TreeController.cs

using Coscine.WaterbutlerHelper;
using Coscine.WaterbutlerHelper.ReturnObjects;
using Coscine.WaterbutlerHelper.Services;
using Coscine.ApiCommons;
using Coscine.ApiCommons.Factories;
using Coscine.Database.DataModel;
using Coscine.Database.Models;
using Coscine.Database.Util;
using Coscine.Logging;
using Coscine.Metadata;
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;
using VDS.RDF.Writing;

namespace Coscine.Api.Tree.Controllers
{
    [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 AnalyticsLogObject _analyticsLogObject;
        private readonly IDataSourceService _dataSourceService;
        private readonly WaterbutlerInterface _waterbutlerInterface;
        private readonly string _blobApiLink;
        private readonly string _prefix;

        public TreeController(ILogger<TreeController> logger, IDataSourceService dataSourceService)
        {
            _authenticator = new Authenticator(this, Program.Configuration);
            _resourceModel = new ResourceModel();
            _rdfStoreConnector = new RdfStoreConnector(Program.Configuration.GetStringAndWait("coscine/local/virtuoso/additional/url"));
            _projectRoleModel = new ProjectRoleModel();
            _projectResourceModel = new ProjectResourceModel();

            _coscineLogger = new CoscineLogger(logger);
            _analyticsLogObject = new AnalyticsLogObject();
            _dataSourceService = dataSourceService;
            _waterbutlerInterface = new WaterbutlerInterface(Program.Configuration, _dataSourceService);

            var rule = Program.Configuration.GetStringAndWait("traefik/frontends/Coscine.Api.Blob/routes/Coscine.Api.Blob/rule");
            var host = rule.Substring("Host:".Length, rule.IndexOf(";") - "Host:".Length);
            var path = rule.Substring(rule.IndexOf("/"));
            _blobApiLink = $"https://{host}{path}/blob/";
            _prefix = Program.Configuration.GetStringAndWait("coscine/global/epic/prefix");
        }

        public Uri GenerateId(string resourceId, string path)
        {
            return new Uri($"https://hdl.handle.net/{_prefix}/{resourceId}@path={Uri.EscapeDataString(path)}");
        }

        [HttpGet("[controller]/{resourceId}/{*path}")]
        public async Task<IActionResult> GetMetadata(string resourceId, string path)
        {
            path = $"/{path}";
            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 (user == null || !_resourceModel.HasAccess(user, resource, UserRoles.Owner, UserRoles.Member))
            {
                return Forbid("User has no Access to this resource.");
            }

            if (check != null)
            {
                return check;
            }

            var resourceTypeOptions = new Dictionary<string, string>();
            if (resource.Type.DisplayName == "rds")
            {
                var data = new RDSResourceTypeModel().GetById((Guid)resource.ResourceTypeOptionId);
                resourceTypeOptions.Add("bucketname", data.BucketName);
            }
            else if (resource.Type.DisplayName == "s3")
            {
                var data = new S3ResourceTypeModel().GetById((Guid)resource.ResourceTypeOptionId);
                resourceTypeOptions.Add("accessKey", data.AccessKey);
                resourceTypeOptions.Add("secretKey", data.SecretKey);
                resourceTypeOptions.Add("bucketname", data.BucketName);
                resourceTypeOptions.Add("resourceUrl", data.ResourceUrl);
            }
            else if (resource.Type.DisplayName == "gitlab")
            {
                var data = new GitlabResourceTypeModel().GetById((Guid)resource.ResourceTypeOptionId);
                resourceTypeOptions.Add("token", data.Token);
                resourceTypeOptions.Add("repositoryUrl", data.RepositoryUrl);
                resourceTypeOptions.Add("repositoryNumber", data.RepositoryNumber.ToString());
            }
            var authHeader = _waterbutlerInterface.BuildAuthHeader(resource.Type.DisplayName, resourceTypeOptions);

            if (authHeader == null)
            {
                return BadRequest($"No provider for: \"{resource.Type.DisplayName}\".");
            }

            var provider = GetResourceTypeName(resource);
            var infos = await _waterbutlerInterface.GetObjectInfoAsync(path, provider, authHeader);

            // Not found
            if (infos == null)
            {
                return NotFound($"Found nothing in waterbutler under \"{path}\".");
            }

            var graphs = new List<JToken>();

            foreach (var info in infos)
            {
                var id = GenerateId(resourceId, info.Path);
                if (_rdfStoreConnector.HasGraph(id.AbsoluteUri))
                {
                    var graph = _rdfStoreConnector.GetGraph(id);
                    graphs.Add(JToken.Parse(VDS.RDF.Writing.StringWriter.Write(graph, new RdfJsonWriter())));
                }
            }

            var jObject = new JObject(
                new JProperty("data", new JObject(
                    new JProperty("metadataStorage", JToken.FromObject(graphs)),
                    new JProperty("fileStorage", JToken.FromObject(infos.Select( x => new ObjectMetaInfoReturnObject(x, _blobApiLink, resource.Id.ToString()))))
                    ))
                );

            LogAnalytics("View MD", resourceId, path, user);
            return Json(jObject);
        }

        [HttpPut("[controller]/{resourceId}/{*path}")]
        public IActionResult StoreMetadataForFile(string resourceId, string path)
        {
            path = $"/{path}";
            if (path.Contains("%2F") || path.Contains("%2f"))
            {
                return BadRequest("Path can not contain the sequence %2F.");
            }

            var innerBlock = ObjectFactory<JToken>.DeserializeFromStream(Request.Body);
            var graphNameUri = GenerateId(resourceId, path);

            var json = new JObject
            {
                [graphNameUri.AbsoluteUri] = innerBlock
            };

            var user = _authenticator.GetUser();
            var resource = _resourceModel.GetById(Guid.Parse(resourceId));

            if (user == null || !_resourceModel.HasAccess(user, resource, UserRoles.Owner, UserRoles.Member))
            {
                return Forbid("User is no project member!");
            }

            if (resource.ApplicationProfile[resource.ApplicationProfile.Length - 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
            JToken root = json.First.First;
            foreach (var node in root)
            {
                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.Subject.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;
                var tripleObjectString = tripleObject.ToString();
                if (tripleObjectString == "{ME}")
                {
                    tripleObjectString = tripleObjectString.Replace("{ME}", user.DisplayName);
                    tripleObject = graph.CreateLiteralNode(tripleObjectString, new Uri(XmlSpecsHelper.XmlSchemaDataTypeString));
                }
                else if (tripleObjectString == "{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);
                LogAnalytics("Update MD", resourceId, path, user);
            }
            else
            {
                _rdfStoreConnector.CreateNamedGraph(graphNameUri);
                LogAnalytics("Upload MD", resourceId, path, user);
            }

            // BaseUri must be set for the sparql query
            graph.BaseUri = graphNameUri;
            _rdfStoreConnector.AddGraph(graph);

            return NoContent();

        }

        private IActionResult CheckResourceIdAndPath(string resourceId, string path, out Resource resource)
        {
            resource = null;

            if (string.IsNullOrWhiteSpace(path))
            {
                return BadRequest($"Your path \"{path}\" is empty.");
            }

            Regex 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)
            {
                ResourceTypeModel resourceTypeModel = new ResourceTypeModel();
                resource.Type = resourceTypeModel.GetById(resource.TypeId);
            }

            // All good
            return null;
        }

        private string GetResourceTypeName(Resource resource)
        {
            if (resource.Type.DisplayName.ToLower().Equals("s3"))
            {
                return "rds";
            }
            else
            {
                return resource.Type.DisplayName.ToLower();
            }
        }

        private void LogAnalytics(string operation, string resourceId, string filename, User user)
        {
            if (CoscineLoggerConfiguration.IsLogLevelActivated(LogType.Analytics))
            {
                _analyticsLogObject.Type = "Action";
                _analyticsLogObject.Operation = operation;
                _analyticsLogObject.FileId = resourceId + "/" + HttpUtility.UrlDecode(filename).Substring(1);
                _analyticsLogObject.ResourceId = resourceId;
                _analyticsLogObject.ProjectId = _projectResourceModel.GetProjectForResource(new Guid(resourceId)).ToString();
                _analyticsLogObject.RoleId = _projectRoleModel.GetGetUserRoleForProject(new Guid(_analyticsLogObject.ProjectId), user.Id).ToString();
                _coscineLogger.AnalyticsLog(_analyticsLogObject);
            }
        }
    }
}