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TreeController.cs
L. Ellenbeck authored and
Petar Hristov
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TreeController.cs 26.53 KiB
using Coscine.Api.Tree.Util;
using Coscine.ApiCommons;
using Coscine.ApiCommons.Factories;
using Coscine.Configuration;
using Coscine.Database.DataModel;
using Coscine.Database.Models;
using Coscine.Database.Util;
using Coscine.Logging;
using Coscine.Metadata;
using Coscine.ResourceTypes;
using Coscine.ResourceTypes.Base;
using Coscine.ResourceTypes.Base.Models;
using Coscine.WaterbutlerHelper;
using Coscine.WaterbutlerHelper.ReturnObjects;
using Microsoft.AspNetCore.Authorization;
using Microsoft.AspNetCore.Mvc;
using Microsoft.Extensions.Logging;
using Newtonsoft.Json.Linq;
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text.RegularExpressions;
using System.Threading.Tasks;
using System.Web;
using VDS.RDF;
using VDS.RDF.Parsing;
namespace Coscine.Api.Tree.Controllers
{
/// <summary>
/// This controller represents the actions which can be taken with a tree object.
/// </summary>
[Authorize]
public class TreeController : Controller
{
private readonly Authenticator _authenticator;
private readonly ResourceModel _resourceModel;
private readonly RdfStoreConnector _rdfStoreConnector;
private readonly ProjectRoleModel _projectRoleModel;
private readonly ProjectResourceModel _projectResourceModel;
private readonly CoscineLogger _coscineLogger;
private readonly string _blobApiLink;
private readonly string _prefix;
private readonly IConfiguration _configuration;
private readonly string _shaclPropertyUrl = "http://www.w3.org/ns/shacl#property";
/// <summary>
/// Tree controller constructor
/// </summary>
/// <param name="logger">Logger</param>
public TreeController(ILogger<TreeController> logger)
{
_configuration = Program.Configuration;
_authenticator = new Authenticator(this, _configuration);
_resourceModel = new ResourceModel();
_rdfStoreConnector = new RdfStoreConnector(_configuration.GetStringAndWait("coscine/local/virtuoso/additional/url"));
_projectRoleModel = new ProjectRoleModel();
_projectResourceModel = new ProjectResourceModel();
_coscineLogger = new CoscineLogger(logger);
var rule = _configuration.GetStringAndWait("traefik/frontends/Coscine.Api.Blob/routes/Coscine.Api.Blob/rule");
var host = rule["Host:".Length..rule.IndexOf(";")];
var path = rule[rule.IndexOf("/")..];
_blobApiLink = $"https://{host}{path}/blob/";
_prefix = _configuration.GetStringAndWait("coscine/global/epic/prefix");
}
/// <summary>
/// Generates Id /// </summary>
/// <param name="resourceId">Id of the resource</param>
/// <param name="path"> Path to file</param>
/// <returns> Uri </returns>
public Uri GenerateId(string resourceId, string path)
{
if (!path.StartsWith("/"))
{
path = "/" + path;
}
return new CustomUri($"https://hdl.handle.net/{_prefix}/{resourceId}@path={Uri.EscapeDataString(path)}");
}
/// <summary>
/// This method retrieves the metadata
/// </summary>
/// <param name="resourceId"> Id of a resource</param>
/// <param name="path">Path to the file</param>
/// <returns> JSON Object with the metadata if OK, otherwise status code 400 or 401 or 404</returns>
[HttpGet("[controller]/{resourceId}/{*path}")]
[ApiExplorerSettings(IgnoreApi = true)]
public async Task<IActionResult> GetMetadataWithPath(string resourceId, string path = "")
{
return await GetMetadata(resourceId, path);
}
/// <summary>
/// This method retrieves the metadata
/// </summary>
/// <param name="resourceId"> Id of a resource</param>
/// <param name="path">Path to the file</param>
/// <param name="mimeType">Requested MimeType of the metadata</param>
/// <returns> JSON Object with the metadata if OK, otherwise status code 400 or 401 or 404</returns>
[HttpGet("[controller]/{resourceId}/")]
public async Task<IActionResult> GetMetadataWithParameter(string resourceId, [FromQuery] string path = "", [FromQuery] string mimeType = "application/rdf+json")
{
// Strip the first slash, to reuse the previous implementation.
if (path.StartsWith("/"))
{
path = path[1..];
}
return await GetMetadata(resourceId, path, mimeType);
}
/// <summary>
/// This method retrieves the metadata
/// </summary>
/// <param name="resourceId"> Id of a resource</param>
/// <param name="path">Path to the file</param>
/// <param name="mimeType">Requested MimeType of the metadata</param>
/// <returns> JSON Object with the metadata if OK, otherwise status code 400 or 401 or 404</returns>
public async Task<IActionResult> GetMetadata(string resourceId, string path = "", string mimeType = "application/rdf+json")
{
if (path.Contains("%2F") || path.Contains("%2f"))
{
return BadRequest("Path can not contain the sequence %2F.");
}
var user = _authenticator.GetUser();
var check = CheckResourceIdAndPath(resourceId, $"/{path}", out Resource resource);
if (check != null)
{
return check;
}
if (resource.ApplicationProfile[^1] != '/')
{
resource.ApplicationProfile += '/'; }
if (user == null || !_resourceModel.HasAccess(user, resource, UserRoles.Owner, UserRoles.Member))
{
return BadRequest("User has no Access to this resource.");
}
try
{
var resourceTypeDefinition = ResourceTypeFactory.Instance.GetResourceType(resource);
if (resourceTypeDefinition == null)
{
return BadRequest($"No provider for: \"{resource.Type.DisplayName}\".");
}
var fileInfos = await resourceTypeDefinition.ListEntries(resourceId, path);
var resourceTypeInformation = resourceTypeDefinition.GetResourceTypeInformation().Result;
var metadataInfos = new List<ResourceEntry>(fileInfos);
// Add to metadata infos, if no "physical" file for it exists
if (!metadataInfos.Any((metadataInfo) => metadataInfo.Key == path))
{
metadataInfos.Add(new ResourceEntry(path, true, 0, GenerateId(resourceId, path).AbsoluteUri, null, DateTime.Now, DateTime.Now));
}
var applicationProfileGraph = _rdfStoreConnector.GetGraph(resource.ApplicationProfile);
var propertyTriples = applicationProfileGraph.GetTriplesWithPredicate(applicationProfileGraph.CreateUriNode(new Uri("http://www.w3.org/ns/shacl#property")));
var properties = propertyTriples.Select((propertyTriple) => applicationProfileGraph.GetTriplesWithSubject(propertyTriple.Object));
var graphs = new List<object>();
int metadataCount = 0;
foreach (var info in metadataInfos)
{
var id = GenerateId(resourceId, info.Key);
if (_rdfStoreConnector.HasGraph(id.AbsoluteUri))
{
var graph = _rdfStoreConnector.GetGraph(id);
// Rewrite the datatype since Virtuoso might convert e.g. decimals to integers
foreach (var property in properties)
{
var shPath = property.FirstOrDefault((triple) => triple.Predicate.ToString() == "http://www.w3.org/ns/shacl#path");
if (shPath != null)
{
var values = graph.GetTriplesWithPredicate(shPath.Object);
var shDatatype = property.FirstOrDefault((triple) => triple.Predicate.ToString() == "http://www.w3.org/ns/shacl#datatype");
if (shDatatype != null)
{
foreach (var value in values)
{
graph.Retract(value);
graph.Assert(
value.Subject,
value.Predicate,
graph.CreateLiteralNode((value.Object as LiteralNode)?.Value, new Uri(shDatatype.Object.ToString()))
);
}
}
}
}
metadataCount = graph.Triples.Count;
var writer = MimeTypesHelper.GetWriter(new List<string>() { mimeType });
var parsedRdf = VDS.RDF.Writing.StringWriter.Write(graph, writer);
// Legacy Support
if (mimeType == "application/rdf+json")
{
graphs.Add(JToken.Parse(parsedRdf));
}
else {
graphs.Add(new JObject
{
[id.AbsoluteUri] = parsedRdf
});
}
}
}
var jObject = new JObject(
new JProperty("data", new JObject(
new JProperty("metadataStorage", JToken.FromObject(graphs)),
new JProperty("fileStorage",
JToken.FromObject(fileInfos.Select(x =>
{
var objectMetaInfo = new ObjectMetaInfo
{
Name = x.Key.Split("/", StringSplitOptions.RemoveEmptyEntries).Last(),
Path = x.Key,
Size = x.BodyBytes,
Kind = x.HasBody ? "file" : "folder",
Provider = resource.Type.DisplayName
};
var objectMetaInfoReturnObject = new ObjectMetaInfoReturnObject(objectMetaInfo, _blobApiLink, resource.Id.ToString());
var obj = new JObject
{
["Name"] = objectMetaInfoReturnObject.Name,
["Path"] = objectMetaInfoReturnObject.Path,
["Size"] = objectMetaInfoReturnObject.Size,
["Kind"] = objectMetaInfoReturnObject.Kind,
["Modified"] = x.HasBody ? x.Modified : null,
["Created"] = x.HasBody ? x.Created : null,
["Provider"] = objectMetaInfoReturnObject.Provider,
["IsFolder"] = !x.HasBody,
["IsFile"] = x.HasBody,
["Action"] = new JObject()
};
if (resourceTypeInformation.CanCreateLinks)
{
obj["Action"] = new JObject
{
["Delete"] = new JObject
{
["Method"] = "DELETE",
["Url"] = resourceTypeDefinition?.GetPresignedUrl(resource.Id.ToString(), objectMetaInfoReturnObject.Path, CoscineHttpVerb.DELETE).Result?.ToString()
},
["Download"] = new JObject
{
["Method"] = "GET",
["Url"] = resourceTypeDefinition?.GetPresignedUrl(resource.Id.ToString(), objectMetaInfoReturnObject.Path, CoscineHttpVerb.GET).Result?.ToString()
},
["Upload"] = new JObject
{
["Method"] = "PUT",
["Url"] = resourceTypeDefinition?.GetPresignedUrl(resource.Id.ToString(), objectMetaInfoReturnObject.Path, CoscineHttpVerb.DELETE).Result?.ToString()
}
};
}
return obj;
})))
))
);
if (CoscineLoggerConfiguration.IsLogLevelActivated(LogType.Analytics) && path != "/")
{
LogAnalyticsViewMd(_projectResourceModel.GetProjectForResource(resource.Id).Value, resource.Id, $"/{path}", user, GetMetadataCompleteness(metadataCount, resource));
}
return Json(jObject);
}
catch (Exception)
{
return BadRequest("Error in communication with the resource");
}
}
/// <summary>
/// This method stores the metadata of the file
/// </summary>
/// <param name="resourceId">Id of the resource</param>
/// <param name="path">Path to the file</param>
/// <returns>If OK status code 204, otherwise status code 400 or 401</returns>
[HttpPut("[controller]/{resourceId}/{*path}")]
[ApiExplorerSettings(IgnoreApi = true)]
public IActionResult StoreMetadataForFileWithPath(string resourceId, string path)
{
return StoreMetadataForFile(resourceId, path);
}
/// <summary>
/// This method stores the metadata of the file
/// </summary>
/// <param name="resourceId">Id of the resource</param>
/// <param name="path">Path to the file</param>
/// <param name="mimeType">Requested MimeType of the metadata</param>
/// <returns>If OK status code 204, otherwise status code 400 or 401</returns>
[HttpPut("[controller]/{resourceId}/")]
public IActionResult StoreMetadataForFileWithParameter(string resourceId, [FromQuery] string path = "", [FromQuery] string mimeType = "application/rdf+json")
{
// Strip the first slash, to reuse the previous implementation.
if (path.StartsWith("/"))
{
path = path[1..];
}
return StoreMetadataForFile(resourceId, path, mimeType);
}
/// <summary>
/// This method stores the metadata of the file
/// </summary>
/// <param name="resourceId">Id of the resource</param>
/// <param name="path">Path to the file</param>
/// <param name="mimeType">Requested MimeType of the metadata</param>
/// <returns>If OK status code 204, otherwise status code 400 or 401</returns>
public IActionResult StoreMetadataForFile(string resourceId, string path, string mimeType = "application/rdf+json")
{
path = $"/{path}";
if (path.Contains("%2F") || path.Contains("%2f"))
{
return BadRequest("Path can not contain the sequence %2F.");
}
// Ducktape solution for supporting multiple mimetypes
var metadataObject = ObjectFactory<JToken>.DeserializeFromStream(Request.Body);
var graphNameUri = GenerateId(resourceId, path);
JObject json;
// Legacy Support
if (mimeType == "application/rdf+json")
{
json = new JObject
{
[graphNameUri.AbsoluteUri] = metadataObject
};
} else
{
var tempGraph = new Graph();
StringParser.Parse(tempGraph, metadataObject.Value<string>("metadata"), MimeTypesHelper.GetParser(mimeType));
var triplesList = tempGraph.Triples.ToArray();
var subjectNode = tempGraph.CreateUriNode(graphNameUri);
foreach (var triple in triplesList)
{
tempGraph.Retract(triple);
tempGraph.Assert(new Triple(subjectNode, triple.Predicate, triple.Object));
}
json = JObject.Parse(VDS.RDF.Writing.StringWriter.Write(tempGraph, MimeTypesHelper.GetWriter("application/rdf+json")));
}
var user = _authenticator.GetUser();
var resource = _resourceModel.GetById(Guid.Parse(resourceId));
if (user == null || !_resourceModel.HasAccess(user, resource, UserRoles.Owner, UserRoles.Member))
{
return BadRequest("User is no project member!");
}
if (resource.Archived == "1")
{
return BadRequest("The resource is read only!");
}
if (resource.ApplicationProfile[^1] != '/')
{
resource.ApplicationProfile += '/';
}
json[graphNameUri.AbsoluteUri]["http://www.w3.org/1999/02/22-rdf-syntax-ns#type"] = new JArray
{
new JObject
{
["value"] = resource.ApplicationProfile,
["type"] = "uri"
}
};
// throw bad request if empty node value is detected
foreach (var node in json.First.First)
{
string nodeValue = node.First.First["value"].ToString().ToLower();
if (string.IsNullOrEmpty(nodeValue))
{
return BadRequest("Empty values in application profile are not accepted.");
}
}
var graph = new Graph();
graph.LoadFromString(json.ToString(), new RdfJsonParser());
var fixedValuesGraph = new Graph();
fixedValuesGraph.LoadFromString(resource.FixedValues, new RdfJsonParser());
var shapesGraph = (Graph)_rdfStoreConnector.GetGraph(resource.ApplicationProfile);
foreach (var triple in fixedValuesGraph.Triples.Where(x => x.Predicate.ToString() == "https://purl.org/coscine/fixedValue"))
{
var shapeTriples = shapesGraph.Triples.Where((shapeTriple) =>
shapeTriple.Object.ToString() == triple.Subject.ToString()
&& shapeTriple.Predicate.ToString() == "http://www.w3.org/ns/shacl#path");
var entry = shapeTriples.First();
// Remove any existing triples
foreach (var triple2 in graph.GetTriplesWithSubjectPredicate(graph.CreateUriNode(graphNameUri), entry.Object).ToList())
{ graph.Retract(triple2);
}
var tripleObject = triple.Object;
if (tripleObject is ILiteralNode)
{
var tripleObjectString = (tripleObject as ILiteralNode)?.Value;
if (tripleObjectString.Equals("{ME}"))
{
tripleObjectString = tripleObjectString.Replace("{ME}", user.DisplayName);
tripleObject = graph.CreateLiteralNode(tripleObjectString, new Uri(XmlSpecsHelper.XmlSchemaDataTypeString));
}
else if (tripleObjectString.Equals("{TODAY}"))
{
tripleObjectString = tripleObjectString.Replace("{TODAY}", DateTime.Today.ToString("yyyy-MM-dd"));
tripleObject = graph.CreateLiteralNode(tripleObjectString, new Uri(XmlSpecsHelper.XmlSchemaDataTypeDate));
}
}
graph.Assert(graph.CreateUriNode(graphNameUri), entry.Object, tripleObject);
}
// Default values is not checked or added
// validate the data
if (!_rdfStoreConnector.ValidateShacl(graph, graphNameUri))
{
return BadRequest("Data has the wrong format!");
}
// store the data
if (_rdfStoreConnector.HasGraph(graphNameUri))
{
_rdfStoreConnector.ClearGraph(graphNameUri);
if (CoscineLoggerConfiguration.IsLogLevelActivated(LogType.Analytics))
{
LogAnalyticsUpdateMd(_projectResourceModel.GetProjectForResource(resource.Id).Value, resource.Id, path, user, GetMetadataCompleteness(graph.Triples.Count, resource));
}
}
else
{
try
{
_rdfStoreConnector.CreateNamedGraph(graphNameUri);
}
#pragma warning disable RCS1075 // Avoid empty catch clause that catches System.Exception.
catch (Exception)
#pragma warning restore RCS1075 // Avoid empty catch clause that catches System.Exception.
{
// Graph creation failed because it has been created before, skip this for now
}
if (CoscineLoggerConfiguration.IsLogLevelActivated(LogType.Analytics))
{
LogAnalyticsUploadMd(_projectResourceModel.GetProjectForResource(resource.Id).Value, resource.Id, path, user, GetMetadataCompleteness(graph.Triples.Count, resource));
}
}
// BaseUri must be set for the sparql query
graph.BaseUri = graphNameUri;
_rdfStoreConnector.AddGraph(graph);
return NoContent();
}
/// <summary>
/// Checks the resource Id and the path
/// </summary>
/// <param name="resourceId">Id of the resource</param>
/// <param name="path">Path to the file</param> /// <param name="resource">Resource</param>
/// <returns>null, otherwise status code 400 or 404 </returns>
private IActionResult CheckResourceIdAndPath(string resourceId, string path, out Resource resource)
{
resource = null;
if (string.IsNullOrWhiteSpace(path))
{
return BadRequest($"Your path \"{path}\" is empty.");
}
var rgx = new Regex(@"[\:?*<>|]+");
if (rgx.IsMatch(path))
{
return BadRequest($"Your path \"{path}\" contains bad characters. The following characters are not permissible: {@"\/:?*<>|"}.");
}
if (!Guid.TryParse(resourceId, out Guid resourceGuid))
{
return BadRequest($"{resourceId} is not a GUID.");
}
try
{
resource = _resourceModel.GetById(resourceGuid);
if (resource == null)
{
return NotFound($"Could not find resource with id: {resourceId}");
}
}
catch (Exception)
{
return NotFound($"Could not find resource with id: {resourceId}");
}
if (resource.Type == null)
{
var resourceTypeModel = new ResourceTypeModel();
resource.Type = resourceTypeModel.GetById(resource.TypeId);
}
// All good
return null;
}
private void LogAnalyticsViewMd(Guid projectId, Guid resourceId, string filename, User user, string metadataCompletness)
{
var analyticsLogObject = new AnalyticsLogObject
{
Type = "Action",
Operation = "View MD",
RoleId = _projectRoleModel.GetGetUserRoleForProject(projectId, user.Id).ToString(),
ProjectId = projectId.ToString(),
ResourceId = resourceId.ToString(),
FileId = resourceId.ToString() + "/" + HttpUtility.UrlDecode(filename)[1..],
ApplicationsProfile = _resourceModel.CreateReturnObjectFromDatabaseObject(_resourceModel.GetById(resourceId)).ApplicationProfile,
MetadataCompleteness = metadataCompletness,
};
_coscineLogger.AnalyticsLog(analyticsLogObject);
}
private void LogAnalyticsUploadMd(Guid projectId, Guid resourceId, string filename, User user, string metadataCompletness)
{
var analyticsLogObject = new AnalyticsLogObject
{
Type = "Action",
Operation = "Upload MD",
RoleId = _projectRoleModel.GetGetUserRoleForProject(projectId, user.Id).ToString(),
ProjectId = projectId.ToString(), ResourceId = resourceId.ToString(),
FileId = resourceId.ToString() + "/" + HttpUtility.UrlDecode(filename)[1..],
ApplicationsProfile = _resourceModel.CreateReturnObjectFromDatabaseObject(_resourceModel.GetById(resourceId)).ApplicationProfile,
MetadataCompleteness = metadataCompletness,
};
_coscineLogger.AnalyticsLog(analyticsLogObject);
}
private void LogAnalyticsUpdateMd(Guid projectId, Guid resourceId, string filename, User user, string metadataCompletness)
{
var analyticsLogObject = new AnalyticsLogObject
{
Type = "Action",
Operation = "Update MD",
RoleId = _projectRoleModel.GetGetUserRoleForProject(projectId, user.Id).ToString(),
ProjectId = projectId.ToString(),
ResourceId = resourceId.ToString(),
FileId = resourceId.ToString() + "/" + HttpUtility.UrlDecode(filename)[1..],
ApplicationsProfile = _resourceModel.CreateReturnObjectFromDatabaseObject(_resourceModel.GetById(resourceId)).ApplicationProfile,
MetadataCompleteness = metadataCompletness,
};
_coscineLogger.AnalyticsLog(analyticsLogObject);
}
private string GetMetadataCompleteness(int metadataCount, Resource resource)
{
var shapesGraph = _rdfStoreConnector.GetGraph(resource.ApplicationProfile);
var nodeFactory = new NodeFactory();
var uriNode = (UriNode)nodeFactory.CreateUriNode(new Uri(_shaclPropertyUrl));
var total = shapesGraph.GetTriplesWithPredicate(uriNode).Count();
var present = metadataCount;
return $"{present}/{total}";
}
}
}