16947417686

Committed 13 Aug 2025 07:32PM UTC coverage: 22.72% (+4.6%) from 18.109%

Build # 16947417686

Build Type

push

github

Committed by

ashleycaselli

Commit Message

test(TripleStore): add unit tests for getRepoConnection method

Run Details

106 of 496 branches covered (21.37%)

Branch coverage included in aggregate %.

295 of 1269 relevant lines covered (23.25%)

1.15 hits per line

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18.29

src/main/java/com/knowledgepixels/query/TripleStore.java

package com.knowledgepixels.query;

import org.apache.commons.exec.environment.EnvironmentUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpUriRequest;
import org.apache.http.client.methods.RequestBuilder;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.BasicResponseHandler;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.eclipse.rdf4j.common.transaction.IsolationLevels;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.repository.Repository;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.eclipse.rdf4j.repository.http.HTTPRepository;
import org.nanopub.NanopubUtils;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.*;
import java.util.Map.Entry;

/**
 * Class to access the database in the form of triple stores.
 */
public class TripleStore {

    /**
     * Name of the admin graph.
     */
    public static final String ADMIN_REPO = "admin";

    private static ValueFactory vf = SimpleValueFactory.getInstance();

    /**
     * IRI for the repo init ID.
     */
    public static final IRI HAS_REPO_INIT_ID = vf.createIRI("http://purl.org/nanopub/admin/hasRepoInitId");

    /**
     * IRI for the nanopub count.
     */
    public static final IRI HAS_NANOPUB_COUNT = vf.createIRI("http://purl.org/nanopub/admin/hasNanopubCount");

    /**
     * IRI for the nanopub checksum.
     */
    public static final IRI HAS_NANOPUB_CHECKSUM = vf.createIRI("http://purl.org/nanopub/admin/hasNanopubChecksum");

    /**
     * IRI for the nanopub load number.
     */
    public static final IRI HAS_LOAD_NUMBER = vf.createIRI("http://purl.org/nanopub/admin/hasLoadNumber");

    /**
     * IRI for the nanopub load checksum.
     */
    public static final IRI HAS_LOAD_CHECKSUM = vf.createIRI("http://purl.org/nanopub/admin/hasLoadChecksum");

    /**
     * IRI for the nanopub load timestamp.
     */
    public static final IRI HAS_LOAD_TIMESTAMP = vf.createIRI("http://purl.org/nanopub/admin/hasLoadTimestamp");

    /**
     * IRI for the nanopub load status.
     */
    public static final IRI HAS_STATUS = vf.createIRI("http://purl.org/nanopub/admin/hasStatus");

    /**
     * IRI for the nanopub registry load counter.
     */
    public static final IRI HAS_REGISTRY_LOAD_COUNTER = vf.createIRI("http://purl.org/nanopub/admin/hasRegistryLoadCounter");

    /**
     * IRI for the nanopub repository ID.
     */
    public static final IRI THIS_REPO_ID = vf.createIRI("http://purl.org/nanopub/admin/thisRepo");

    /**
     * IRI for the nanopub coverage item.
     */
    public static final IRI HAS_COVERAGE_ITEM = vf.createIRI("http://purl.org/nanopub/admin/hasCoverageItem");

    /**
     * IRI for the nanopub coverage hash.
     */
    public static final IRI HAS_COVERAGE_HASH = vf.createIRI("http://purl.org/nanopub/admin/hasCoverageHash");

    /**
     * IRI for the nanopub coverage filter.
     */
    public static final IRI HAS_COVERAGE_FILTER = vf.createIRI("http://purl.org/nanopub/admin/hasCoverageFilter");

    private final Map<String, Repository> repositories = new LinkedHashMap<>();

    private String endpointBase = null;
    private String endpointType = null;

    private static TripleStore tripleStoreInstance;

    /**
     * Returns singleton triple store instance.
     *
     * @return Triple store instance
     */
    public static TripleStore get() {
        if (tripleStoreInstance == null) {
            try {
                tripleStoreInstance = new TripleStore();
            } catch (IOException ex) {
                ex.printStackTrace();
            }
        }
        return tripleStoreInstance;
    }

    private TripleStore() throws IOException {
        Map<String, String> env = EnvironmentUtils.getProcEnvironment();
        endpointBase = env.get("ENDPOINT_BASE");
        System.err.println("Endpoint base: " + endpointBase);
        endpointType = env.get("ENDPOINT_TYPE");

        getRepository("empty");  // Make sure empty repo exists
    }

    private final CloseableHttpClient httpclient = HttpClients.createDefault();

    Repository getRepository(String name) {
        synchronized (this) {
            while (repositories.size() > 100) {
                Entry<String, Repository> e = repositories.entrySet().iterator().next();
                repositories.remove(e.getKey());
                System.err.println("Shutting down repo: " + e.getKey());
                e.getValue().shutDown();
                System.err.println("Shutdown complete");
            }
            if (repositories.containsKey(name)) {
                // Move to the end of the list:
                Repository repo = repositories.remove(name);
                repositories.put(name, repo);
            } else {
                Repository repository = null;
                if (endpointType == null || endpointType.equals("rdf4j")) {
                    HTTPRepository hr = new HTTPRepository(endpointBase + "repositories/" + name);
                    hr.setHttpClient(httpclient);
                    repository = hr;
//                        } else if (endpointType.equals("virtuoso")) {
//                                repository = new VirtuosoRepository(endpointBase + name, username, password);
                } else {
                    throw new RuntimeException("Unknown repository type: " + endpointType);
                }
                repositories.put(name, repository);
                createRepo(name);
                getRepoConnection(name).close();
            }
            return repositories.get(name);
        }
    }

    /**
     * Return the repository connection for the given repository name.
     *
     * @param name repository name
     * @return repository connection
     */
    public RepositoryConnection getRepoConnection(String name) {
        Repository repo = getRepository(name);
        if (repo == null) {
            return null;
        }
        return repo.getConnection();
    }

    private void createRepo(String repoName) {
        if (!repoName.equals(ADMIN_REPO)) {
            getRepository(ADMIN_REPO);  // make sure admin repo is loaded first
        }
        try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
            //System.err.println("Trying to creating repo " + name);

            // TODO new syntax somehow doesn't work for the Lucene case:

//                        String createRegularRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n"
//                                        + "@prefix config: <tag:rdf4j.org,2023:config/>.\n"
//                                        + "[] a config:Repository ;\n"
//                                        + "    config:rep.id \"" + name + "\" ;\n"
//                                        + "    rdfs:label \"" + name + " native store\" ;\n"
//                                        + "    config:rep.impl [\n"
//                                        + "        config:rep.type \"openrdf:SailRepository\" ;\n"
//                                        + "        config:sail.impl [\n"
//                                        + "            config:sail.type \"openrdf:NativeStore\" ;\n"
//                                        + "            config:sail.iterationCacheSyncThreshold \"10000\";\n"
//                                        + "            config:native.tripleIndexes \"spoc,posc,ospc,opsc,psoc,sopc,spoc,cpos,cosp,cops,cpso,csop\" ;\n"
//                                        + "            config:sail.defaultQueryEvaluationMode \"STANDARD\"\n"
//                                        + "        ]\n"
//                                        + "    ].";
//                        String createTextRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n"
//                                        + "@prefix config: <tag:rdf4j.org,2023:config/>.\n"
//                                        + "[] a config:Repository ;\n"
//                                        + "    config:rep.id \"" + name + "\" ;\n"
//                                        + "    rdfs:label \"" + name + " native store\" ;\n"
//                                        + "    config:rep.impl [\n"
//                                        + "        config:rep.type \"openrdf:SailRepository\" ;\n"
//                                        + "        config:sail.impl [\n"
//                                        + "            config:sail.type \"openrdf:LuceneSail\" ;\n"
//                                        + "            config:sail.lucene.indexDir \"index/\" ;\n"
//                                        + "            config:delegate [\n"
//                                        + "                config:rep.type \"openrdf:SailRepository\" ;\n"
//                                        + "                config:sail.impl [\n"
//                                        + "                    config:sail.type \"openrdf:NativeStore\" ;\n"
//                                        + "                    config:sail.iterationCacheSyncThreshold \"10000\";\n"
//                                        + "                    config:native.tripleIndexes \"spoc,posc,ospc,opsc,psoc,sopc,spoc,cpos,cosp,cops,cpso,csop\" ;\n"
//                                        + "                    config:sail.defaultQueryEvaluationMode \"STANDARD\"\n"
//                                        + "                ]\n"
//                                        + "            ]\n"
//                                        + "        ]\n"
//                                        + "    ].";

            String indexTypes = "spoc,posc,ospc,cspo,cpos,cosp";
            if (repoName.startsWith("meta") || repoName.startsWith("text")) {
                indexTypes = "spoc,posc,ospc";
            }

            String createRegularRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n" + "@prefix rep: <http://www.openrdf.org/config/repository#>.\n" + "@prefix sr: <http://www.openrdf.org/config/repository/sail#>.\n" + "@prefix sail: <http://www.openrdf.org/config/sail#>.\n" + "@prefix sail-luc: <http://www.openrdf.org/config/sail/lucene#>.\n" + "@prefix lmdb: <http://rdf4j.org/config/sail/lmdb#>.\n" + "@prefix sb: <http://www.openrdf.org/config/sail/base#>.\n" + "\n" + "[] a rep:Repository ;\n" + "    rep:repositoryID \"" + repoName + "\" ;\n" + "    rdfs:label \"" + repoName + " LMDB store\" ;\n" + "    rep:repositoryImpl [\n" + "        rep:repositoryType \"openrdf:SailRepository\" ;\n" + "        sr:sailImpl [\n" + "            sail:sailType \"rdf4j:LmdbStore\" ;\n" + "            sail:iterationCacheSyncThreshold \"10000\";\n" + "            lmdb:tripleIndexes \"" + indexTypes + "\" ;\n" + "            sb:defaultQueryEvaluationMode \"STANDARD\"\n" + "        ]\n" + "    ].\n";

            // TODO Index npa:hasFilterLiteral predicate too (see https://groups.google.com/g/rdf4j-users/c/epF4Af1jXGU):
            String createTextRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n" + "@prefix rep: <http://www.openrdf.org/config/repository#>.\n" + "@prefix sr: <http://www.openrdf.org/config/repository/sail#>.\n" + "@prefix sail: <http://www.openrdf.org/config/sail#>.\n" + "@prefix sail-luc: <http://www.openrdf.org/config/sail/lucene#>.\n" + "@prefix lmdb: <http://rdf4j.org/config/sail/lmdb#>.\n" + "@prefix sb: <http://www.openrdf.org/config/sail/base#>.\n" + "\n" + "[] a rep:Repository ;\n" + "    rep:repositoryID \"" + repoName + "\" ;\n" + "    rdfs:label \"" + repoName + " store\" ;\n" + "    rep:repositoryImpl [\n" + "        rep:repositoryType \"openrdf:SailRepository\" ;\n" + "        sr:sailImpl [\n" + "            sail:sailType \"openrdf:LuceneSail\" ;\n" + "            sail-luc:indexDir \"index/\" ;\n" + "            sail:delegate [" + "              sail:sailType \"rdf4j:LmdbStore\" ;\n" + "              sail:iterationCacheSyncThreshold \"10000\";\n" + "              lmdb:tripleIndexes \"" + indexTypes + "\" ;\n" + "              sb:defaultQueryEvaluationMode \"STANDARD\"\n" + "            ]\n" + "        ]\n" + "    ].";

            String createRepoQueryString = createRegularRepoQueryString;
            if (repoName.startsWith("text")) {
                createRepoQueryString = createTextRepoQueryString;
            }

            HttpUriRequest createRepoRequest = RequestBuilder.put().setUri(endpointBase + "repositories/" + repoName).addHeader("Content-Type", "text/turtle").setEntity(new StringEntity(createRepoQueryString)).build();

            HttpResponse response = httpclient.execute(createRepoRequest);
            int statusCode = response.getStatusLine().getStatusCode();
            if (statusCode == 409) {
                //System.err.println("Already exists.");
                getRepository(repoName).init();
            } else if (statusCode >= 200 && statusCode < 300) {
                //System.err.println("Successfully created.");
                initNewRepo(repoName);
            } else {
                System.err.println("Status code: " + response.getStatusLine().getStatusCode());
                System.err.println(response.getStatusLine().getReasonPhrase());
                System.err.println("Response: " + new BasicResponseHandler().handleResponse(response));
            }
        } catch (IOException ex) {
            ex.printStackTrace();
        }
    }

    /**
     * Sends shutdown signal to all repositories.
     */
    public void shutdownRepositories() {
        for (Repository repo : repositories.values()) {
            if (repo != null && repo.isInitialized()) {
                repo.shutDown();
            }
        }
    }

    /**
     * Returns admin repo connection.
     *
     * @return repository connection to admin repository
     */
    public RepositoryConnection getAdminRepoConnection() {
        return get().getRepoConnection(ADMIN_REPO);
    }

    /**
     * Returns set of all repository names.
     *
     * @return Repository name set
     */
    public Set<String> getRepositoryNames() {
        Map<String, Boolean> repositoryNames = null;
        try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
            HttpResponse resp = httpclient.execute(RequestBuilder.get()
                    .setUri(endpointBase + "/repositories")
                    .addHeader("Content-Type", "text/csv")
                    .build());
            BufferedReader reader = new BufferedReader(new InputStreamReader(resp.getEntity().getContent()));
            int code = resp.getStatusLine().getStatusCode();
            if (code < 200 || code >= 300) return null;
            repositoryNames = new HashMap<>();
            int lineCount = 0;
            while (true) {
                String line = reader.readLine();
                if (line == null) break;
                if (lineCount > 0) {
                    String repoName = line.split(",")[1];
                    repositoryNames.put(repoName, true);
                }
                lineCount = lineCount + 1;
            }
        } catch (IOException ex) {
            ex.printStackTrace();
            return null;
        }
        return repositoryNames.keySet();
    }

    private void initNewRepo(String repoName) {
        String repoInitId = new Random().nextLong() + "";
        getRepository(repoName).init();
        if (!repoName.equals("empty")) {
            RepositoryConnection conn = getRepoConnection(repoName);
            try (conn) {
                // Full isolation, just in case.
                conn.begin(IsolationLevels.SERIALIZABLE);
                conn.add(THIS_REPO_ID, HAS_REPO_INIT_ID, vf.createLiteral(repoInitId), NanopubLoader.ADMIN_GRAPH);
                conn.add(THIS_REPO_ID, HAS_NANOPUB_COUNT, vf.createLiteral(0L), NanopubLoader.ADMIN_GRAPH);
                conn.add(THIS_REPO_ID, HAS_NANOPUB_CHECKSUM, vf.createLiteral(NanopubUtils.INIT_CHECKSUM), NanopubLoader.ADMIN_GRAPH);
                if (repoName.startsWith("pubkey_") || repoName.startsWith("type_")) {
                    String h = repoName.replaceFirst("^[^_]+_", "");
                    conn.add(THIS_REPO_ID, HAS_COVERAGE_ITEM, Utils.getObjectForHash(h), NanopubLoader.ADMIN_GRAPH);
                    conn.add(THIS_REPO_ID, HAS_COVERAGE_HASH, vf.createLiteral(h), NanopubLoader.ADMIN_GRAPH);
                    conn.add(THIS_REPO_ID, HAS_COVERAGE_FILTER, vf.createLiteral("_" + repoName), NanopubLoader.ADMIN_GRAPH);
                }
                conn.commit();
            }
        }
    }

}

1	package com.knowledgepixels.query;
2
3	import org.apache.commons.exec.environment.EnvironmentUtils;
4	import org.apache.http.HttpResponse;
5	import org.apache.http.client.methods.HttpUriRequest;
6	import org.apache.http.client.methods.RequestBuilder;
7	import org.apache.http.entity.StringEntity;
8	import org.apache.http.impl.client.BasicResponseHandler;
9	import org.apache.http.impl.client.CloseableHttpClient;
10	import org.apache.http.impl.client.HttpClients;
11	import org.eclipse.rdf4j.common.transaction.IsolationLevels;
12	import org.eclipse.rdf4j.model.IRI;
13	import org.eclipse.rdf4j.model.ValueFactory;
14	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
15	import org.eclipse.rdf4j.repository.Repository;
16	import org.eclipse.rdf4j.repository.RepositoryConnection;
17	import org.eclipse.rdf4j.repository.http.HTTPRepository;
18	import org.nanopub.NanopubUtils;
19
20	import java.io.BufferedReader;
21	import java.io.IOException;
22	import java.io.InputStreamReader;
23	import java.util.*;
24	import java.util.Map.Entry;
25
26	/**
27	* Class to access the database in the form of triple stores.
28	*/
29	public class TripleStore {
30
31	/**
32	* Name of the admin graph.
33	*/
34	public static final String ADMIN_REPO = "admin";
35
36	private static ValueFactory vf = SimpleValueFactory.getInstance();	2✔
37
38	/**
39	* IRI for the repo init ID.
40	*/
41	public static final IRI HAS_REPO_INIT_ID = vf.createIRI("http://purl.org/nanopub/admin/hasRepoInitId");	4✔
42
43	/**
44	* IRI for the nanopub count.
45	*/
46	public static final IRI HAS_NANOPUB_COUNT = vf.createIRI("http://purl.org/nanopub/admin/hasNanopubCount");	4✔
47
48	/**
49	* IRI for the nanopub checksum.
50	*/
51	public static final IRI HAS_NANOPUB_CHECKSUM = vf.createIRI("http://purl.org/nanopub/admin/hasNanopubChecksum");	4✔
52
53	/**
54	* IRI for the nanopub load number.
55	*/
56	public static final IRI HAS_LOAD_NUMBER = vf.createIRI("http://purl.org/nanopub/admin/hasLoadNumber");	4✔
57
58	/**
59	* IRI for the nanopub load checksum.
60	*/
61	public static final IRI HAS_LOAD_CHECKSUM = vf.createIRI("http://purl.org/nanopub/admin/hasLoadChecksum");	4✔
62
63	/**
64	* IRI for the nanopub load timestamp.
65	*/
66	public static final IRI HAS_LOAD_TIMESTAMP = vf.createIRI("http://purl.org/nanopub/admin/hasLoadTimestamp");	4✔
67
68	/**
69	* IRI for the nanopub load status.
70	*/
71	public static final IRI HAS_STATUS = vf.createIRI("http://purl.org/nanopub/admin/hasStatus");	4✔
72
73	/**
74	* IRI for the nanopub registry load counter.
75	*/
76	public static final IRI HAS_REGISTRY_LOAD_COUNTER = vf.createIRI("http://purl.org/nanopub/admin/hasRegistryLoadCounter");	4✔
77
78	/**
79	* IRI for the nanopub repository ID.
80	*/
81	public static final IRI THIS_REPO_ID = vf.createIRI("http://purl.org/nanopub/admin/thisRepo");	4✔
82
83	/**
84	* IRI for the nanopub coverage item.
85	*/
86	public static final IRI HAS_COVERAGE_ITEM = vf.createIRI("http://purl.org/nanopub/admin/hasCoverageItem");	4✔
87
88	/**
89	* IRI for the nanopub coverage hash.
90	*/
91	public static final IRI HAS_COVERAGE_HASH = vf.createIRI("http://purl.org/nanopub/admin/hasCoverageHash");	4✔
92
93	/**
94	* IRI for the nanopub coverage filter.
95	*/
96	public static final IRI HAS_COVERAGE_FILTER = vf.createIRI("http://purl.org/nanopub/admin/hasCoverageFilter");	5✔
97
98	private final Map<String, Repository> repositories = new LinkedHashMap<>();	5✔
99
100	private String endpointBase = null;	3✔
101	private String endpointType = null;	3✔
102
103	private static TripleStore tripleStoreInstance;
104
105	/**
106	* Returns singleton triple store instance.
107	*
108	* @return Triple store instance
109	*/
110	public static TripleStore get() {
111	if (tripleStoreInstance == null) {	2!
112	try {
113	tripleStoreInstance = new TripleStore();	×
114	} catch (IOException ex) {	×
115	ex.printStackTrace();	×
116	}	×
117	}
118	return tripleStoreInstance;	×
119	}
120
121	private TripleStore() throws IOException {	2✔
122	Map<String, String> env = EnvironmentUtils.getProcEnvironment();	2✔
123	endpointBase = env.get("ENDPOINT_BASE");	6✔
124	System.err.println("Endpoint base: " + endpointBase);	5✔
125	endpointType = env.get("ENDPOINT_TYPE");	6✔
126
127	getRepository("empty"); // Make sure empty repo exists	×
128	}	×
129
130	private final CloseableHttpClient httpclient = HttpClients.createDefault();	3✔
131
132	Repository getRepository(String name) {
133	synchronized (this) {	4✔
134	while (repositories.size() > 100) {	5!
135	Entry<String, Repository> e = repositories.entrySet().iterator().next();	×
136	repositories.remove(e.getKey());	×
137	System.err.println("Shutting down repo: " + e.getKey());	×
138	e.getValue().shutDown();	×
139	System.err.println("Shutdown complete");	×
140	}	×
141	if (repositories.containsKey(name)) {	5!
142	// Move to the end of the list:
143	Repository repo = repositories.remove(name);	×
144	repositories.put(name, repo);	×
145	} else {	×
146	Repository repository = null;	2✔
147	if (endpointType == null \|\| endpointType.equals("rdf4j")) {	3!
148	HTTPRepository hr = new HTTPRepository(endpointBase + "repositories/" + name);	×
149	hr.setHttpClient(httpclient);	×
150	repository = hr;	×
151	// } else if (endpointType.equals("virtuoso")) {
152	// repository = new VirtuosoRepository(endpointBase + name, username, password);
153	} else {	×
154	throw new RuntimeException("Unknown repository type: " + endpointType);	×
155	}
156	repositories.put(name, repository);	×
157	createRepo(name);	×
158	getRepoConnection(name).close();	×
159	}
160	return repositories.get(name);	×
161	}
162	}
163
164	/**
165	* Return the repository connection for the given repository name.
166	*
167	* @param name repository name
168	* @return repository connection
169	*/
170	public RepositoryConnection getRepoConnection(String name) {
171	Repository repo = getRepository(name);	×
172	if (repo == null) {	×
173	return null;	×
174	}
175	return repo.getConnection();	×
176	}
177
178	private void createRepo(String repoName) {
179	if (!repoName.equals(ADMIN_REPO)) {	×
180	getRepository(ADMIN_REPO); // make sure admin repo is loaded first	×
181	}
182	try (CloseableHttpClient httpclient = HttpClients.createDefault()) {	×
183	//System.err.println("Trying to creating repo " + name);
184
185	// TODO new syntax somehow doesn't work for the Lucene case:
186
187	// String createRegularRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n"
188	// + "@prefix config: <tag:rdf4j.org,2023:config/>.\n"
189	// + "[] a config:Repository ;\n"
190	// + " config:rep.id \"" + name + "\" ;\n"
191	// + " rdfs:label \"" + name + " native store\" ;\n"
192	// + " config:rep.impl [\n"
193	// + " config:rep.type \"openrdf:SailRepository\" ;\n"
194	// + " config:sail.impl [\n"
195	// + " config:sail.type \"openrdf:NativeStore\" ;\n"
196	// + " config:sail.iterationCacheSyncThreshold \"10000\";\n"
197	// + " config:native.tripleIndexes \"spoc,posc,ospc,opsc,psoc,sopc,spoc,cpos,cosp,cops,cpso,csop\" ;\n"
198	// + " config:sail.defaultQueryEvaluationMode \"STANDARD\"\n"
199	// + " ]\n"
200	// + " ].";
201	// String createTextRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n"
202	// + "@prefix config: <tag:rdf4j.org,2023:config/>.\n"
203	// + "[] a config:Repository ;\n"
204	// + " config:rep.id \"" + name + "\" ;\n"
205	// + " rdfs:label \"" + name + " native store\" ;\n"
206	// + " config:rep.impl [\n"
207	// + " config:rep.type \"openrdf:SailRepository\" ;\n"
208	// + " config:sail.impl [\n"
209	// + " config:sail.type \"openrdf:LuceneSail\" ;\n"
210	// + " config:sail.lucene.indexDir \"index/\" ;\n"
211	// + " config:delegate [\n"
212	// + " config:rep.type \"openrdf:SailRepository\" ;\n"
213	// + " config:sail.impl [\n"
214	// + " config:sail.type \"openrdf:NativeStore\" ;\n"
215	// + " config:sail.iterationCacheSyncThreshold \"10000\";\n"
216	// + " config:native.tripleIndexes \"spoc,posc,ospc,opsc,psoc,sopc,spoc,cpos,cosp,cops,cpso,csop\" ;\n"
217	// + " config:sail.defaultQueryEvaluationMode \"STANDARD\"\n"
218	// + " ]\n"
219	// + " ]\n"
220	// + " ]\n"
221	// + " ].";
222
223	String indexTypes = "spoc,posc,ospc,cspo,cpos,cosp";	×
224	if (repoName.startsWith("meta") \|\| repoName.startsWith("text")) {	×
225	indexTypes = "spoc,posc,ospc";	×
226	}
227
228	String createRegularRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n" + "@prefix rep: <http://www.openrdf.org/config/repository#>.\n" + "@prefix sr: <http://www.openrdf.org/config/repository/sail#>.\n" + "@prefix sail: <http://www.openrdf.org/config/sail#>.\n" + "@prefix sail-luc: <http://www.openrdf.org/config/sail/lucene#>.\n" + "@prefix lmdb: <http://rdf4j.org/config/sail/lmdb#>.\n" + "@prefix sb: <http://www.openrdf.org/config/sail/base#>.\n" + "\n" + "[] a rep:Repository ;\n" + " rep:repositoryID \"" + repoName + "\" ;\n" + " rdfs:label \"" + repoName + " LMDB store\" ;\n" + " rep:repositoryImpl [\n" + " rep:repositoryType \"openrdf:SailRepository\" ;\n" + " sr:sailImpl [\n" + " sail:sailType \"rdf4j:LmdbStore\" ;\n" + " sail:iterationCacheSyncThreshold \"10000\";\n" + " lmdb:tripleIndexes \"" + indexTypes + "\" ;\n" + " sb:defaultQueryEvaluationMode \"STANDARD\"\n" + " ]\n" + " ].\n";	×
229
230	// TODO Index npa:hasFilterLiteral predicate too (see https://groups.google.com/g/rdf4j-users/c/epF4Af1jXGU):
231	String createTextRepoQueryString = "@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.\n" + "@prefix rep: <http://www.openrdf.org/config/repository#>.\n" + "@prefix sr: <http://www.openrdf.org/config/repository/sail#>.\n" + "@prefix sail: <http://www.openrdf.org/config/sail#>.\n" + "@prefix sail-luc: <http://www.openrdf.org/config/sail/lucene#>.\n" + "@prefix lmdb: <http://rdf4j.org/config/sail/lmdb#>.\n" + "@prefix sb: <http://www.openrdf.org/config/sail/base#>.\n" + "\n" + "[] a rep:Repository ;\n" + " rep:repositoryID \"" + repoName + "\" ;\n" + " rdfs:label \"" + repoName + " store\" ;\n" + " rep:repositoryImpl [\n" + " rep:repositoryType \"openrdf:SailRepository\" ;\n" + " sr:sailImpl [\n" + " sail:sailType \"openrdf:LuceneSail\" ;\n" + " sail-luc:indexDir \"index/\" ;\n" + " sail:delegate [" + " sail:sailType \"rdf4j:LmdbStore\" ;\n" + " sail:iterationCacheSyncThreshold \"10000\";\n" + " lmdb:tripleIndexes \"" + indexTypes + "\" ;\n" + " sb:defaultQueryEvaluationMode \"STANDARD\"\n" + " ]\n" + " ]\n" + " ].";	×
232
233	String createRepoQueryString = createRegularRepoQueryString;	×
234	if (repoName.startsWith("text")) {	×
235	createRepoQueryString = createTextRepoQueryString;	×
236	}
237
238	HttpUriRequest createRepoRequest = RequestBuilder.put().setUri(endpointBase + "repositories/" + repoName).addHeader("Content-Type", "text/turtle").setEntity(new StringEntity(createRepoQueryString)).build();	×
239
240	HttpResponse response = httpclient.execute(createRepoRequest);	×
241	int statusCode = response.getStatusLine().getStatusCode();	×
242	if (statusCode == 409) {	×
243	//System.err.println("Already exists.");
244	getRepository(repoName).init();	×
245	} else if (statusCode >= 200 && statusCode < 300) {	×
246	//System.err.println("Successfully created.");
247	initNewRepo(repoName);	×
248	} else {
249	System.err.println("Status code: " + response.getStatusLine().getStatusCode());	×
250	System.err.println(response.getStatusLine().getReasonPhrase());	×
251	System.err.println("Response: " + new BasicResponseHandler().handleResponse(response));	×
252	}
253	} catch (IOException ex) {	×
254	ex.printStackTrace();	×
255	}	×
256	}	×
257
258	/**
259	* Sends shutdown signal to all repositories.
260	*/
261	public void shutdownRepositories() {
262	for (Repository repo : repositories.values()) {	×
263	if (repo != null && repo.isInitialized()) {	×
264	repo.shutDown();	×
265	}
266	}	×
267	}	×
268
269	/**
270	* Returns admin repo connection.
271	*
272	* @return repository connection to admin repository
273	*/
274	public RepositoryConnection getAdminRepoConnection() {
275	return get().getRepoConnection(ADMIN_REPO);	×
276	}
277
278	/**
279	* Returns set of all repository names.
280	*
281	* @return Repository name set
282	*/
283	public Set<String> getRepositoryNames() {
284	Map<String, Boolean> repositoryNames = null;	×
285	try (CloseableHttpClient httpclient = HttpClients.createDefault()) {	×
286	HttpResponse resp = httpclient.execute(RequestBuilder.get()	×
287	.setUri(endpointBase + "/repositories")	×
288	.addHeader("Content-Type", "text/csv")	×
289	.build());	×
290	BufferedReader reader = new BufferedReader(new InputStreamReader(resp.getEntity().getContent()));	×
291	int code = resp.getStatusLine().getStatusCode();	×
292	if (code < 200 \|\| code >= 300) return null;	×
293	repositoryNames = new HashMap<>();	×
294	int lineCount = 0;	×
295	while (true) {
296	String line = reader.readLine();	×
297	if (line == null) break;	×
298	if (lineCount > 0) {	×
299	String repoName = line.split(",")[1];	×
300	repositoryNames.put(repoName, true);	×
301	}
302	lineCount = lineCount + 1;	×
303	}	×
304	} catch (IOException ex) {	×
305	ex.printStackTrace();	×
306	return null;	×
307	}	×
308	return repositoryNames.keySet();	×
309	}
310
311	private void initNewRepo(String repoName) {
312	String repoInitId = new Random().nextLong() + "";	×
313	getRepository(repoName).init();	×
314	if (!repoName.equals("empty")) {	×
315	RepositoryConnection conn = getRepoConnection(repoName);	×
316	try (conn) {	×
317	// Full isolation, just in case.
318	conn.begin(IsolationLevels.SERIALIZABLE);	×
319	conn.add(THIS_REPO_ID, HAS_REPO_INIT_ID, vf.createLiteral(repoInitId), NanopubLoader.ADMIN_GRAPH);	×
320	conn.add(THIS_REPO_ID, HAS_NANOPUB_COUNT, vf.createLiteral(0L), NanopubLoader.ADMIN_GRAPH);	×
321	conn.add(THIS_REPO_ID, HAS_NANOPUB_CHECKSUM, vf.createLiteral(NanopubUtils.INIT_CHECKSUM), NanopubLoader.ADMIN_GRAPH);	×
322	if (repoName.startsWith("pubkey_") \|\| repoName.startsWith("type_")) {	×
323	String h = repoName.replaceFirst("^[^_]+_", "");	×
324	conn.add(THIS_REPO_ID, HAS_COVERAGE_ITEM, Utils.getObjectForHash(h), NanopubLoader.ADMIN_GRAPH);	×
325	conn.add(THIS_REPO_ID, HAS_COVERAGE_HASH, vf.createLiteral(h), NanopubLoader.ADMIN_GRAPH);	×
326	conn.add(THIS_REPO_ID, HAS_COVERAGE_FILTER, vf.createLiteral("_" + repoName), NanopubLoader.ADMIN_GRAPH);	×
327	}
328	conn.commit();	×
329	}
330	}
331	}	×
332
333	}

knowledgepixels / nanopub-query / 16947417686

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