytes
.../java/at/tuwien/auth/AuthTokenFilter.java | 2 +-
.../java/at/tuwien/config/GatewayConfig.java | 12 +-
.../at/tuwien/config/WebSecurityConfig.java | 1 -
.../exception/CommitFileUploadException.java | 21 +
.../tuwien/exception/FileUploadException.java | 21 +
.../at/tuwien/gateway/DocumentGateway.java | 20 +-
.../AuthenticationServiceGatewayImpl.java | 10 +-
.../impl/InvenioDocumentGatewayImpl.java | 128 ++++--
.../java/at/tuwien/mapper/DocumentMapper.java | 6 +
.../at/tuwien/service/DocumentService.java | 10 +-
.../java/at/tuwien/service/FileService.java | 10 +-
.../service/impl/InvenioDraftServiceImpl.java | 22 +-
.../service/impl/InvenioFileServiceImpl.java | 15 +-
.../gatewayservice/config/GatewayConfig.java | 5 +
.../FdaIdentifierServiceApplication.java | 1 -
.../src/main/resources/application.yml | 1 +
.../api/document/file/FileAnnounceDto.java | 37 ++
.../at/tuwien/api/document/file/FileDto.java | 72 ++++
.../api/document/file/FileEntryDto.java | 43 ++
.../tuwien/api/document/file/FileKeyDto.java | 23 ++
.../record/{DraftDto.java => RecordDto.java} | 2 +-
fda-ui/server-middleware/index.js | 8 +-
44 files changed, 975 insertions(+), 172 deletions(-)
rename .invenio/{analyze.ipynb => deposit.ipynb} (82%)
mode change 100644 => 100755 .invenio/dev.py
create mode 100644 .invenio/feature_extract.ipynb
create mode 100644 fda-document-service/rest-service/src/test/resources/images/mock.png
create mode 100644 fda-document-service/services/src/main/java/at/tuwien/exception/CommitFileUploadException.java
create mode 100644 fda-document-service/services/src/main/java/at/tuwien/exception/FileUploadException.java
create mode 100644 fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileAnnounceDto.java
create mode 100644 fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileDto.java
create mode 100644 fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileEntryDto.java
create mode 100644 fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileKeyDto.java
rename fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/{DraftDto.java => RecordDto.java} (98%)
diff --git a/.invenio/.gitignore b/.invenio/.gitignore
index ed8ebf583f..150c6f7559 100644
--- a/.invenio/.gitignore
+++ b/.invenio/.gitignore
@@ -1 +1,3 @@
-__pycache__
\ No newline at end of file
+__pycache__
+
+features.csv
\ No newline at end of file
diff --git a/.invenio/api_authentication/configuration.py b/.invenio/api_authentication/configuration.py
index a35f4efa83..2638b5e36f 100644
--- a/.invenio/api_authentication/configuration.py
+++ b/.invenio/api_authentication/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9097"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/api_container/configuration.py b/.invenio/api_container/configuration.py
index b93a7ea5d3..23d21b8381 100644
--- a/.invenio/api_container/configuration.py
+++ b/.invenio/api_container/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9091"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/api_database/configuration.py b/.invenio/api_database/configuration.py
index 758efb3300..5ee4406b93 100644
--- a/.invenio/api_database/configuration.py
+++ b/.invenio/api_database/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9092"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/api_document/configuration.py b/.invenio/api_document/configuration.py
index bb7e50accf..3acecd4c60 100644
--- a/.invenio/api_document/configuration.py
+++ b/.invenio/api_document/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9099"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/api_identifier/configuration.py b/.invenio/api_identifier/configuration.py
index 7845c1cc68..28b5cf8755 100644
--- a/.invenio/api_identifier/configuration.py
+++ b/.invenio/api_identifier/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9096"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/api_query/api/table_data_endpoint_api.py b/.invenio/api_query/api/table_data_endpoint_api.py
index 12101dabc2..34b6434bf0 100644
--- a/.invenio/api_query/api/table_data_endpoint_api.py
+++ b/.invenio/api_query/api/table_data_endpoint_api.py
@@ -259,7 +259,7 @@ class TableDataEndpointApi(object):
auth_settings = [] # noqa: E501
return self.api_client.call_api(
- '/api/container/{id}/database/{databaseId}/table/{tableId}/data', 'HEAD',
+ '/api/container/{id}/database/{databaseId}/table/{tableId}/data', 'GET',
path_params,
query_params,
header_params,
@@ -380,7 +380,7 @@ class TableDataEndpointApi(object):
auth_settings = [] # noqa: E501
return self.api_client.call_api(
- '/api/container/{id}/database/{databaseId}/table/{tableId}/data', 'GET',
+ '/api/container/{id}/database/{databaseId}/table/{tableId}/data', 'HEAD',
path_params,
query_params,
header_params,
diff --git a/.invenio/api_query/configuration.py b/.invenio/api_query/configuration.py
index 1b566374df..2991fff8bf 100644
--- a/.invenio/api_query/configuration.py
+++ b/.invenio/api_query/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9093"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/api_table/configuration.py b/.invenio/api_table/configuration.py
index f24b34599f..557adf4db5 100644
--- a/.invenio/api_table/configuration.py
+++ b/.invenio/api_table/configuration.py
@@ -46,7 +46,7 @@ class Configuration(six.with_metaclass(TypeWithDefault, object)):
def __init__(self):
"""Constructor"""
# Default Base url
- self.host = "http://localhost:9094"
+ self.host = "http://localhost:9095"
# Temp file folder for downloading files
self.temp_folder_path = None
diff --git a/.invenio/analyze.ipynb b/.invenio/deposit.ipynb
similarity index 82%
rename from .invenio/analyze.ipynb
rename to .invenio/deposit.ipynb
index 542a3613a6..6fe7d9c770 100644
--- a/.invenio/analyze.ipynb
+++ b/.invenio/deposit.ipynb
@@ -2,15 +2,11 @@
"cells": [
{
"cell_type": "markdown",
+ "source": [],
"metadata": {
- "collapsed": true,
- "pycharm": {
- "name": "#%% md\n"
- }
+ "collapsed": false
},
- "source": [
- "# Test"
- ]
+ "outputs": []
}
],
"metadata": {
diff --git a/.invenio/dev.py b/.invenio/dev.py
old mode 100644
new mode 100755
index aa0cb1af32..81a94da41a
--- a/.invenio/dev.py
+++ b/.invenio/dev.py
@@ -1,67 +1,34 @@
#!/usr/bin/env python3
-import json
-
+import re
+import csv
import requests
-from api_authentication.api.authentication_endpoint_api import AuthenticationEndpointApi
-from api_authentication.api.user_endpoint_api import UserEndpointApi
-from api_container.api.container_endpoint_api import ContainerEndpointApi
-from api_database.api.container_database_endpoint_api import ContainerDatabaseEndpointApi
+doi = '10.5281/zenodo.5649276'
+headers = {
+ 'Authorize': 'Bearer djCvqkoOW69keHajybZiwE8bBjyir2QSZOLKpAtc4S1Wp17KXgcHmMoWJwft'
+}
-authentication = AuthenticationEndpointApi()
-user = UserEndpointApi()
-container = ContainerEndpointApi()
-database = ContainerDatabaseEndpointApi()
+# Resolve DOI
+response = requests.get('https://doi.org/' + doi)
+id = re.findall('/([a-z0-9-]+)$', response.url)[0]
+host = re.findall('^https?:\/\/([a-z0-9]+\.[a-z]+)', response.url)[0]
+print("Resolved DOI to", host, "and record id", id)
-# # Create account
-# response = user.register({
-# 'username': 'mweise',
-# 'password': 'fda',
-# 'email': 'martin.weise@tuwien.ac.at'
-# })
-# print('Created account with username %s' % response.username)
-#
-# # Create authentication
-# response = authentication.authenticate_user1({
-# 'username': 'mweise',
-# 'password': 'fda'
-# })
-# container.api_client.default_headers = {
-# 'Authorization': 'Bearer ' + response.token
-# }
-# database.api_client.default_headers = {
-# 'Authorization': 'Bearer ' + response.token
-# }
-#
-# # Create container
-# response = container.create1({
-# 'name': 'MIR ' + str(uuid.uuid1()),
-# 'repository': 'mariadb',
-# 'tag': '10.5'
-# })
-# cid = response.id
-# print('Created container with id %d' % cid)
-#
-# # Start container
-# response = container.modify({
-# 'action': 'START'
-# }, cid)
-# time.sleep(5)
-# print('Started container with id %d' % cid)
-#
-# # Create database
-# response = database.create({
-# 'name': 'MIR ' + str(uuid.uuid1()),
-# 'description': 'Music Information Retrieval',
-# 'is_public': True
-# }, cid)
-# dbid = response.id
-# print('Created database with id %d' % dbid)
+# Find files
+url = 'https://' + host + '/api/records/' + id
+response = requests.get(url, headers=headers)
+record = response.json()
-# Analyse Table
-response = requests.post('http://localhost:5000/api/analyse/determinedt', json={
- 'filepath': '/tmp/test.csv',
-})
-data = json.loads(response.content)
-print('Determined data types')
-print(response)
+# Write some .csv
+i = 0
+with open('./features.csv', 'w') as f:
+ writer = csv.writer(f)
+ writer.writerow(['key', 'size', 'link'])
+ for file in record['files']:
+ requests.get(file['links']['self'])
+ print("... feature extract from", file['links']['self'])
+ writer.writerow([file['key'], file['size'], file['links']['self']])
+ i += 1
+ if i > 10:
+ break
+print("Generated a feature .csv")
diff --git a/.invenio/feature_extract.ipynb b/.invenio/feature_extract.ipynb
new file mode 100644
index 0000000000..9de40c112c
--- /dev/null
+++ b/.invenio/feature_extract.ipynb
@@ -0,0 +1,367 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "collapsed": true,
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
+ "source": [
+ "# Feature Extraction & Deposit\n",
+ "\n",
+ "In this notebook we define an example of creating a database from a .csv and perform feature extraction of audio files. The APIs are auto-generated from the Swagger Endpoint documentations using [`generate.sh`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-docs/-/blob/master/swagger/generate.sh). Steps we perform:\n",
+ "\n",
+ " 1. Download a music file from a public repository\n",
+ " 2. Perform feature extraction\n",
+ " 3. Create an account at DBRepo\n",
+ " 4. Create an authentication token\n",
+ " 5. Create a mariadb container\n",
+ " 6. Start the mariadb container\n",
+ " 7. Create a database within the mariadb container\n",
+ " 8. Import the feature .csv (manually)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "outputs": [],
+ "source": [
+ "import os.path\n",
+ "import uuid\n",
+ "import time\n",
+ "import re\n",
+ "import csv\n",
+ "import requests as rq\n",
+ "from api_authentication.api.authentication_endpoint_api import AuthenticationEndpointApi\n",
+ "from api_authentication.api.user_endpoint_api import UserEndpointApi\n",
+ "from api_container.api.container_endpoint_api import ContainerEndpointApi\n",
+ "from api_database.api.container_database_endpoint_api import ContainerDatabaseEndpointApi\n",
+ "from api_table.api.table_endpoint_api import TableEndpointApi\n",
+ "\n",
+ "authentication = AuthenticationEndpointApi()\n",
+ "user = UserEndpointApi()\n",
+ "container = ContainerEndpointApi()\n",
+ "database = ContainerDatabaseEndpointApi()\n",
+ "table = TableEndpointApi()\n",
+ "\n",
+ "doi = \"10.5281/zenodo.5649276\"\n",
+ "email = \"some@example.com\""
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 1. Download wav\n",
+ "\n",
+ "Resolve the DOI to URI"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Resolved DOI to zenodo.org and record id 5649276\n"
+ ]
+ }
+ ],
+ "source": [
+ "response = rq.get(\"https://doi.org/\" + doi)\n",
+ "id = re.findall(\"/([a-z0-9-]+)$\", response.url)[0]\n",
+ "host = re.findall(\"^https?:\\/\\/([a-z0-9]+\\.[a-z]+)\", response.url)[0]\n",
+ "print(\"Resolved DOI to\", host, \"and record id\", id)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 2. Perform feature extraction"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0044_20200518133554_1_m4a_1.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0044_20200518133554_2_m4a_1.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200611134530_1_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200611134530_2_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200612072315_1_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200612072315_2_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200613082517_1_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200613082517_2_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200614080017_1_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200614080017_2_m4a_0.wav\n",
+ "... feature extract from https://zenodo.org/api/files/22d69a63-2aff-47ae-b818-be78a23e9889/colive.0066_20200615070238_1_m4a_0.wav\n",
+ "Generated a feature .csv in your home directory\n"
+ ]
+ }
+ ],
+ "source": [
+ "response = rq.get(\"https://\" + host + \"/api/records/\" + id)\n",
+ "record = response.json()\n",
+ "\n",
+ "i = 0\n",
+ "with open(os.path.expanduser(\"~/features.csv\"), \"w\") as f:\n",
+ " writer = csv.writer(f)\n",
+ " writer.writerow([\"key\", \"size\", \"link\"])\n",
+ " for file in record[\"files\"]:\n",
+ " rq.get(file[\"links\"][\"self\"])\n",
+ " print(\"... feature extract from\", file[\"links\"][\"self\"])\n",
+ " writer.writerow([file[\"key\"], file[\"size\"], file[\"links\"][\"self\"]])\n",
+ " i += 1\n",
+ " if i > 10:\n",
+ " break\n",
+ "print(\"Generated a feature .csv in your home directory\")"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 3. Create an account at DBRepo"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{'authorities': [{'authority': 'ROLE_RESEARCHER'}],\n",
+ " 'containers': None,\n",
+ " 'databases': None,\n",
+ " 'email': 'martinweiseat@gmail.com',\n",
+ " 'firstname': None,\n",
+ " 'id': 2,\n",
+ " 'identifiers': None,\n",
+ " 'lastname': None,\n",
+ " 'titles_after': None,\n",
+ " 'titles_before': None,\n",
+ " 'username': 'user'}\n"
+ ]
+ }
+ ],
+ "source": [
+ "response = user.register({\n",
+ " \"username\": \"user\",\n",
+ " \"password\": \"user\",\n",
+ " \"email\": email\n",
+ "})\n",
+ "print(response)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 4. Create an authentication token"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "outputs": [],
+ "source": [
+ "response = authentication.authenticate_user1({\n",
+ " \"username\": \"user\",\n",
+ " \"password\": \"user\"\n",
+ "})\n",
+ "container.api_client.default_headers = {\"Authorization\": \"Bearer \" + response.token}\n",
+ "database.api_client.default_headers = {\"Authorization\": \"Bearer \" + response.token}\n",
+ "table.api_client.default_headers = {\"Authorization\": \"Bearer \" + response.token}"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 5. Create a mariadb container"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{'hash': 'f5a649a71aae3748e62228721c44627ffc866f665d677bb890c37b9111590ffa',\n",
+ " 'id': 2,\n",
+ " 'internal_name': 'fda-userdb-mir-1010b964-f6fa-11ec-9f77-64bc58900b78',\n",
+ " 'is_public': None,\n",
+ " 'name': 'MIR 1010b964-f6fa-11ec-9f77-64bc58900b78'}\n"
+ ]
+ }
+ ],
+ "source": [
+ "response = container.create1({\n",
+ " \"name\": \"MIR \" + str(uuid.uuid1()),\n",
+ " \"repository\": \"mariadb\",\n",
+ " \"tag\": \"10.5\"\n",
+ "})\n",
+ "container_id = response.id\n",
+ "print(response)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 6. Start the mariadb container"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "{'hash': 'f5a649a71aae3748e62228721c44627ffc866f665d677bb890c37b9111590ffa',\n",
+ " 'id': 2,\n",
+ " 'internal_name': 'fda-userdb-mir-1010b964-f6fa-11ec-9f77-64bc58900b78',\n",
+ " 'is_public': None,\n",
+ " 'name': 'MIR 1010b964-f6fa-11ec-9f77-64bc58900b78'}\n"
+ ]
+ }
+ ],
+ "source": [
+ "response = container.modify({\n",
+ " \"action\": \"START\"\n",
+ "}, container_id)\n",
+ "time.sleep(5)\n",
+ "print(response)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 7. Create a database within the mariadb container"
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "outputs": [],
+ "source": [
+ "response = database.create({\n",
+ " \"name\": \"MIR \" + str(uuid.uuid1()),\n",
+ " \"description\": \"Music Information Retrieval\",\n",
+ " \"is_public\": True\n",
+ "}, container_id)\n",
+ "database_id = response.id"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## 8. Import the feature .csv\n",
+ "\n",
+ "Now open [http://localhost:3000/](http://localhost:3000/) and import the .csv file by clicking the database. After successful creation of the table, come back here."
+ ],
+ "metadata": {
+ "collapsed": false
+ }
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
\ No newline at end of file
diff --git a/.invenio/requirements.txt b/.invenio/requirements.txt
index 47f78a7d88..cead3141b6 100644
--- a/.invenio/requirements.txt
+++ b/.invenio/requirements.txt
@@ -1,2 +1 @@
-invenio-client==0.1.0
-six==1.16.0
\ No newline at end of file
+requests==2.28.0
\ No newline at end of file
diff --git a/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/DocumentEndpoint.java b/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/DocumentEndpoint.java
index 2436b9748b..395e77b5a3 100644
--- a/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/DocumentEndpoint.java
+++ b/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/DocumentEndpoint.java
@@ -1,7 +1,7 @@
package at.tuwien.endpoints;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
import at.tuwien.exception.DraftRecordCreateException;
import at.tuwien.service.DocumentService;
import io.swagger.v3.oas.annotations.Operation;
@@ -20,9 +20,8 @@ import java.security.Principal;
@Log4j2
-@RestController
@CrossOrigin(origins = "*")
-@ControllerAdvice
+@RestController
@RequestMapping("/api/document")
public class DocumentEndpoint {
@@ -37,9 +36,9 @@ public class DocumentEndpoint {
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
@Operation(summary = "Create a draft", security = @SecurityRequirement(name = "bearerAuth"))
- public ResponseEntity<DraftDto> create(@NotNull @Valid @RequestBody CreateDraftDto data,
+ public ResponseEntity<RecordDto> create(@NotNull @Valid @RequestBody CreateDraftDto data,
@NotNull Principal principal) throws DraftRecordCreateException {
- final DraftDto document = documentService.create(data, principal);
+ final RecordDto document = documentService.create(data, principal);
return ResponseEntity.status(HttpStatus.CREATED)
.body(document);
}
@@ -48,22 +47,33 @@ public class DocumentEndpoint {
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
@Operation(summary = "Find a draft", security = @SecurityRequirement(name = "bearerAuth"))
- public ResponseEntity<DraftDto> find(@NotNull @PathVariable("id") String documentId,
+ public ResponseEntity<RecordDto> find(@NotNull @PathVariable("id") String documentId,
@NotNull Principal principal) throws DraftRecordCreateException {
- final DraftDto document = documentService.findById(documentId, principal);
+ final RecordDto document = documentService.findById(documentId, principal);
log.info("Found draft record with id {}", documentId);
log.debug("found draft record {}", document);
return ResponseEntity.status(HttpStatus.OK)
.body(document);
}
+ @PutMapping("/{id}/publish")
+ @PreAuthorize("hasRole('ROLE_RESEARCHER')")
+ @Transactional(readOnly = true)
+ @Operation(summary = "Publish a draft", security = @SecurityRequirement(name = "bearerAuth"))
+ public ResponseEntity<RecordDto> publish(@NotNull @PathVariable("id") String documentId,
+ @NotNull Principal principal) throws DraftRecordCreateException {
+ final RecordDto document = documentService.publish(documentId, principal);
+ return ResponseEntity.status(HttpStatus.ACCEPTED)
+ .body(document);
+ }
+
@PostMapping("/{id}")
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
@Operation(summary = "Reserve draft DOI", security = @SecurityRequirement(name = "bearerAuth"))
- public ResponseEntity<DraftDto> reserve(@NotNull @PathVariable("id") String documentId,
+ public ResponseEntity<RecordDto> reserve(@NotNull @PathVariable("id") String documentId,
@NotNull Principal principal) throws DraftRecordCreateException {
- final DraftDto document = documentService.reserveDoi(documentId, principal);
+ final RecordDto document = documentService.reserveDoi(documentId, principal);
return ResponseEntity.status(HttpStatus.CREATED)
.body(document);
}
diff --git a/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/FileEndpoint.java b/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/FileEndpoint.java
index 5457e3c67a..402d37ed3b 100644
--- a/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/FileEndpoint.java
+++ b/fda-document-service/rest-service/src/main/java/at/tuwien/endpoints/FileEndpoint.java
@@ -1,6 +1,8 @@
package at.tuwien.endpoints;
-import at.tuwien.api.document.file.FileStartDto;
+import at.tuwien.api.document.file.FileDto;
+import at.tuwien.exception.FileUploadException;
+import at.tuwien.exception.CommitFileUploadException;
import at.tuwien.exception.DraftRecordCreateException;
import at.tuwien.service.FileService;
import io.swagger.v3.oas.annotations.Operation;
@@ -12,6 +14,7 @@ import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.*;
+import org.springframework.web.multipart.MultipartFile;
import javax.validation.constraints.NotNull;
import java.security.Principal;
@@ -20,7 +23,6 @@ import java.security.Principal;
@Log4j2
@RestController
@CrossOrigin(origins = "*")
-@ControllerAdvice
@RequestMapping("/api/document/{id}/file")
public class FileEndpoint {
@@ -34,11 +36,14 @@ public class FileEndpoint {
@PostMapping
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
- @Operation(summary = "Start draft files", security = @SecurityRequirement(name = "bearerAuth"))
- public ResponseEntity<FileStartDto> start(@NotNull @PathVariable("id") String documentId,
- @NotNull Principal principal) throws DraftRecordCreateException {
- final FileStartDto document = fileService.start(documentId, principal);
- return ResponseEntity.status(HttpStatus.CREATED)
+ @Operation(summary = "Upload file", security = @SecurityRequirement(name = "bearerAuth"))
+ public ResponseEntity<FileDto> uploadFile(@NotNull @PathVariable("id") String documentId,
+ @NotNull @RequestParam("file") MultipartFile file,
+ @NotNull Principal principal)
+ throws DraftRecordCreateException, CommitFileUploadException, FileUploadException,
+ org.apache.tomcat.util.http.fileupload.FileUploadException {
+ final FileDto document = fileService.uploadFile(documentId, file, principal);
+ return ResponseEntity.status(HttpStatus.ACCEPTED)
.body(document);
}
diff --git a/fda-document-service/rest-service/src/main/resources/application-docker.yml b/fda-document-service/rest-service/src/main/resources/application-docker.yml
index 46f56dc08b..6cc0944799 100644
--- a/fda-document-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-document-service/rest-service/src/main/resources/application-docker.yml
@@ -30,5 +30,6 @@ eureka:
fda:
mount.path: /tmp
ready.path: /ready
+ gateway.endpoint: http://fda-gateway-service:9095
document.endpoint: https://test.researchdata.tuwien.ac.at
dev.token: "${TOKEN}"
\ No newline at end of file
diff --git a/fda-document-service/rest-service/src/main/resources/application.yml b/fda-document-service/rest-service/src/main/resources/application.yml
index 47db505983..bf035c9f11 100644
--- a/fda-document-service/rest-service/src/main/resources/application.yml
+++ b/fda-document-service/rest-service/src/main/resources/application.yml
@@ -7,7 +7,7 @@ spring:
username: postgres
password: postgres
jpa:
- show-sql: false
+ show-sql: true
database-platform: org.hibernate.dialect.PostgreSQLDialect
hibernate:
ddl-auto: validate
@@ -16,7 +16,6 @@ spring:
name: fda-document-service
cloud:
loadbalancer.ribbon.enabled: false
-springdoc.swagger-ui.enabled: true
server.port: 9099
logging:
pattern.console: "%d %highlight(%-5level) %msg%n"
@@ -31,5 +30,6 @@ eureka:
fda:
mount.path: /tmp
ready.path: ./ready
+ gateway.endpoint: http://localhost:9095
document.endpoint: https://test.researchdata.tuwien.ac.at
dev.token: "${TOKEN}"
\ No newline at end of file
diff --git a/fda-document-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java b/fda-document-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
index 7f4f0cc7eb..c772a6be5d 100644
--- a/fda-document-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
+++ b/fda-document-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
@@ -2,6 +2,8 @@ package at.tuwien;
import at.tuwien.api.document.metadata.*;
import at.tuwien.api.document.record.*;
+import at.tuwien.api.user.UserDetailsDto;
+import org.springframework.security.core.userdetails.UserDetails;
import org.springframework.test.context.TestPropertySource;
import java.time.Instant;
@@ -11,30 +13,58 @@ import java.util.List;
@TestPropertySource(locations = "classpath:application.properties")
public abstract class BaseUnitTest {
+ public final static Long USER_1_ID = 1L;
public final static String USER_1_USERNAME = "junit";
+ public final static UserDetails USER_1_DETAILS = UserDetailsDto.builder()
+ .id(USER_1_ID)
+ .username(USER_1_USERNAME)
+ .build();
+
public final static AccessTypeDto DOCUMENT_1_RECORD_TYPE = AccessTypeDto.PUBLIC;
public final static FileTypeDto DOCUMENT_1_FILE_TYPE = FileTypeDto.PUBLIC;
+ public final static AccessTypeDto DOCUMENT_2_RECORD_TYPE = AccessTypeDto.PUBLIC;
+ public final static FileTypeDto DOCUMENT_2_FILE_TYPE = FileTypeDto.RESTRICTED;
+
public final static AccessOptionsDto DOCUMENT_1_ACCESS_OPTIONS = AccessOptionsDto.builder()
.record(DOCUMENT_1_RECORD_TYPE)
.files(DOCUMENT_1_FILE_TYPE)
.build();
- public final static Boolean DOCUMENT_1_FILES_ENABLED = true;
+ public final static AccessOptionsDto DOCUMENT_2_ACCESS_OPTIONS = AccessOptionsDto.builder()
+ .record(DOCUMENT_2_RECORD_TYPE)
+ .files(DOCUMENT_2_FILE_TYPE)
+ .build();
+
+ public final static Boolean DOCUMENT_1_FILES_ENABLED = false;
+
+ public final static Boolean DOCUMENT_2_FILES_ENABLED = true;
public final static FilesOptionsDto DOCUMENT_1_FILES_OPTIONS = FilesOptionsDto.builder()
.enabled(DOCUMENT_1_FILES_ENABLED)
.build();
- public final static String DOCUMENT_1_TITLE = "Test Draft";
+ public final static FilesOptionsDto DOCUMENT_2_FILES_OPTIONS = FilesOptionsDto.builder()
+ .enabled(DOCUMENT_2_FILES_ENABLED)
+ .build();
+
+ public final static String DOCUMENT_1_TITLE = "Public Test-Record";
public final static String DOCUMENT_1_RESOURCE_TYPE_TYPE = "other";
public final static Date DOCUMENT_1_PUBLICATION_DATE = Date.from(Instant.now());
+ public final static String DOCUMENT_2_TITLE = "Restricted Test-Record";
+ public final static String DOCUMENT_2_RESOURCE_TYPE_TYPE = "other";
+ public final static Date DOCUMENT_2_PUBLICATION_DATE = Date.from(Instant.now());
+
public final static ResourceTypeDto DOCUMENT_1_RESOURCE_TYPE = ResourceTypeDto.builder()
.id(DOCUMENT_1_RESOURCE_TYPE_TYPE)
.build();
+ public final static ResourceTypeDto DOCUMENT_2_RESOURCE_TYPE = ResourceTypeDto.builder()
+ .id(DOCUMENT_2_RESOURCE_TYPE_TYPE)
+ .build();
+
public final static String IDENTIFIER_1_IDENTIFIER = "0000-0003-4216-302X";
public final static IdentifierTypeDto IDENTIFIER_1_TYPE = IdentifierTypeDto.ORCID;
@@ -72,10 +102,23 @@ public abstract class BaseUnitTest {
.creators(List.of(CREATOR_1))
.build();
+ public final static MetadataDto DOCUMENT_2_METADATA = MetadataDto.builder()
+ .title(DOCUMENT_2_TITLE)
+ .resourceType(DOCUMENT_2_RESOURCE_TYPE)
+ .publicationDate(DOCUMENT_2_PUBLICATION_DATE)
+ .creators(List.of(CREATOR_1))
+ .build();
+
public final static CreateDraftDto DOCUMENT_1_CREATE_DRAFT = CreateDraftDto.builder()
.access(DOCUMENT_1_ACCESS_OPTIONS)
.files(DOCUMENT_1_FILES_OPTIONS)
.metadata(DOCUMENT_1_METADATA)
.build();
+ public final static CreateDraftDto DOCUMENT_2_CREATE_DRAFT = CreateDraftDto.builder()
+ .access(DOCUMENT_2_ACCESS_OPTIONS)
+ .files(DOCUMENT_2_FILES_OPTIONS)
+ .metadata(DOCUMENT_2_METADATA)
+ .build();
+
}
diff --git a/fda-document-service/rest-service/src/test/java/at/tuwien/endpoint/DocumentEndpointUnitTest.java b/fda-document-service/rest-service/src/test/java/at/tuwien/endpoint/DocumentEndpointUnitTest.java
index 0965a30b1e..534038dbad 100644
--- a/fda-document-service/rest-service/src/test/java/at/tuwien/endpoint/DocumentEndpointUnitTest.java
+++ b/fda-document-service/rest-service/src/test/java/at/tuwien/endpoint/DocumentEndpointUnitTest.java
@@ -1,13 +1,52 @@
package at.tuwien.endpoint;
import at.tuwien.BaseUnitTest;
+import at.tuwien.api.document.record.CreateDraftDto;
+import at.tuwien.api.document.record.RecordDto;
+import at.tuwien.endpoints.DocumentEndpoint;
+import at.tuwien.exception.DraftRecordCreateException;
+import at.tuwien.gateway.AuthenticationServiceGateway;
+import org.apache.http.auth.BasicUserPrincipal;
+import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.test.context.support.WithMockUser;
import org.springframework.test.context.junit.jupiter.SpringExtension;
+import java.security.Principal;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.when;
+
@ExtendWith(SpringExtension.class)
@SpringBootTest
public class DocumentEndpointUnitTest extends BaseUnitTest {
+ @Autowired
+ private DocumentEndpoint documentEndpoint;
+
+ @MockBean
+ private AuthenticationServiceGateway authenticationServiceGateway;
+
+
+ @Test
+ @WithMockUser(username = USER_1_USERNAME, authorities = {"ROLE_RESEARCHER"})
+ public void create_succeed() throws DraftRecordCreateException {
+ final CreateDraftDto request = DOCUMENT_1_CREATE_DRAFT;
+ final Principal principal = new BasicUserPrincipal(USER_1_USERNAME);
+
+ /* mock */
+ when(authenticationServiceGateway.validate(anyString()))
+ .thenReturn(USER_1_DETAILS);
+
+ /* test */
+ final ResponseEntity<RecordDto> response = documentEndpoint.create(request, principal);
+ assertEquals(HttpStatus.CREATED, response.getStatusCode());
+ }
}
diff --git a/fda-document-service/rest-service/src/test/java/at/tuwien/service/DocumentServiceIntegrationTest.java b/fda-document-service/rest-service/src/test/java/at/tuwien/service/DocumentServiceIntegrationTest.java
index 055fd45ca2..cdef81d0dc 100644
--- a/fda-document-service/rest-service/src/test/java/at/tuwien/service/DocumentServiceIntegrationTest.java
+++ b/fda-document-service/rest-service/src/test/java/at/tuwien/service/DocumentServiceIntegrationTest.java
@@ -2,7 +2,7 @@ package at.tuwien.service;
import at.tuwien.BaseUnitTest;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
import at.tuwien.exception.DraftRecordCreateException;
import lombok.extern.log4j.Log4j2;
import org.apache.http.auth.BasicUserPrincipal;
@@ -35,7 +35,7 @@ public class DocumentServiceIntegrationTest extends BaseUnitTest {
/* mock */
/* test */
- final DraftDto response = documentService.create(request, principal);
+ final RecordDto response = documentService.create(request, principal);
assertEquals(DOCUMENT_1_TITLE, response.getMetadata().getTitle());
}
@@ -47,8 +47,8 @@ public class DocumentServiceIntegrationTest extends BaseUnitTest {
/* mock */
/* test */
- final DraftDto document = documentService.create(request, principal);
- final DraftDto response = documentService.reserveDoi(document.getId(), principal);
+ final RecordDto document = documentService.create(request, principal);
+ final RecordDto response = documentService.reserveDoi(document.getId(), principal);
assertNotNull(response.getPids().getDoi());
}
diff --git a/fda-document-service/rest-service/src/test/java/at/tuwien/service/FileServiceIntegrationTest.java b/fda-document-service/rest-service/src/test/java/at/tuwien/service/FileServiceIntegrationTest.java
index 9172889617..b694b019aa 100644
--- a/fda-document-service/rest-service/src/test/java/at/tuwien/service/FileServiceIntegrationTest.java
+++ b/fda-document-service/rest-service/src/test/java/at/tuwien/service/FileServiceIntegrationTest.java
@@ -1,21 +1,31 @@
package at.tuwien.service;
import at.tuwien.BaseUnitTest;
-import at.tuwien.api.document.file.FileStartDto;
+import at.tuwien.api.document.file.FileDto;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
+import at.tuwien.exception.FileUploadException;
+import at.tuwien.exception.CommitFileUploadException;
import at.tuwien.exception.DraftRecordCreateException;
import lombok.extern.log4j.Log4j2;
+import org.apache.commons.io.FileUtils;
import org.apache.http.auth.BasicUserPrincipal;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.mock.web.MockMultipartFile;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension;
+import org.springframework.web.multipart.MultipartFile;
+import java.io.File;
+import java.io.IOException;
import java.security.Principal;
+import static org.junit.jupiter.api.Assertions.*;
+
+
@Log4j2
@DirtiesContext(classMode = DirtiesContext.ClassMode.BEFORE_EACH_TEST_METHOD)
@ExtendWith(SpringExtension.class)
@@ -29,15 +39,35 @@ public class FileServiceIntegrationTest extends BaseUnitTest {
private FileService fileService;
@Test
- public void start_succeeds() throws DraftRecordCreateException {
+ public void upload_succeeds()
+ throws DraftRecordCreateException, IOException, CommitFileUploadException, FileUploadException {
+ final CreateDraftDto request = DOCUMENT_2_CREATE_DRAFT;
+ final Principal principal = new BasicUserPrincipal(USER_1_USERNAME);
+ final File mockFile = new File("src/test/resources/images/mock.png");
+
+ /* mock */
+ final MultipartFile file = new MockMultipartFile(mockFile.getName(), FileUtils.openInputStream(mockFile)
+ .readAllBytes());
+ final RecordDto document = documentService.create(request, principal);
+ assertFalse(document.getIsPublished());
+
+ /* test */
+ final FileDto response = fileService.uploadFile(document.getId(), file, principal);
+ assertEquals(file.getName(), response.getKey());
+ }
+ @Test
+ public void publish_succeeds()
+ throws DraftRecordCreateException {
final CreateDraftDto request = DOCUMENT_1_CREATE_DRAFT;
final Principal principal = new BasicUserPrincipal(USER_1_USERNAME);
/* mock */
- final DraftDto document = documentService.create(request, principal);
+ final RecordDto document = documentService.create(request, principal);
/* test */
- final FileStartDto response = fileService.start(document.getId(), principal);
+ final RecordDto response = documentService.publish(document.getId(), principal);
+ assertTrue(response.getIsPublished());
+ assertNotNull(response.getPids().getDoi());
}
}
diff --git a/fda-document-service/rest-service/src/test/resources/images/mock.png b/fda-document-service/rest-service/src/test/resources/images/mock.png
new file mode 100644
index 0000000000000000000000000000000000000000..4094aa6f22d95544339040f01f4f3d19f587d1d3
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HcmV?d00001
diff --git a/fda-document-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java b/fda-document-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java
index e33f0dba4d..4d819a1786 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java
@@ -55,4 +55,4 @@ public class AuthTokenFilter extends OncePerRequestFilter {
}
return null;
}
-}
\ No newline at end of file
+}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/config/GatewayConfig.java b/fda-document-service/services/src/main/java/at/tuwien/config/GatewayConfig.java
index 006541ad8c..776e4aa5d8 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/config/GatewayConfig.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/config/GatewayConfig.java
@@ -9,11 +9,21 @@ import org.springframework.web.util.DefaultUriBuilderFactory;
@Configuration
public class GatewayConfig {
+ @Value("${fda.gateway.endpoint}")
+ private String gatewayEndpoint;
+
@Value("${fda.document.endpoint}")
private String documentEndpoint;
@Bean
- public RestTemplate restTemplate() {
+ public RestTemplate gatewayRestTemplate() {
+ final RestTemplate restTemplate = new RestTemplate();
+ restTemplate.setUriTemplateHandler(new DefaultUriBuilderFactory(gatewayEndpoint));
+ return restTemplate;
+ }
+
+ @Bean
+ public RestTemplate documentRestTemplate() {
final RestTemplate restTemplate = new RestTemplate();
restTemplate.setUriTemplateHandler(new DefaultUriBuilderFactory(documentEndpoint));
return restTemplate;
diff --git a/fda-document-service/services/src/main/java/at/tuwien/config/WebSecurityConfig.java b/fda-document-service/services/src/main/java/at/tuwien/config/WebSecurityConfig.java
index 70dac68fcd..472089fc21 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/config/WebSecurityConfig.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/config/WebSecurityConfig.java
@@ -65,7 +65,6 @@ public class WebSecurityConfig extends WebSecurityConfigurerAdapter {
/* set permissions on endpoints */
http.authorizeRequests()
/* our public endpoints */
- .antMatchers(HttpMethod.GET, "/api/document/**").permitAll()
.antMatchers("/v3/api-docs.yaml",
"/v3/api-docs/**",
"/swagger-ui/**",
diff --git a/fda-document-service/services/src/main/java/at/tuwien/exception/CommitFileUploadException.java b/fda-document-service/services/src/main/java/at/tuwien/exception/CommitFileUploadException.java
new file mode 100644
index 0000000000..430f7bba54
--- /dev/null
+++ b/fda-document-service/services/src/main/java/at/tuwien/exception/CommitFileUploadException.java
@@ -0,0 +1,21 @@
+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.CONFLICT)
+public class CommitFileUploadException extends Exception {
+
+ public CommitFileUploadException(String msg) {
+ super(msg);
+ }
+
+ public CommitFileUploadException(String msg, Throwable thr) {
+ super(msg, thr);
+ }
+
+ public CommitFileUploadException(Throwable thr) {
+ super(thr);
+ }
+
+}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/exception/FileUploadException.java b/fda-document-service/services/src/main/java/at/tuwien/exception/FileUploadException.java
new file mode 100644
index 0000000000..590060826f
--- /dev/null
+++ b/fda-document-service/services/src/main/java/at/tuwien/exception/FileUploadException.java
@@ -0,0 +1,21 @@
+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.FAILED_DEPENDENCY)
+public class FileUploadException extends Exception {
+
+ public FileUploadException(String msg) {
+ super(msg);
+ }
+
+ public FileUploadException(String msg, Throwable thr) {
+ super(msg, thr);
+ }
+
+ public FileUploadException(Throwable thr) {
+ super(thr);
+ }
+
+}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/gateway/DocumentGateway.java b/fda-document-service/services/src/main/java/at/tuwien/gateway/DocumentGateway.java
index fe6a27d6d5..36d86d6d02 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/gateway/DocumentGateway.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/gateway/DocumentGateway.java
@@ -1,18 +1,26 @@
package at.tuwien.gateway;
-import at.tuwien.api.document.file.FileStartDto;
+import at.tuwien.api.document.file.FileDto;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
+import at.tuwien.exception.FileUploadException;
+import at.tuwien.exception.CommitFileUploadException;
import at.tuwien.exception.DraftRecordCreateException;
+import org.springframework.web.multipart.MultipartFile;
public interface DocumentGateway {
- DraftDto createDraft(CreateDraftDto data, String token) throws DraftRecordCreateException;
+ RecordDto createDraft(CreateDraftDto data, String token) throws DraftRecordCreateException;
- DraftDto reserveDraftDoi(String id, String token) throws DraftRecordCreateException;
+ RecordDto reserveDraftDoi(String id, String token) throws DraftRecordCreateException;
- DraftDto findDraft(String id, String token) throws DraftRecordCreateException;
+ RecordDto findDraft(String id, String token) throws DraftRecordCreateException;
- FileStartDto startUpload(String id, String token) throws DraftRecordCreateException;
+ RecordDto publishDraft(String id, String token) throws DraftRecordCreateException;
+
+ FileDto uploadFile(String id, MultipartFile file, String token)
+ throws DraftRecordCreateException, FileUploadException,
+ org.apache.tomcat.util.http.fileupload.FileUploadException,
+ CommitFileUploadException;
void delete(String id, String token) throws DraftRecordCreateException;
}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/AuthenticationServiceGatewayImpl.java b/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/AuthenticationServiceGatewayImpl.java
index 56d691a6c8..5492233420 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/AuthenticationServiceGatewayImpl.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/AuthenticationServiceGatewayImpl.java
@@ -18,20 +18,20 @@ import org.springframework.web.client.RestTemplate;
public class AuthenticationServiceGatewayImpl implements AuthenticationServiceGateway {
private final UserMapper userMapper;
- private final RestTemplate restTemplate;
+ private final RestTemplate gatewayRestTemplate;
@Autowired
- public AuthenticationServiceGatewayImpl(UserMapper userMapper, RestTemplate restTemplate) {
+ public AuthenticationServiceGatewayImpl(UserMapper userMapper, RestTemplate gatewayRestTemplate) {
this.userMapper = userMapper;
- this.restTemplate = restTemplate;
+ this.gatewayRestTemplate = gatewayRestTemplate;
}
@Override
public UserDetails validate(String token) {
final HttpHeaders headers = new HttpHeaders();
headers.set("Authorization", "Bearer " + token);
- final ResponseEntity<UserDto> response = restTemplate.exchange("/api/auth", HttpMethod.PUT,
- new HttpEntity<>("", headers), UserDto.class);
+ final ResponseEntity<UserDto> response = gatewayRestTemplate.exchange("/api/auth", HttpMethod.PUT,
+ new HttpEntity<>(null, headers), UserDto.class);
return userMapper.userDtoToUserDetailsDto(response.getBody());
}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/InvenioDocumentGatewayImpl.java b/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/InvenioDocumentGatewayImpl.java
index 318594ee12..bca9d5b863 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/InvenioDocumentGatewayImpl.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/gateway/impl/InvenioDocumentGatewayImpl.java
@@ -1,36 +1,49 @@
package at.tuwien.gateway.impl;
-import at.tuwien.api.document.file.FileStartDto;
+import at.tuwien.api.document.file.FileAnnounceDto;
+import at.tuwien.api.document.file.FileDto;
+import at.tuwien.api.document.file.FileKeyDto;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
+import at.tuwien.exception.FileUploadException;
+import at.tuwien.exception.CommitFileUploadException;
import at.tuwien.exception.DraftRecordCreateException;
import at.tuwien.gateway.DocumentGateway;
+import at.tuwien.mapper.DocumentMapper;
import lombok.extern.slf4j.Slf4j;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.*;
import org.springframework.stereotype.Component;
import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.RestTemplate;
+import org.springframework.web.multipart.MultipartFile;
+
+import java.io.IOException;
+import java.util.List;
@Slf4j
@Component
public class InvenioDocumentGatewayImpl implements DocumentGateway {
- private RestTemplate restTemplate;
+ private final static String OCTET_STREAM = "application/octet-stream";
+
+ private final DocumentMapper documentMapper;
+ private final RestTemplate documentRestTemplate;
@Autowired
- public InvenioDocumentGatewayImpl(RestTemplate restTemplate) {
- this.restTemplate = restTemplate;
+ public InvenioDocumentGatewayImpl(DocumentMapper documentMapper, RestTemplate documentRestTemplate) {
+ this.documentMapper = documentMapper;
+ this.documentRestTemplate = documentRestTemplate;
}
@Override
- public DraftDto createDraft(CreateDraftDto data, String token) throws DraftRecordCreateException {
+ public RecordDto createDraft(CreateDraftDto data, String token) throws DraftRecordCreateException {
log.trace("sending {}", data);
final String url = "/api/records";
- final ResponseEntity<DraftDto> response;
+ final ResponseEntity<RecordDto> response;
try {
- response = restTemplate.exchange(url, HttpMethod.POST,
- new HttpEntity<>(data, headers(token)), DraftDto.class);
+ response = documentRestTemplate.exchange(url, HttpMethod.POST,
+ new HttpEntity<>(data, headers(token)), RecordDto.class);
} catch (HttpClientErrorException.BadRequest e) {
log.error("Failed to create draft record");
throw new DraftRecordCreateException("Failed to create draft record", e);
@@ -39,12 +52,12 @@ public class InvenioDocumentGatewayImpl implements DocumentGateway {
}
@Override
- public DraftDto reserveDraftDoi(String id, String token) throws DraftRecordCreateException {
+ public RecordDto reserveDraftDoi(String id, String token) throws DraftRecordCreateException {
final String url = "/api/records/" + id + "/draft/pids/doi";
- final ResponseEntity<DraftDto> response;
+ final ResponseEntity<RecordDto> response;
try {
- response = restTemplate.exchange(url, HttpMethod.POST,
- new HttpEntity<>(null, headers(token)), DraftDto.class);
+ response = documentRestTemplate.exchange(url, HttpMethod.POST,
+ new HttpEntity<>(null, headers(token)), RecordDto.class);
} catch (HttpClientErrorException.BadRequest e) {
log.error("Failed to reserve draft doi");
throw new DraftRecordCreateException("Failed to reserve draft doi", e);
@@ -53,12 +66,12 @@ public class InvenioDocumentGatewayImpl implements DocumentGateway {
}
@Override
- public DraftDto findDraft(String id, String token) throws DraftRecordCreateException {
+ public RecordDto findDraft(String id, String token) throws DraftRecordCreateException {
final String url = "/api/records/" + id + "/draft";
- final ResponseEntity<DraftDto> response;
+ final ResponseEntity<RecordDto> response;
try {
- response = restTemplate.exchange(url, HttpMethod.GET,
- new HttpEntity<>(null, headers(token)), DraftDto.class);
+ response = documentRestTemplate.exchange(url, HttpMethod.GET,
+ new HttpEntity<>(null, headers(token)), RecordDto.class);
} catch (HttpClientErrorException.BadRequest e) {
log.error("Failed to find draft record");
throw new DraftRecordCreateException("Failed to create find record", e);
@@ -67,24 +80,76 @@ public class InvenioDocumentGatewayImpl implements DocumentGateway {
}
@Override
- public FileStartDto startUpload(String id, String token) throws DraftRecordCreateException {
- final String url = "/api/records/" + id + "/draft/files";
- final ResponseEntity<FileStartDto> response;
+ public RecordDto publishDraft(String id, String token) throws DraftRecordCreateException {
+ final String url = "/api/records/" + id + "/draft/actions/publish";
+ final ResponseEntity<RecordDto> response;
try {
- response = restTemplate.exchange(url, HttpMethod.POST,
- new HttpEntity<>(null, headers(token)), FileStartDto.class);
+ response = documentRestTemplate.exchange(url, HttpMethod.POST,
+ new HttpEntity<>(null, headers(token)), RecordDto.class);
} catch (HttpClientErrorException.BadRequest e) {
- log.error("Failed to start draft files");
- throw new DraftRecordCreateException("Failed to start draft files", e);
+ log.error("Failed to publish draft record");
+ throw new DraftRecordCreateException("Failed to publish find record", e);
}
return response.getBody();
}
+ @Override
+ public FileDto uploadFile(String id, MultipartFile file, String token)
+ throws FileUploadException {
+ /* announce */
+ final String url1 = "/api/records/" + id + "/draft/files";
+ final List<FileKeyDto> files = List.of(documentMapper.stringToFileKeyDto(file.getName()));
+ final ResponseEntity<FileAnnounceDto> response1;
+ try {
+ response1 = documentRestTemplate.exchange(url1, HttpMethod.POST,
+ new HttpEntity<>(files, headers(token)), FileAnnounceDto.class);
+ } catch (HttpClientErrorException.BadRequest e) {
+ log.error("Failed to announce draft file");
+ throw new FileUploadException("Failed to announce draft file", e);
+ }
+ if (response1.getStatusCode() != HttpStatus.CREATED) {
+ log.error("Failed to announce file upload");
+ throw new FileUploadException("Failed to announce file upload");
+ }
+ /* upload */
+ final String url2 = "/api/records/" + id + "/draft/files/" + file.getName() + "/content";
+ final ResponseEntity<Void> response2;
+ try {
+ response2 = documentRestTemplate.exchange(url2, HttpMethod.PUT,
+ new HttpEntity<>(file.getBytes(), headers(token, OCTET_STREAM)), Void.class);
+ } catch (HttpClientErrorException.BadRequest e) {
+ log.error("Failed to upload draft file");
+ throw new FileUploadException("Failed to upload draft file", e);
+ } catch (IOException e) {
+ log.error("Failed to get draft file bytes");
+ throw new FileUploadException("Failed to get draft file bytes", e);
+ }
+ if (response2.getStatusCode() != HttpStatus.OK) {
+ log.error("Failed to upload file");
+ throw new FileUploadException("Failed to upload file");
+ }
+ /* commit */
+ final String url3 = "/api/records/" + id + "/draft/files/" + file.getName() + "/commit";
+ final ResponseEntity<FileDto> response3;
+ try {
+ response3 = documentRestTemplate.exchange(url3, HttpMethod.POST,
+ new HttpEntity<>(null, headers(token)), FileDto.class);
+ } catch (HttpClientErrorException.BadRequest e) {
+ log.error("Failed to commit draft file");
+ throw new FileUploadException("Failed to commit draft file", e);
+ }
+ if (response3.getStatusCode() != HttpStatus.OK) {
+ log.error("Failed to commit file");
+ throw new FileUploadException("Failed to commit file");
+ }
+ return response3.getBody();
+ }
+
@Override
public void delete(String id, String token) throws DraftRecordCreateException {
final String url = "/api/records" + id + "/draft";
try {
- restTemplate.exchange(url, HttpMethod.DELETE,
+ documentRestTemplate.exchange(url, HttpMethod.DELETE,
new HttpEntity<>(null, headers(token)), Void.class);
} catch (HttpClientErrorException.BadRequest e) {
log.error("Failed to delete draft record");
@@ -99,9 +164,20 @@ public class InvenioDocumentGatewayImpl implements DocumentGateway {
* @return The headers.
*/
private HttpHeaders headers(String token) {
+ return headers(token, "application/json");
+ }
+
+ /**
+ * Prepares the headers for all requests to authorize with the bearer token and content type.
+ *
+ * @param token The token.
+ * @param contentType The content type.
+ * @return The headers.
+ */
+ private HttpHeaders headers(String token, String contentType) {
final HttpHeaders headers = new HttpHeaders();
headers.add("Authorization", "Bearer " + token);
- headers.add("Content-Type", "application/json");
+ headers.add("Content-Type", contentType);
return headers;
}
}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/mapper/DocumentMapper.java b/fda-document-service/services/src/main/java/at/tuwien/mapper/DocumentMapper.java
index 0132073b62..2457da7cec 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/mapper/DocumentMapper.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/mapper/DocumentMapper.java
@@ -1,10 +1,16 @@
package at.tuwien.mapper;
+import at.tuwien.api.document.file.FileKeyDto;
import org.mapstruct.*;
@Mapper(componentModel = "spring")
public interface DocumentMapper {
+ default FileKeyDto stringToFileKeyDto(String data) {
+ return FileKeyDto.builder()
+ .key(data)
+ .build();
+ }
}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/service/DocumentService.java b/fda-document-service/services/src/main/java/at/tuwien/service/DocumentService.java
index 5d102b335c..182feb2d5b 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/service/DocumentService.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/service/DocumentService.java
@@ -1,18 +1,20 @@
package at.tuwien.service;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
import at.tuwien.exception.DraftRecordCreateException;
import java.security.Principal;
public interface DocumentService {
- DraftDto findById(String id, Principal principal) throws DraftRecordCreateException;
+ RecordDto findById(String id, Principal principal) throws DraftRecordCreateException;
- DraftDto create(CreateDraftDto data, Principal principal) throws DraftRecordCreateException;
+ RecordDto create(CreateDraftDto data, Principal principal) throws DraftRecordCreateException;
- DraftDto reserveDoi(String id, Principal principal) throws DraftRecordCreateException;
+ RecordDto publish(String id, Principal principal) throws DraftRecordCreateException;
+
+ RecordDto reserveDoi(String id, Principal principal) throws DraftRecordCreateException;
void delete(String id, Principal principal) throws DraftRecordCreateException;
}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/service/FileService.java b/fda-document-service/services/src/main/java/at/tuwien/service/FileService.java
index 5113be20f9..67fb8932b5 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/service/FileService.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/service/FileService.java
@@ -1,11 +1,17 @@
package at.tuwien.service;
-import at.tuwien.api.document.file.FileStartDto;
+import at.tuwien.api.document.file.FileDto;
+import at.tuwien.exception.FileUploadException;
+import at.tuwien.exception.CommitFileUploadException;
import at.tuwien.exception.DraftRecordCreateException;
+import org.springframework.web.multipart.MultipartFile;
import java.security.Principal;
public interface FileService {
- FileStartDto start(String id, Principal principal) throws DraftRecordCreateException;
+
+ FileDto uploadFile(String id, MultipartFile file, Principal principal)
+ throws DraftRecordCreateException, CommitFileUploadException, FileUploadException,
+ org.apache.tomcat.util.http.fileupload.FileUploadException;
}
diff --git a/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioDraftServiceImpl.java b/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioDraftServiceImpl.java
index 456fd6b540..06c038521a 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioDraftServiceImpl.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioDraftServiceImpl.java
@@ -1,7 +1,7 @@
package at.tuwien.service.impl;
import at.tuwien.api.document.record.CreateDraftDto;
-import at.tuwien.api.document.record.DraftDto;
+import at.tuwien.api.document.record.RecordDto;
import at.tuwien.config.InvenioConfig;
import at.tuwien.exception.DraftRecordCreateException;
import at.tuwien.gateway.DocumentGateway;
@@ -26,27 +26,37 @@ public class InvenioDraftServiceImpl implements DocumentService {
}
@Override
- public DraftDto findById(String id, Principal principal) throws DraftRecordCreateException {
+ public RecordDto findById(String id, Principal principal) throws DraftRecordCreateException {
/* get token */
/* remote */
return documentGateway.findDraft(id, invenioConfig.getDebugToken());
}
@Override
- public DraftDto create(CreateDraftDto data, Principal principal) throws DraftRecordCreateException {
+ public RecordDto create(CreateDraftDto data, Principal principal) throws DraftRecordCreateException {
/* get token */
/* remote */
- final DraftDto document = documentGateway.createDraft(data, invenioConfig.getDebugToken());
+ final RecordDto document = documentGateway.createDraft(data, invenioConfig.getDebugToken());
log.info("Created draft record with id {}", document.getId());
log.debug("created draft record {}", document);
return document;
}
@Override
- public DraftDto reserveDoi(String id, Principal principal) throws DraftRecordCreateException {
+ public RecordDto publish(String id, Principal principal) throws DraftRecordCreateException {
/* get token */
/* remote */
- final DraftDto document = documentGateway.reserveDraftDoi(id, invenioConfig.getDebugToken());
+ final RecordDto document = documentGateway.publishDraft(id, invenioConfig.getDebugToken());
+ log.info("Published draft record with id {}", document.getId());
+ log.debug("published draft record {}", document);
+ return document;
+ }
+
+ @Override
+ public RecordDto reserveDoi(String id, Principal principal) throws DraftRecordCreateException {
+ /* get token */
+ /* remote */
+ final RecordDto document = documentGateway.reserveDraftDoi(id, invenioConfig.getDebugToken());
log.info("Reserved DOI {} for draft record with id {}", document.getPids().getDoi(), document.getId());
log.debug("reserved PID {} for draft record with id {}", document.getPids(), document);
return document;
diff --git a/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioFileServiceImpl.java b/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioFileServiceImpl.java
index 459454f346..4110d07846 100644
--- a/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioFileServiceImpl.java
+++ b/fda-document-service/services/src/main/java/at/tuwien/service/impl/InvenioFileServiceImpl.java
@@ -1,13 +1,16 @@
package at.tuwien.service.impl;
-import at.tuwien.api.document.file.FileStartDto;
+import at.tuwien.api.document.file.FileDto;
import at.tuwien.config.InvenioConfig;
+import at.tuwien.exception.FileUploadException;
+import at.tuwien.exception.CommitFileUploadException;
import at.tuwien.exception.DraftRecordCreateException;
import at.tuwien.gateway.DocumentGateway;
import at.tuwien.service.FileService;
import lombok.extern.slf4j.Slf4j;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
+import org.springframework.web.multipart.MultipartFile;
import java.security.Principal;
@@ -25,12 +28,14 @@ public class InvenioFileServiceImpl implements FileService {
}
@Override
- public FileStartDto start(String id, Principal principal) throws DraftRecordCreateException {
+ public FileDto uploadFile(String id, MultipartFile file, Principal principal)
+ throws DraftRecordCreateException, CommitFileUploadException, FileUploadException,
+ org.apache.tomcat.util.http.fileupload.FileUploadException {
/* get token */
/* remote */
- final FileStartDto document = documentGateway.startUpload(id, invenioConfig.getDebugToken());
- log.info("Started draft files with id {}", id);
- log.debug("started draft files {}", document);
+ final FileDto document = documentGateway.uploadFile(id, file, invenioConfig.getDebugToken());
+ log.info("Deposited draft file content for record with id {}", id);
+ log.debug("Deposited draft file content for record {}", document);
return document;
}
diff --git a/fda-gateway-service/gateway/src/main/java/at/tuwien/gatewayservice/config/GatewayConfig.java b/fda-gateway-service/gateway/src/main/java/at/tuwien/gatewayservice/config/GatewayConfig.java
index 040bbb0e96..27a3863e80 100644
--- a/fda-gateway-service/gateway/src/main/java/at/tuwien/gatewayservice/config/GatewayConfig.java
+++ b/fda-gateway-service/gateway/src/main/java/at/tuwien/gatewayservice/config/GatewayConfig.java
@@ -56,6 +56,11 @@ public class GatewayConfig {
.method("POST", "GET", "PUT", "DELETE")
.and()
.uri("lb://fda-units-service"))
+ .route("fda-document-service", r -> r.path("/api/document/**")
+ .and()
+ .method("POST", "GET", "PUT", "DELETE")
+ .and()
+ .uri("lb://fda-document-service"))
.build();
}
diff --git a/fda-identifier-service/rest-service/src/main/java/at/tuwien/FdaIdentifierServiceApplication.java b/fda-identifier-service/rest-service/src/main/java/at/tuwien/FdaIdentifierServiceApplication.java
index 185a41efc0..56712b0f03 100644
--- a/fda-identifier-service/rest-service/src/main/java/at/tuwien/FdaIdentifierServiceApplication.java
+++ b/fda-identifier-service/rest-service/src/main/java/at/tuwien/FdaIdentifierServiceApplication.java
@@ -8,7 +8,6 @@ import org.springframework.data.jpa.repository.config.EnableJpaAuditing;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.transaction.annotation.EnableTransactionManagement;
-
@SpringBootApplication
@EnableJpaAuditing
@EnableTransactionManagement
diff --git a/fda-identifier-service/rest-service/src/main/resources/application.yml b/fda-identifier-service/rest-service/src/main/resources/application.yml
index 11335fa111..e71ce69b3f 100644
--- a/fda-identifier-service/rest-service/src/main/resources/application.yml
+++ b/fda-identifier-service/rest-service/src/main/resources/application.yml
@@ -22,6 +22,7 @@ logging:
level:
root: warn
at.tuwien.: debug
+ at.tuwien.gateway.: trace
org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver: debug
eureka:
instance.hostname: fda-identifier-service
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileAnnounceDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileAnnounceDto.java
new file mode 100644
index 0000000000..c2941ccdec
--- /dev/null
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileAnnounceDto.java
@@ -0,0 +1,37 @@
+
+package at.tuwien.api.document.file;
+
+import at.tuwien.api.document.links.LinksDto;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import io.swagger.v3.oas.annotations.Parameter;
+import lombok.*;
+
+import javax.validation.constraints.NotNull;
+import java.util.List;
+
+@Getter
+@Setter
+@ToString
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class FileAnnounceDto {
+
+ @JsonProperty("default_preview")
+ @Parameter(name = "file name")
+ private String defaultPreview;
+
+ @NotNull
+ @Parameter(name = "file enabled")
+ private Boolean enabled;
+
+ @NotNull
+ @Parameter(name = "file entries")
+ private List<FileEntryDto> entries;
+
+ @Parameter(name = "file links")
+ private LinksDto links;
+
+}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileDto.java
new file mode 100644
index 0000000000..63f820e372
--- /dev/null
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileDto.java
@@ -0,0 +1,72 @@
+package at.tuwien.api.document.file;
+
+import at.tuwien.api.document.links.LinksDto;
+import com.fasterxml.jackson.annotation.JsonFormat;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import io.swagger.v3.oas.annotations.Parameter;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+import java.time.Instant;
+
+
+@Getter
+@Setter
+@ToString
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class FileDto {
+
+ @NotBlank
+ @JsonProperty("bucket_id")
+ @Parameter(name = "bucket id", description = "Bucket id.")
+ private String bucketId;
+
+ @NotBlank
+ @Parameter(name = "file checksum", description = "File checksum.", example = "md5:ef8fcf1f046bb24f1db1f1a376ddbfbb")
+ private String checksum;
+
+ @NotNull
+ @JsonFormat(pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSXXX", timezone = "UTC+2")
+ @Parameter(name = "file creation timestamp")
+ private Instant created;
+
+ @NotNull
+ @JsonFormat(pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSXXX", timezone = "UTC+2")
+ @Parameter(name = "file updated timestamp")
+ private Instant updated;
+
+ @NotBlank
+ @JsonProperty("file_id")
+ @Parameter(name = "file id")
+ private String fileId;
+
+ @NotBlank
+ @Parameter(name = "file key", example = "mock.png")
+ private String key;
+
+ @NotNull
+ @Parameter(name = "file links")
+ private LinksDto links;
+
+ @Parameter(name = "file mimetype")
+ private String mimetype;
+
+ @Parameter(name = "file size")
+ private Long size;
+
+ @Parameter(name = "file status")
+ private String status;
+
+ @JsonProperty("storage_class")
+ @Parameter(name = "file storage class", example = "S")
+ private String storageClass;
+
+ @JsonProperty("version_id")
+ @Parameter(name = "file version id")
+ private String versionId;
+}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileEntryDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileEntryDto.java
new file mode 100644
index 0000000000..d4c7909d5a
--- /dev/null
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileEntryDto.java
@@ -0,0 +1,43 @@
+
+package at.tuwien.api.document.file;
+
+import at.tuwien.api.document.links.LinksDto;
+import com.fasterxml.jackson.annotation.JsonFormat;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import io.swagger.v3.oas.annotations.Parameter;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+import java.time.Instant;
+
+@Getter
+@Setter
+@ToString
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class FileEntryDto {
+
+ @NotBlank
+ @Parameter(name = "file name", description = "Name of the file.")
+ private String key;
+
+ @NotNull
+ @JsonFormat(pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSXXX", timezone = "UTC+2")
+ @Parameter(name = "file updated")
+ private Instant updated;
+
+ @NotNull
+ @JsonFormat(pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSXXX", timezone = "UTC+2")
+ @Parameter(name = "file created")
+ private Instant created;
+
+ @Parameter(name = "file status")
+ private String status;
+
+ @Parameter(name = "file links")
+ private LinksDto links;
+
+}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileKeyDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileKeyDto.java
new file mode 100644
index 0000000000..79c7f3d7b7
--- /dev/null
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/file/FileKeyDto.java
@@ -0,0 +1,23 @@
+
+package at.tuwien.api.document.file;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import io.swagger.v3.oas.annotations.Parameter;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+
+@Getter
+@Setter
+@ToString
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class FileKeyDto {
+
+ @NotBlank
+ @Parameter(name = "file name", description = "Name of the file.", example = "mock.png")
+ private String key;
+
+}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/DraftDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/RecordDto.java
similarity index 98%
rename from fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/DraftDto.java
rename to fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/RecordDto.java
index d754f22fce..0f41c523bb 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/DraftDto.java
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/document/record/RecordDto.java
@@ -18,7 +18,7 @@ import java.time.Instant;
@AllArgsConstructor
@NoArgsConstructor
@JsonInclude(JsonInclude.Include.NON_NULL)
-public class DraftDto {
+public class RecordDto {
@NotNull(message = "access is required")
@Parameter(name = "access")
diff --git a/fda-ui/server-middleware/index.js b/fda-ui/server-middleware/index.js
index b74dab0892..819f649f24 100644
--- a/fda-ui/server-middleware/index.js
+++ b/fda-ui/server-middleware/index.js
@@ -25,6 +25,7 @@ app.post('/table_from_csv', upload.single('file'), async (req, res) => {
// send path to analyse service
let analysis
+ let json
try {
const analyseUrl = `${process.env.API}/api/analyse/determinedt`
analysis = await fetch(analyseUrl, {
@@ -35,9 +36,8 @@ app.post('/table_from_csv', upload.single('file'), async (req, res) => {
console.error('data type determination failed', error)
throw error
})
- const json = await analysis.json()
- analysis = JSON.parse(json)
- if (!analysis.columns) {
+ json = await analysis.json()
+ if (!json.columns) {
return res.json({ success: false, message: 'Columns array missing' })
}
} catch (error) {
@@ -47,7 +47,7 @@ app.post('/table_from_csv', upload.single('file'), async (req, res) => {
// map messytables / CoMi's `determine_dt` column types to ours
// e.g. "Integer" -> "NUMBER"
- let entries = Object.entries(analysis.columns)
+ let entries = Object.entries(json.columns)
entries = entries.map(([k, v]) => {
if (colTypeMap[v]) {
v = colTypeMap[v]
--
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