Ep extensions merge

gsrs-module-substance-example/pom.xml

@@ -329,13 +329,6 @@
             <artifactId>log4j-core</artifactId>
             <version>${log4j2.version}</version>
         </dependency>
-         <dependency>
-            <groupId>io.burt</groupId>
-            <artifactId>jmespath</artifactId>
-            <version>0.4.0</version>
-            <type>pom</type>
-        </dependency>
-
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>

gsrs-module-substances-core/pom.xml

@@ -331,6 +331,16 @@
             <artifactId>batik-svg-dom</artifactId>
             <version>1.17</version>
         </dependency>
+        <dependency>
+            <groupId>io.burt</groupId>
+            <artifactId>jmespath-core</artifactId>
+            <version>0.6.0</version>
+        </dependency>
+        <dependency>
+            <groupId>io.burt</groupId>
+            <artifactId>jmespath-jackson</artifactId>
+            <version>0.6.0</version>
+        </dependency>
         <dependency>
             <groupId>gov.fda.gsrs</groupId>
             <artifactId>Featureize-Nitrosamines</artifactId>

gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/GsrsApiExporter.java

@@ -0,0 +1,118 @@
+package gsrs.module.substance.exporters;
+
+import com.fasterxml.jackson.databind.ObjectWriter;
+import ix.core.controllers.EntityFactory;
+import ix.core.validator.GinasProcessingMessage;
+import ix.core.validator.ValidationResponse;
+import ix.ginas.exporters.Exporter;
+import ix.ginas.models.v1.Substance;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.util.Date;
+import java.util.Map;
+import java.util.Objects;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.web.client.HttpClientErrorException;
+import org.springframework.web.client.RestTemplate;
+import lombok.extern.slf4j.Slf4j;
+
+/**
+ * Created by Egor Puzanov on 10/18/22.
+ */
+@Slf4j
+public class GsrsApiExporter implements Exporter<Substance> {
+
+    private final HttpHeaders headers;
+    private final BufferedWriter out;
+    private final RestTemplate restTemplate;
+    private final boolean allowedExport;
+    private final boolean validate;
+    private final String newAuditor;
+    private final String changeReason;
+    private final ObjectWriter writer = EntityFactory.EntityMapper.FULL_ENTITY_MAPPER().writer();
+    private final Pattern AUDIT_PAT = Pattern.compile("edBy\":\"[^\"]*\"");
+
+    public GsrsApiExporter(OutputStream out, RestTemplate restTemplate, Map<String, String> headers, boolean allowedExport,  boolean validate, String newAuditor, String changeReason) throws IOException {
+        Objects.requireNonNull(out);
+        this.out = new BufferedWriter(new OutputStreamWriter(out));
+        Objects.requireNonNull(restTemplate);
+        this.restTemplate = restTemplate;
+        HttpHeaders h = new HttpHeaders();
+        h.setContentType(MediaType.APPLICATION_JSON);
+        for (Map.Entry<String, String> entry : headers.entrySet()) {
+            h.set(entry.getKey(), entry.getValue());
+        }
+        this.headers = h;
+        this.allowedExport = allowedExport;
+        this.validate = validate;
+        this.newAuditor = newAuditor != null ? "edBy\":\"" + newAuditor + "\"" : null;
+        this.changeReason = changeReason;
+        log.debug("BaseUrl: " + restTemplate.getUriTemplateHandler().expand("/") + " Headers: " + h.toString());
+    }
+
+    private HttpEntity<String> makeRequest(Substance obj) throws Exception {
+        String jsonStr = writer.writeValueAsString(obj);
+        if (newAuditor != null) {
+            jsonStr = AUDIT_PAT.matcher(jsonStr).replaceAll(newAuditor);
+        }
+        HttpEntity<String> request = new HttpEntity<String>(jsonStr, headers);
+        if (validate) {
+            ValidationResponse vr = restTemplate.postForObject("/@validate", request, ValidationResponse.class);
+            if (vr.getValidationMessages().isEmpty()) throw new Exception("GSRS API not found");
+            if (vr.hasError()) throw new Exception(vr.toString());
+        }
+        return request;
+    }
+
+    @Override
+    public void export(Substance obj) throws IOException {
+        HttpEntity<String> request;
+        Date date = new Date();
+        try {
+            if (!allowedExport) {
+                throw new Exception("Export denied");
+            }
+            if (changeReason != null && obj.version != null) {
+                obj.changeReason = changeReason.replace("{{version}}", obj.version).replace("{{changeReason}}", obj.changeReason != null ? obj.changeReason : "").trim();
+            }
+            try {
+                obj.version = restTemplate.getForObject("/{uuid}/version", String.class, obj.getUuid().toString()).replace("\"", "");
+                request = makeRequest(obj);
+                restTemplate.put("/", request);
+            } catch (HttpClientErrorException.NotFound ex) {
+                if (!ex.getMessage().contains("{\"message\":\"not found\",\"status\":404}")) {
+                    throw new Exception(ex.getMessage());
+                }
+                obj.version = "1";
+                String approvalID = obj.getApprovalID();
+                if (approvalID != null) {
+                    obj.approvalID = null;
+                }
+                request = makeRequest(obj);
+                Substance newObj = restTemplate.postForObject("/", request, Substance.class);
+                if (newObj.getUuid() == null) throw new Exception("GSRS API not found");
+                if (approvalID != null) {
+                    obj.approvalID = approvalID;
+                    request = makeRequest(obj);
+                    restTemplate.put("/", request);
+                }
+            }
+            out.write(String.format("%tF %tT Substance: %s %s - SUCCESS", date, date, obj.getUuid().toString(), obj.getName()));
+        } catch (Exception ex) {
+            out.write(String.format("%tF %tT Substance: %s %s - ERROR: %s", date, date, obj.getUuid().toString(), obj.getName(), ex.getMessage()));
+        }
+        out.newLine();
+    }
+
+    @Override
+    public void close() throws IOException {
+        out.close();
+    }
+}

gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/GsrsApiExporterFactory.java

@@ -0,0 +1,173 @@
+package gsrs.module.substance.exporters;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import gsrs.repository.UserProfileRepository;
+import ix.core.models.Role;
+import ix.core.models.UserProfile;
+import ix.ginas.exporters.Exporter;
+import ix.ginas.exporters.ExporterFactory;
+import ix.ginas.exporters.OutputFormat;
+import ix.ginas.models.v1.Substance;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.security.SecureRandom;
+import java.security.cert.X509Certificate;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+import javax.net.ssl.SSLContext;
+import javax.net.ssl.TrustManager;
+import javax.net.ssl.X509TrustManager;
+
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.config.RequestConfig;
+import org.apache.http.conn.ssl.SSLConnectionSocketFactory;
+import org.apache.http.conn.ssl.NoopHostnameVerifier;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.client.HttpClients;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.client.ClientHttpRequestFactory;
+import org.springframework.http.client.HttpComponentsClientHttpRequestFactory;
+import org.springframework.web.client.RestTemplate;
+import org.springframework.web.util.DefaultUriBuilderFactory;
+
+
+/**
+ * Created by Egor Puzanov on 10/18/22.
+ */
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class GsrsApiExporterFactory implements ExporterFactory {
+
+    @Autowired
+    private UserProfileRepository userProfileRepository;
+
+    private OutputFormat format = new OutputFormat("gsrsapi", "Send to ...");
+    private int timeout = 120000;
+    private boolean trustAllCerts = false;
+    private boolean validate = true;
+    private Role allowedRole = null;
+    private String newAuditor = null;
+    private String changeReason = null;
+    private String baseUrl = "http://localhost:8080/api/v1/substances";
+    private Map<String, String> headers = new HashMap<String, String>();
+    private final TrustManager[] trustAllCertificates = new TrustManager[]{
+        new X509TrustManager() {
+            public X509Certificate[] getAcceptedIssuers() {
+                return null;
+            }
+            public void checkClientTrusted(
+               X509Certificate[] certs, String authType) {
+            }
+            public void checkServerTrusted(
+               X509Certificate[] certs, String authType) {
+           }
+        }
+    };
+
+    private Map<String, String> getHeaders(UserProfile profile) {
+        Map<String, String> userHeaders = new HashMap<String, String>();
+        for (Map.Entry<String, String> entry : headers.entrySet()) {
+            String value = entry.getValue();
+            switch(value) {
+                case "{{user.name}}":
+                    value = profile.getIdentifier();
+                    break;
+                case "{{user.email}}":
+                    value = profile.user.email;
+                    break;
+                case "{{user.apikey}}":
+                    value = profile.getKey();
+                    break;
+                default:
+                    break;
+            }
+            userHeaders.put(entry.getKey(), value);
+        }
+        return userHeaders;
+    }
+
+    public void setFormat(Map<String, String> m) {
+        this.format = new OutputFormat(m.get("extension"), m.get("displayName"));
+    }
+
+    public void setTimeout(Integer timeout) {
+        this.timeout = timeout.intValue();
+    }
+
+    public void setTrustAllCerts(boolean trustAllCerts) {
+        this.trustAllCerts = trustAllCerts;
+    }
+
+    public void setValidate(boolean validate) {
+        this.validate = validate;
+    }
+
+    public void setBaseUrl(String baseUrl) {
+        this.baseUrl = baseUrl;
+    }
+
+    public void setHeaders(Map<String, String> headers) {
+        this.headers = headers;
+    }
+
+    public void setAllowedRole(String allowedRole) {
+        this.allowedRole = Role.valueOf(allowedRole);
+    }
+
+    public void setNewAuditor(String newAuditor) {
+        this.newAuditor = newAuditor;
+    }
+
+    public void setChangeReason(String changeReason) {
+        this.changeReason = changeReason;
+    }
+
+    @Override
+    public boolean supports(Parameters params) {
+        return params.getFormat().equals(format);
+    }
+
+    @Override
+    public Set<OutputFormat> getSupportedFormats() {
+        return Collections.singleton(format);
+    }
+
+    @Override
+    public Exporter<Substance> createNewExporter(OutputStream out, Parameters params) throws IOException {
+        RequestConfig requestConfig = RequestConfig.custom()
+            .setConnectionRequestTimeout(timeout)
+            .build();
+        HttpClientBuilder client = HttpClients.custom()
+            .useSystemProperties()
+            .setDefaultRequestConfig(requestConfig);
+        if (trustAllCerts) {
+            try {
+                SSLContext sslContext = SSLContext.getInstance("TLS");
+                sslContext.init(null, trustAllCertificates, new SecureRandom());
+                SSLConnectionSocketFactory connectionFactory = new SSLConnectionSocketFactory(sslContext, new NoopHostnameVerifier());
+                client = client.setSSLSocketFactory(connectionFactory);
+            } catch (Exception ex) {
+            }
+        }
+        ClientHttpRequestFactory clientFactory = new HttpComponentsClientHttpRequestFactory(client.build());
+        RestTemplate restTemplate = new RestTemplate(clientFactory);
+        restTemplate.setUriTemplateHandler(new DefaultUriBuilderFactory(baseUrl));
+        UserProfile profile = userProfileRepository.findByUser_UsernameIgnoreCase(params.getUsername());
+        boolean allowedExport = (allowedRole == null || profile.hasRole(allowedRole)) ? true : false;
+        return new GsrsApiExporter(out, restTemplate, getHeaders(profile), allowedExport, validate, newAuditor, changeReason);
+    }
+
+    @Override
+    public JsonNode getSchema() {
+        ObjectNode parameters = JsonNodeFactory.instance.objectNode();
+        return parameters;
+    }
+}