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Commit fbbb75d6 authored by Matija Obreza's avatar Matija Obreza
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Merge branch '9-accession-api-v1' into 'master' 

Resolve "Accession API v1"

Closes #9

See merge request !9
parents f442311b e75f511d
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    src/main/java/org/genesys2/client/oauth/CLI.java deleted 100644 → 0
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    /*
    * Copyright 2016 Global Crop Diversity Trust
    *
    * Licensed under the Apache License, Version 2.0 (the "License");
    * you may not use this file except in compliance with the License.
    * You may obtain a copy of the License at
    *
    * http://www.apache.org/licenses/LICENSE-2.0
    *
    * Unless required by applicable law or agreed to in writing, software
    * distributed under the License is distributed on an "AS IS" BASIS,
    * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    * See the License for the specific language governing permissions and
    * limitations under the License.
    */
    package org.genesys2.client.oauth;
    import java.io.File;
    import java.io.FileInputStream;
    import java.io.FileNotFoundException;
    import java.io.FileOutputStream;
    import java.io.IOException;
    import java.util.HashSet;
    import java.util.Iterator;
    import java.util.Map.Entry;
    import java.util.Properties;
    import java.util.Scanner;
    import java.util.Set;
    import com.fasterxml.jackson.core.JsonProcessingException;
    import com.fasterxml.jackson.databind.JsonNode;
    import com.fasterxml.jackson.databind.ObjectMapper;
    import com.fasterxml.jackson.databind.node.ArrayNode;
    import com.fasterxml.jackson.databind.node.DoubleNode;
    import com.fasterxml.jackson.databind.node.IntNode;
    import com.fasterxml.jackson.databind.node.NullNode;
    import com.fasterxml.jackson.databind.node.ObjectNode;
    import com.fasterxml.jackson.databind.node.TextNode;
    import com.github.scribejava.core.model.Verb;
    import org.apache.commons.io.IOUtils;
    import org.apache.commons.lang.StringUtils;
    import org.slf4j.Logger;
    import org.slf4j.LoggerFactory;
    /**
    * Simple command line interface to Genesys.
    *
    * @author matijaobreza
    */
    public class CLI {
    /** The Constant LOG. */
    private static final Logger LOG = LoggerFactory.getLogger(CLI.class);
    /** The properties file. */
    private File propertiesFile;
    /** The properties. */
    private Properties properties;
    /** The in. */
    private final Scanner in = new Scanner(System.in);
    /** The mapper. */
    private static ObjectMapper mapper = new ObjectMapper();
    /** The genesys client. */
    private GenesysClient genesysClient;
    /** The ignored fields. */
    private static Set<String> ignoredFields;
    static {
    ignoredFields = new HashSet<String>();
    ignoredFields.add("id");
    ignoredFields.add("createdBy");
    ignoredFields.add("createdDate");
    ignoredFields.add("lastModifiedBy");
    ignoredFields.add("lastModifiedDate");
    ignoredFields.add("version");
    }
    /**
    * The main method.
    *
    * @param args the arguments
    */
    public static void main(final String[] args) {
    LOG.info("Hello World!");
    final CLI cli = new CLI();
    cli.genesysClient = GenesysClient.build(cli.loadProperties("client.properties"));
    cli.run();
    }
    /**
    * Run.
    */
    private void run() {
    checkPreconditions();
    try {
    System.out.println("/me: " + genesysClient.query("/me"));
    properties.put("access.token", genesysClient.getTokens().getAccessToken());
    saveProperties();
    } catch (final OAuthAuthenticationException e) {
    LOG.error("Failed to fetch /me", e);
    try {
    authenticate();
    } catch (OAuthAuthenticationException e1) {
    LOG.error("Failed to authenticate", e1);
    return;
    }
    } catch (final Throwable e) {
    LOG.error(e.getMessage(), e);
    return;
    }
    try {
    doWork();
    } catch (final Throwable e) {
    LOG.error(e.getMessage(), e);
    }
    }
    /**
    * Do work.
    *
    * @throws GenesysApiException the genesys api exception
    * @throws PleaseRetryException the please retry exception
    * @throws IOException Signals that an I/O exception has occurred.
    */
    private void doWork() throws GenesysApiException, PleaseRetryException, IOException {
    String line = null;
    do {
    System.out.println("1 Datasets");
    System.out.println("2 Traits");
    System.out.println("3 Crops");
    System.out.println("0 Custom");
    System.out.println("Q QUIT");
    line = in.nextLine();
    if ("1".equals(line)) {
    doDatasets();
    } else if ("2".equals(line)) {
    doTraits();
    } else if ("3".equals(line)) {
    doCrops();
    } else if ("0".equals(line)) {
    doCustom();
    }
    } while (!"Q".equalsIgnoreCase(line));
    }
    /**
    * Update json data.
    *
    * @param label the label
    * @param n the n
    */
    private void updateJsonData(final String label, final JsonNode n) {
    if (n.isArray()) {
    updateJsonArray(label, (ArrayNode) n);
    } else if (n.isObject()) {
    updateJsonObject(label, n);
    }
    }
    /**
    * Update json object.
    *
    * @param label the label
    * @param n the n
    */
    private void updateJsonObject(final String label, final JsonNode n) {
    final Iterator<Entry<String, JsonNode>> f = n.fields();
    while (f.hasNext()) {
    final Entry<String, JsonNode> field = f.next();
    System.out.print(label + "." + StringUtils.capitalize(field.getKey()) + ":");
    System.out.println(field.getValue());
    if (ignoredFields.contains(field.getKey())) {
    continue;
    }
    if (field.getValue().isObject() || field.getValue().isArray()) {
    System.out.println("Edit subobject ?");
    if (StringUtils.equalsIgnoreCase("y", in.nextLine())) {
    updateJsonData(label + "." + field.getKey(), field.getValue());
    }
    continue;
    }
    final String val = in.nextLine();
    if (!field.getValue().isNull() && val.length() == 0) {
    continue;
    }
    if (val.startsWith("i ")) {
    field.setValue(new IntNode(Integer.parseInt(val.substring(2))));
    } else if (val.startsWith("d ")) {
    field.setValue(new DoubleNode(Double.parseDouble(val.substring(2))));
    } else if (StringUtils.isBlank(val)) {
    field.setValue(NullNode.getInstance());
    } else {
    field.setValue(new TextNode(val.trim()));
    }
    }
    System.out.println("Done editing " + label);
    }
    /**
    * Update json array.
    *
    * @param label the label
    * @param n the n
    */
    private void updateJsonArray(final String label, final ArrayNode n) {
    System.out.println("Array: " + n);
    final ArrayNode na = n.arrayNode();
    String val;
    do {
    val = in.nextLine().trim();
    if (val.startsWith("i ")) {
    na.add(Integer.parseInt(val.substring(2)));
    } else if (val.startsWith("d ")) {
    na.add(Double.parseDouble(val.substring(2)));
    } else if (val.startsWith("o ")) {
    try {
    final Object o = Class.forName("org.genesys2.client.rest.model." + val.substring(2)).newInstance();
    final JsonNode newNode = mapper.readTree(mapper.writeValueAsString(o));
    System.out.println(newNode);
    updateJsonObject(label + "." + val.substring(2), newNode);
    na.add(newNode);
    } catch (final ClassNotFoundException e) {
    System.err.println(e.getMessage());
    } catch (final JsonProcessingException e) {
    System.err.println(e.getMessage());
    } catch (final IOException e) {
    System.err.println(e.getMessage());
    } catch (final InstantiationException e) {
    System.err.println(e.getMessage());
    } catch (final IllegalAccessException e) {
    System.err.println(e.getMessage());
    }
    } else if (StringUtils.isBlank(val)) {
    break;
    } else {
    na.add(val);
    }
    } while (StringUtils.isNotBlank(val));
    n.removeAll();
    n.addAll(na);
    System.out.println("Done editing array " + label);
    }
    /**
    * Do custom.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void doCustom() throws GenesysApiException {
    System.out.print("URL: ");
    final String url = in.nextLine();
    System.out.print("Method [GET]: ");
    final String method = StringUtils.defaultIfBlank(in.nextLine(), "GET");
    System.out.println("JSON: ");
    final String data = StringUtils.defaultIfBlank(in.nextLine(), null);
    // Exec
    System.out.println(genesysClient.query(Verb.valueOf(method), url, null, data));
    }
    /**
    * Do crops.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void doCrops() throws GenesysApiException {
    String line = null;
    do {
    System.out.println("1 List crops");
    System.out.println("2 Update crop");
    System.out.println("3 Update crop rules");
    System.out.println("0 Back");
    line = in.nextLine();
    if ("1".equals(line)) {
    System.out.println("/crops: " + genesysClient.query("/crops"));
    } else if ("2".equals(line)) {
    updateCrop();
    } else if ("3".equals(line)) {
    updateCropRules();
    } else if ("9".equals(line)) {
    System.out.println("/methods: " + genesysClient.query("/methods"));
    } else if ("0".equalsIgnoreCase(line)) {
    return;
    }
    } while (!"0".equalsIgnoreCase(line));
    }
    /**
    * Update crop rules.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void updateCropRules() throws GenesysApiException {
    System.out.println("Crop shortName: ");
    final String shortName = in.nextLine().trim();
    final String rules = genesysClient.query("/crops/" + shortName + "/rules");
    System.out.println("Crop rules: " + rules);
    final String newRules = StringUtils.defaultIfBlank(in.nextLine().trim(), rules);
    if (StringUtils.equals(newRules, rules)) {
    System.out.println("No change.");
    return;
    }
    ArrayNode arr;
    try {
    arr = (ArrayNode) mapper.readTree(newRules);
    } catch (final Throwable e) {
    System.err.println(e.getMessage());
    return;
    }
    System.out.println(arr.toString());
    // make a crop
    System.out.println("New rules: " + genesysClient.query(Verb.POST, "/crops/" + shortName + "/rules", null, arr.toString()));
    }
    /**
    * Update crop.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void updateCrop() throws GenesysApiException {
    System.out.println("Crop shortName: ");
    final String shortName = in.nextLine().trim();
    ObjectNode cropJson = null;
    try {
    cropJson = (ObjectNode) mapper.readTree(genesysClient.getCrop(shortName));
    cropJson.remove("rules");
    } catch (final IOException e) {
    System.err.println(e.getMessage());
    }
    if (cropJson == null) {
    cropJson = mapper.createObjectNode();
    cropJson.put("shortName", shortName);
    cropJson.put("name", "");
    cropJson.put("i18n", "{}");
    }
    System.out.println(">> " + cropJson.toString());
    System.out.println("Name [" + cropJson.get("name").textValue() + "]: ");
    cropJson.put("name", StringUtils.defaultIfBlank(in.nextLine().trim(), cropJson.get("name").textValue()));
    System.out.println("i18n [" + cropJson.get("i18n").textValue() + "]: ");
    cropJson.put("i18n", StringUtils.defaultIfBlank(in.nextLine().trim(), cropJson.get("i18n").textValue()));
    System.out.println(cropJson.toString());
    // make a crop
    System.out.println("Put method: " + genesysClient.query(Verb.PUT, "/crops", null, cropJson.toString()));
    }
    /**
    * Do traits.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void doTraits() throws GenesysApiException {
    String line = null;
    do {
    System.out.println("1 List parameters");
    System.out.println("2 List my methods");
    System.out.println("9 List all methods");
    System.out.println("3 Add method");
    System.out.println("0 Back");
    line = in.nextLine();
    if ("1".equals(line)) {
    System.out.println("/parameters: " + genesysClient.query("/descriptors"));
    } else if ("2".equals(line)) {
    System.out.println("/mymethods: " + genesysClient.query("/mymethods"));
    } else if ("3".equals(line)) {
    addMethod();
    } else if ("9".equals(line)) {
    System.out.println("/methods: " + genesysClient.query("/methods"));
    } else if ("0".equalsIgnoreCase(line)) {
    return;
    }
    } while (!"0".equalsIgnoreCase(line));
    }
    /**
    * Do datasets.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void doDatasets() throws GenesysApiException {
    String line = null;
    do {
    System.out.println("1 List");
    System.out.println("2 Add");
    System.out.println("3 Add data");
    System.out.println("4 Add RAW");
    System.out.println("0 Back");
    line = in.nextLine();
    if ("1".equals(line)) {
    System.out.println("/datasets: " + genesysClient.query("/datasets"));
    } else if ("2".equals(line)) {
    addDataset();
    } else if ("3".equals(line)) {
    addDatasetData();
    } else if ("4".equals(line)) {
    addDatasetRaw();
    } else if ("0".equalsIgnoreCase(line)) {
    return;
    }
    } while (!"0".equalsIgnoreCase(line));
    }
    /**
    * Adds the method.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void addMethod() throws GenesysApiException {
    final ObjectNode datasetJson = mapper.createObjectNode();
    System.out.println("Method description: ");
    datasetJson.put("description", in.nextLine());
    System.out.println("UOM: ");
    datasetJson.put("unit", StringUtils.defaultIfBlank(in.nextLine(), null));
    System.out.println("Field name: ");
    datasetJson.put("fieldName", StringUtils.defaultIfBlank(in.nextLine(), null));
    System.out.println("Field type: (0=String, 1=Double, 2=Long)");
    final int fieldType = Integer.parseInt(in.nextLine());
    datasetJson.put("fieldType", fieldType);
    if (fieldType == 0) {
    System.out.println("Field size: ");
    datasetJson.put("fieldSize", Integer.parseInt(in.nextLine()));
    }
    System.out.println("Options: ");
    datasetJson.put("options", StringUtils.defaultIfBlank(in.nextLine(), null));
    System.out.println("Range: ");
    datasetJson.put("range", StringUtils.defaultIfBlank(in.nextLine(), null));
    System.err.println(datasetJson.toString());
    // make a dataset
    System.out.println("Put method: " + genesysClient.query(Verb.PUT, "/methods", null, datasetJson.toString()));
    }
    /**
    * Adds the dataset.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void addDataset() throws GenesysApiException {
    final ObjectNode datasetJson = mapper.createObjectNode();
    System.out.println("WIEWS Code: ");
    datasetJson.put("institute", in.nextLine());
    System.out.println("Dataset title: ");
    datasetJson.put("title", in.nextLine());
    System.out.println("Dataset description: ");
    datasetJson.put("description", in.nextLine());
    System.err.println(datasetJson.toString());
    // make a dataset
    System.out.println("Put dataset: " + genesysClient.query(Verb.PUT, "/datasets", null, datasetJson.toString()));
    }
    /**
    * Adds the dataset data.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void addDatasetData() throws GenesysApiException {
    final ObjectNode datasetJson = mapper.createObjectNode();
    System.out.println("Dataset ID: ");
    final long datasetId = Long.parseLong(in.nextLine());
    System.out.println("WIEWS Code: ");
    datasetJson.put("instCode", in.nextLine());
    System.out.println("Data data: ");
    datasetJson.put("data", in.nextLine());
    System.err.println(datasetJson.toString());
    // make a dataset
    System.out.println("Put dataset: " + genesysClient.query(Verb.PUT, "/datasets/" + datasetId + "/data", null, datasetJson.toString()));
    }
    /**
    * Adds the dataset raw.
    *
    * @throws GenesysApiException the genesys api exception
    */
    private void addDatasetRaw() throws GenesysApiException {
    System.out.println("Dataset ID: ");
    final long datasetId = Long.parseLong(in.nextLine());
    System.out.println("JSON: ");
    final String json = in.nextLine();
    System.err.println(json);
    // make a dataset
    System.out.println("Put dataset: " + genesysClient.query(Verb.PUT, "/datasets/" + datasetId + "/data", null, json));
    }
    /**
    * Check preconditions.
    */
    private void checkPreconditions() {
    boolean restart = false;
    if (StringUtils.isBlank(properties.getProperty("client.key"))) {
    System.out.print("Provide client key: ");
    properties.put("client.key", in.nextLine());
    restart = true;
    }
    if (StringUtils.isBlank(properties.getProperty("client.secret"))) {
    System.out.print("Provide client secret: ");
    properties.put("client.secret", in.nextLine());
    restart = true;
    }
    if (StringUtils.isBlank(properties.getProperty("api.url"))) {
    System.out.print("Provide API url: ");
    properties.put("api.url", in.nextLine());
    restart = true;
    }
    if (restart) {
    saveProperties();
    LOG.warn("Properties udpated, please restart CLI application");
    System.exit(-1);
    }
    }
    /**
    * Authenticate.
    *
    * @throws OAuthAuthenticationException
    */
    private void authenticate() throws OAuthAuthenticationException {
    final String authorizationUrl = genesysClient.getAuthorizationUrl();
    System.out.println("Authorization URL: \n" + authorizationUrl);
    System.out.print("\nVerifier: ");
    final String verifierCode = in.nextLine();
    System.out.println();
    // Trade the Request Token and Verifier for the Access Token
    genesysClient.authenticate(verifierCode);
    properties.put("access.token", genesysClient.getTokens().getAccessToken());
    // Get refresh token ()
    properties.put("refresh.token", genesysClient.getTokens().getRefreshToken());
    saveProperties();
    }