diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 5f2f72a3ec2a684fb9e7907df0cd65b3b73973bb..10be575a25520beec4fe724c567f70db0dd23694 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -14,13 +14,7 @@ spring:
username: {{ default .Env.META_DB_USER "postgres" }}
password: {{ .Env.META_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
- featuresDatasource:
- url: {{ default .Env.FEATURES_DB_URL "jdbc:postgresql://172.22.0.1:5433/features" }}
- schema: {{ default .Env.FEATURES_DB_SCHEMA "public" }}
- main-table: {{ default .Env.FEATURES_DB_MAIN_TABLE "features" }}
- username: {{ default .Env.FEATURES_DB_USER "postgres" }}
- password: {{ .Env.FEATURES_DB_PASSWORD }}
- driver-class-name: org.postgresql.Driver
+
data:
jpa:
repositories:
@@ -96,5 +90,5 @@ services:
workflowAuthorization: {{ default .Env.WORKFLOW_AUTHORIZATION "undefined" }}
galaxy:
galaxyUsername: {{ default .Env.GALAXY_USERNAME "admin" }}
- galaxyPassword: {{ default .Env.GALAXY_PASSWORD "admin" }}
+ galaxyPassword: {{ default .Env.GALAXY_PASSWORD "password" }}
diff --git a/src/main/java/eu/hbp/mip/StartupTasks.java b/src/main/java/eu/hbp/mip/StartupTasks.java
deleted file mode 100644
index d7dc3e0958bc1613ee6afa13fbb4a8d6b9ddc836..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/StartupTasks.java
+++ /dev/null
@@ -1,87 +0,0 @@
-package eu.hbp.mip;
-
-import ch.chuv.lren.woken.messages.datasets.Dataset;
-import com.google.gson.Gson;
-import eu.hbp.mip.controllers.DatasetsApi;
-import eu.hbp.mip.controllers.MiningApi;
-import eu.hbp.mip.controllers.VariablesApi;
-import eu.hbp.mip.model.Variable;
-import eu.hbp.mip.repositories.VariableRepository;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.context.event.ApplicationReadyEvent;
-import org.springframework.context.ApplicationListener;
-import org.springframework.context.annotation.DependsOn;
-import org.springframework.stereotype.Component;
-
-
-@Component
-public class StartupTasks implements ApplicationListener<ApplicationReadyEvent> {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(StartupTasks.class);
- private static final Gson gson = new Gson();
-
- @Autowired
- private VariableRepository variableRepository;
-
- @Autowired
- private DatasetsApi datasetsApi;
-
- @Autowired
- private VariablesApi variablesApi;
-
- @Autowired
- private MiningApi miningApi;
-
- @Override
- public void onApplicationEvent(ApplicationReadyEvent event) {
-
- boolean variablesRepositoryOk = false;
-
- // Pre-fill the local variable repository with the list of datasets, interpreted here as variables
- // (a bit like a categorical variable can be split into a set of variables (a.k.a one hot encoding in Data science) )
- // Try 5 times, to be more robust in the face of cluster failures / slow startup
- // LOGGER.info("Prefill variable repository with datasets...");
- // for (int i = 0; i < 5; i++) {
- // try {
- // StringBuilder fetchedDatasets = new StringBuilder();
- // for (Dataset dataset : datasetsApi.fetchDatasets()) {
- // final String code = dataset.id().code();
- // fetchedDatasets.append(code).append(' ');
- // Variable v = variableRepository.findOne(code);
- // if (v == null) {
- // LOGGER.info("Store additional variable {}", code);
- // v = new Variable(code);
- // variableRepository.save(v);
- // }
- // }
- // LOGGER.info("Datasets fetched from Woken: " + fetchedDatasets.toString());
- // variablesRepositoryOk = true;
- // break;
- // } catch (Exception e) {
- // variablesRepositoryOk = false;
- // LOGGER.error("Cannot initialise the variable repository. Is the connection to Woken working?", e);
- // }
- // }
-
- // if (!variablesRepositoryOk) {
- // System.exit(1);
- // }
-
- /*
- for (String variableJson: variablesApi.loadVariables()) {
- String code = gson.fromJson(variableJson, Variable.class).getCode();
- MiningQuery histogram = new MiningQuery();
- histogram.setAlgorithm(new Algorithm("histogram", "histogram", false));
- histogram.setVariables(Collections.singletonList(new Variable(code)));
- histogram.setCovariables(Collections.emptyList());
- histogram.setGrouping(Collections.emptyList());
- // TODO: need to get groupings from Woken
- }
- */
-
- LOGGER.info("[OK] MIP Portal backend is ready!");
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index a1525ee96e44b2bfecc8a94ba73935ab46834ba8..20b6fb7dce662714140497d47058ef943a1a7dea 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -1,6 +1,5 @@
package eu.hbp.mip.configuration;
-import eu.hbp.mip.utils.DataUtil;
import org.flywaydb.core.Flyway;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
@@ -26,9 +25,6 @@ import javax.sql.DataSource;
@EntityScan(basePackages = "eu.hbp.mip.model")
public class PersistenceConfiguration {
- @Value("#{'${spring.featuresDatasource.main-table:features}'}")
- private String featuresMainTable;
-
@Primary
@Bean(name = "portalDatasource")
@ConfigurationProperties(prefix="spring.portalDatasource")
@@ -42,12 +38,6 @@ public class PersistenceConfiguration {
return DataSourceBuilder.create().build();
}
- @Bean(name = "featuresDatasource")
- @ConfigurationProperties(prefix="spring.featuresDatasource")
- public DataSource featuresDataSource() {
- return DataSourceBuilder.create().build();
- }
-
@Bean
@Autowired
@Qualifier("metaJdbcTemplate")
@@ -55,13 +45,6 @@ public class PersistenceConfiguration {
return new JdbcTemplate(metaDataSource());
}
- @Bean
- @Autowired
- @Qualifier("featuresJdbcTemplate")
- public JdbcTemplate featuresJdbcTemplate() {
- return new JdbcTemplate(featuresDataSource());
- }
-
@Bean(name = "entityManagerFactory")
@DependsOn("flyway")
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
@@ -80,10 +63,4 @@ public class PersistenceConfiguration {
return flyway;
}
- @Bean(name = "dataUtil")
- @Scope("singleton")
- public DataUtil dataUtil() {
- return new DataUtil(featuresJdbcTemplate(), featuresMainTable);
- }
-
}
diff --git a/src/main/java/eu/hbp/mip/controllers/GroupsApi.java b/src/main/java/eu/hbp/mip/controllers/GroupsApi.java
deleted file mode 100644
index dd71e18f4d57f75588071703140ffa40a6ff2e7d..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/GroupsApi.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/**
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-import com.google.gson.Gson;
-import com.google.gson.JsonArray;
-import com.google.gson.JsonElement;
-import com.google.gson.JsonObject;
-import eu.hbp.mip.model.Group;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import org.postgresql.util.PGobject;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.cache.annotation.Cacheable;
-import org.springframework.http.ResponseEntity;
-import org.springframework.jdbc.core.JdbcTemplate;
-import org.springframework.jdbc.support.rowset.SqlRowSet;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/groups", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/groups", description = "the groups API")
-public class GroupsApi {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(GroupsApi.class);
-
- private static final Gson gson = new Gson();
-
- @Autowired
- @Qualifier("metaJdbcTemplate")
- private JdbcTemplate metaJdbcTemplate;
-
- @Value("#{'${spring.featuresDatasource.main-table:features}'}")
- private String featuresMainTable;
-
-
- @ApiOperation(value = "Get the root group (containing all subgroups)", response = Group.class)
- @Cacheable("groups")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<Object> getTheRootGroup() {
- LOGGER.info("Get root group and its whole sub-groups tree");
-
- return ResponseEntity.ok(gson.fromJson(loadGroups(), Object.class));
- }
-
- private String loadGroups() {
- String sqlQuery = String.format(
- "SELECT * FROM meta_variables where target_table='%s'", featuresMainTable.toUpperCase());
- SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
-
- JsonObject root = new JsonObject();
- if (data.next()) {
- String json = ((PGobject) data.getObject("hierarchy")).getValue();
- root = gson.fromJson(json, JsonObject.class);
- removeVariablesRecursive(root);
- }
- return gson.toJson(root);
- }
-
- private void removeVariablesRecursive(JsonObject element) {
- if (element.has("groups")){
- for(JsonElement child : element.getAsJsonArray("groups")) {
- removeVariablesRecursive(child.getAsJsonObject());
- }
- }
- else {
- element.add("groups", new JsonArray()); // Only for compatibility with olf frontend
- }
- if(element.has("variables")) {
- element.remove("variables");
- }
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
index 3ac19450cccf0b5b709d3380a9c87443659e4f5c..f0107618159215f3f663f5bfacea9bc88532a921 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
@@ -13,7 +13,6 @@ import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.model.Variable;
import eu.hbp.mip.repositories.*;
-import eu.hbp.mip.utils.DataUtil;
import io.swagger.annotations.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -54,11 +53,6 @@ public class ModelsApi {
@Autowired
private VariableRepository variableRepository;
- @Autowired
- @Qualifier("dataUtil")
- private DataUtil dataUtil;
-
-
@ApiOperation(value = "Get models", response = Model.class, responseContainer = "List")
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<List> getModels(
@@ -95,7 +89,7 @@ public class ModelsApi {
models = models != null ? models : new LinkedList<>();
for (Model m : models) {
m.setDataset(datasetRepository.findOne(m.getDataset().getCode()));
- modelsList.add(getModelWithDataset(m));
+ modelsList.add(m);
}
return ResponseEntity.ok(modelsList);
@@ -224,7 +218,7 @@ public class ModelsApi {
Collection<String> yAxisVarsColl = new LinkedHashSet<>(yAxisVars);
model.getConfig().setyAxisVariables(new LinkedList<>(yAxisVarsColl));
- return ResponseEntity.ok(getModelWithDataset(model));
+ return ResponseEntity.ok(model);
}
@@ -285,24 +279,4 @@ public class ModelsApi {
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
- private Model getModelWithDataset(Model model)
- {
- List<String> allVars = new LinkedList<>();
- allVars.addAll(model.getDataset().getVariable());
- allVars.addAll(model.getDataset().getHeader());
- allVars.addAll(model.getDataset().getGrouping());
-
- // WokenConversions conv = new WokenConversions();
- // String filtersJson = model.getQuery().getFilters();
- // Option<FilterRule> filters = conv.toFilterRule(filtersJson);
- // String filtersSQL = conv.toSqlWhere(filters);
-
- // Gson gson = new Gson();
- // JsonObject jsonModel = gson.fromJson(gson.toJson(model, Model.class), JsonObject.class);
- // jsonModel.get("dataset").getAsJsonObject()
- // .add("data", dataUtil.getDataFromVariables(allVars, filtersSQL));
-
- return model; //gson.fromJson(jsonModel, Model.class);
- }
-
}
diff --git a/src/main/java/eu/hbp/mip/controllers/RequestsApi.java b/src/main/java/eu/hbp/mip/controllers/RequestsApi.java
index 777eac0c51ec2ed47f68d485fdbbb48dcb2df5e9..a848ff951f77bbff853780347731a55cb71c3eb3 100644
--- a/src/main/java/eu/hbp/mip/controllers/RequestsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/RequestsApi.java
@@ -11,12 +11,9 @@ import com.google.gson.JsonObject;
import eu.hbp.mip.model.Dataset;
import eu.hbp.mip.model.Query;
import eu.hbp.mip.model.StringDtoResponse;
-import eu.hbp.mip.utils.DataUtil;
import io.swagger.annotations.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -42,11 +39,6 @@ public class RequestsApi {
private static final Pattern variableExpression = Pattern.compile("\\w+");
- @Autowired
- @Qualifier("dataUtil")
- private DataUtil dataUtil;
-
-
@ApiOperation(value = "Post a request", response = Dataset.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.POST)
@@ -79,7 +71,6 @@ public class RequestsApi {
dataset.add("variable", gson.toJsonTree(variables));
dataset.add("grouping", gson.toJsonTree(groupings));
dataset.add("header", gson.toJsonTree(covariables));
- dataset.add("data", dataUtil.getDataFromVariables(allVars, filters));
return ResponseEntity.ok(gson.fromJson(dataset, Object.class));
}
diff --git a/src/main/java/eu/hbp/mip/controllers/StatsApi.java b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
index daf1b117fd5a4588d9d4d879eb37d02987cb7aaa..d09c032bc75659c18100a4f58ca3965c2e4b4933 100644
--- a/src/main/java/eu/hbp/mip/controllers/StatsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/StatsApi.java
@@ -7,7 +7,6 @@ package eu.hbp.mip.controllers;
import eu.hbp.mip.model.GeneralStats;
import eu.hbp.mip.repositories.ArticleRepository;
import eu.hbp.mip.repositories.UserRepository;
-import eu.hbp.mip.utils.DataUtil;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.slf4j.Logger;
@@ -34,10 +33,6 @@ public class StatsApi {
@Autowired
private ArticleRepository articleRepository;
- @Autowired
- @Qualifier("dataUtil")
- private DataUtil dataUtil;
-
@ApiOperation(value = "Get general statistics", response = GeneralStats.class)
@RequestMapping(method = RequestMethod.GET)
@@ -48,7 +43,6 @@ public class StatsApi {
stats.setUsers(userRepository.count());
stats.setArticles(articleRepository.count());
- stats.setVariables(dataUtil.countVariables());
return ResponseEntity.ok(stats);
}
diff --git a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
deleted file mode 100644
index 0eae7e7cf5bfcd84f75505f7d9dfb2f0596d6469..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
+++ /dev/null
@@ -1,212 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-
-import ch.chuv.lren.woken.messages.variables.VariableMetaData;
-import ch.chuv.lren.woken.messages.variables.VariablesForDatasetsQuery;
-import ch.chuv.lren.woken.messages.variables.VariablesForDatasetsResponse;
-import com.google.gson.Gson;
-import com.google.gson.JsonArray;
-import com.google.gson.JsonElement;
-import com.google.gson.JsonObject;
-
-import eu.hbp.mip.model.Algorithm;
-import eu.hbp.mip.model.MiningQuery;
-import eu.hbp.mip.model.Variable;
-import io.swagger.annotations.*;
-import org.postgresql.util.PGobject;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.cache.annotation.Cacheable;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.jdbc.core.JdbcTemplate;
-import org.springframework.jdbc.support.rowset.SqlRowSet;
-import org.springframework.web.bind.annotation.*;
-import scala.collection.JavaConversions;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.stream.Collectors;
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-@RestController
-@RequestMapping(value = "/variables", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/variables", description = "the variables API")
-public class VariablesApi {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(VariablesApi.class);
-
- private static final Gson gson = new Gson();
-
- @Autowired
- @Qualifier("metaJdbcTemplate")
- private JdbcTemplate metaJdbcTemplate;
-
- @Value("#{'${spring.featuresDatasource.main-table:features}'}")
- private String featuresMainTable;
-
- @ApiOperation(value = "Get variables", response = List.class, responseContainer = "List")
- @Cacheable("variables")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<Iterable> getVariables(
- @ApiParam(value = "List of groups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "group", required = false) String group,
- @ApiParam(value = "List of subgroups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "subgroup", required = false) String subgroup,
- @ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isVariable", required = false) String isVariable,
- @ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isGrouping", required = false) String isGrouping,
- @ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isCovariable", required = false) String isCovariable,
- @ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isFilter", required = false) String isFilter
- ) {
- LOGGER.info("Get variables");
-
- LinkedList<Object> variablesObjects = new LinkedList<>();
-
- for (String var : loadVariables())
- {
- variablesObjects.add(gson.fromJson(var, Object.class));
- }
-
- return ResponseEntity.ok(variablesObjects);
- }
-
-
-
- @ApiOperation(value = "Get a variable", response = Object.class)
- @Cacheable("variable")
- @RequestMapping(value = "/{code}", method = RequestMethod.GET)
- public ResponseEntity<Object> getAVariable(
- @ApiParam(value = "code of the variable ( multiple codes are allowed, separated by \",\" )", required = true) @PathVariable("code") String code
- ) {
- LOGGER.info("Get a variable");
-
- for (String var : loadVariables())
- {
- JsonObject varObj = gson.fromJson(var, JsonElement.class).getAsJsonObject();
- if (varObj.get("code").getAsString().equals(code))
- {
- return ResponseEntity.ok(gson.fromJson(varObj, Object.class));
- }
- }
-
- LOGGER.warn("Variable " + code + " not found ! ");
-
- return ResponseEntity.ok(null);
- }
-
-
- @ApiOperation(value = "Get values from a variable", response = List.class, responseContainer = "List")
- @Cacheable("values")
- @RequestMapping(value = "/{code}/values", method = RequestMethod.GET)
- public ResponseEntity<Iterable> getValuesFromAVariable(
- @ApiParam(value = "code", required = true) @PathVariable("code") String code,
- @ApiParam(value = "Pattern to match") @RequestParam(value = "q", required = false) String q
- ) {
- LOGGER.info("Get values from a variable");
-
- for (String var : loadVariables())
- {
- JsonObject varObj = gson.fromJson(var, JsonElement.class).getAsJsonObject();
- if (varObj.get("code").getAsString().equals(code))
- {
- JsonArray values = varObj.get("enumerations").getAsJsonArray();
- LinkedList<Object> valuesObjects = new LinkedList<>();
- for (JsonElement value : values){
- valuesObjects.add(gson.fromJson(value, Object.class));
- }
- return ResponseEntity.ok(valuesObjects);
- }
- }
-
- LOGGER.warn("Variable " + code + " not found ! ");
-
- return ResponseEntity.ok(null);
- }
-
- @ApiOperation(value = "Get groups and variables hierarchy", response = Object.class)
- @Cacheable("vars_hierarchy")
- @RequestMapping(value = "/hierarchy", method = RequestMethod.GET)
- public ResponseEntity<Object> getVariablesHierarchy(
- ) {
- LOGGER.info("Get groups and variables hierarchy");
-
- String sqlQuery = String.format(
- "SELECT * FROM meta_variables where upper(target_table)='%s'", featuresMainTable.toUpperCase());
- SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
- data.next();
- String json = ((PGobject) data.getObject("hierarchy")).getValue();
-
- Object hierarchy = gson.fromJson(json, Object.class);
-
- return ResponseEntity.ok(hierarchy);
- }
-
- @ApiOperation(value = "Get query for histograms", response = Object.class)
- @Cacheable("vars_histogram_query")
- @RequestMapping(value = "/{code}/histogram_query", method = RequestMethod.GET)
- public ResponseEntity<MiningQuery> getHistogramQuery(
- @ApiParam(value = "code", required = true) @PathVariable("code") String code
- ) {
- LOGGER.info("Get query for histograms");
-
- String sqlQuery = String.format(
- "SELECT histogram_groupings FROM meta_variables where upper(target_table)='%s'", featuresMainTable.toUpperCase());
- SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
- data.next();
- String histogramGroupings = data.getString("histogram_groupings");
-
- MiningQuery query = new MiningQuery();
- query.addVariable(new Variable(code));
- List<String> newGroups = Arrays.asList(histogramGroupings.split(","));
- List<Variable> groupings = query.getGrouping();
- groupings.addAll(newGroups.stream().map(Variable::new).collect(Collectors.toList()));
- query.setGrouping(groupings);
- query.setAlgorithm(new Algorithm("histograms", "Histograms", false));
-
- return ResponseEntity.ok(query);
- }
-
-
- public List<String> loadVariables() {
- String sqlQuery = String.format(
- "SELECT * FROM meta_variables where upper(target_table)='%s'", featuresMainTable.toUpperCase());
- SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
-
- List<String> variables = new LinkedList<>();
- if (data.next()) {
- String json = ((PGobject) data.getObject("hierarchy")).getValue();
- JsonObject root = gson.fromJson(json, JsonObject.class);
- extractVariablesRecursive(root, variables);
- }
-
- return variables;
- }
-
- private void extractVariablesRecursive(JsonObject element, List<String> variables) {
- if (element.has("groups")){
- for(JsonElement child : element.getAsJsonArray("groups")) {
- extractVariablesRecursive(child.getAsJsonObject(), variables);
- }
- }
- if (element.has("variables")){
- for (JsonElement var : element.getAsJsonArray("variables")){
- JsonObject grp = new JsonObject();
- grp.addProperty("code", element.getAsJsonPrimitive("code").getAsString());
- grp.addProperty("label", element.getAsJsonPrimitive("label").getAsString());
- var.getAsJsonObject().add("group", grp);
- var.getAsJsonObject().addProperty("isVariable", true);
- variables.add(gson.toJson(var));
- }
- }
- }
-
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/GeneralStats.java b/src/main/java/eu/hbp/mip/model/GeneralStats.java
index 939ca27de29f3bc9d21dcdd60eb343a953c71e2d..302cf8edd320149c560b5fb252bb8ab3e4fece26 100644
--- a/src/main/java/eu/hbp/mip/model/GeneralStats.java
+++ b/src/main/java/eu/hbp/mip/model/GeneralStats.java
@@ -13,7 +13,6 @@ public class GeneralStats {
private Long users = null;
private Long articles = null;
- private Long variables = null;
public GeneralStats() {
@@ -39,13 +38,4 @@ public class GeneralStats {
public void setArticles(Long articles) {
this.articles = articles;
}
-
-
- public Long getVariables() {
- return variables;
- }
-
- public void setVariables(Long variables) {
- this.variables = variables;
- }
}
diff --git a/src/main/java/eu/hbp/mip/utils/DataUtil.java b/src/main/java/eu/hbp/mip/utils/DataUtil.java
deleted file mode 100644
index 1bad9d966f8f7e86b2ed3621b5e2140fec7c429b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/utils/DataUtil.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package eu.hbp.mip.utils;
-
-import com.google.gson.JsonArray;
-import com.google.gson.JsonObject;
-import org.springframework.cache.annotation.Cacheable;
-import org.springframework.jdbc.core.JdbcTemplate;
-
-import java.util.List;
-
-/**
- * Created by mirco on 14.09.16.
- */
-
-public class DataUtil {
-
- private static final int MAX_NB_SAMPLES = 200;
-
- private JdbcTemplate jdbcTemplate;
- private String featuresMainTable;
-
- public DataUtil(JdbcTemplate jdbcTemplate, String featuresMainTable)
- {
- this.jdbcTemplate = jdbcTemplate;
- this.featuresMainTable = featuresMainTable;
- }
-
- @Cacheable("varsdata")
- public JsonObject getDataFromVariables(List<String> vars, String filterSQL)
- {
- JsonObject data = new JsonObject();
- String filters = "";
-
- if (filterSQL != null && filterSQL.length() > 0) {
- filters = String.format(
- " AND %s",
- filterSQL.replaceAll("\\\\'", "''")); // Quick and dirty workaround
- }
-
- for (String var : vars) {
- JsonArray currentVarData = new JsonArray();
-
- long nbRows = countDatasetRows();
-
- if (nbRows >= 1) {
- List<Object> queryResult;
- synchronized(this){
- // Dirty
- jdbcTemplate.execute("SELECT SETSEED(0.42)");
- // Dirty
- queryResult = jdbcTemplate.queryForList(
- String.format("SELECT %s FROM %s WHERE %s IS NOT NULL %s ORDER BY Random() LIMIT %d",
- var, featuresMainTable, var, filters, MAX_NB_SAMPLES),
- Object.class);
- }
- for (Object value : queryResult) {
- if (value == null) {
- currentVarData.add((String) null);
- } else {
- if (value instanceof Double) {
- currentVarData.add((Double) value);
- } else if (value instanceof Float) {
- currentVarData.add((Float) value);
- } else if (value instanceof Integer) {
- currentVarData.add((Integer) value);
- } else if (value instanceof Long) {
- currentVarData.add((Long) value);
- } else {
- String strValue = String.valueOf(value);
- try {
- double numValue = Double.parseDouble(strValue);
- currentVarData.add(numValue);
- } catch (NumberFormatException e2) {
- currentVarData.add(strValue);
- }
- }
- }
- }
- data.add(var, currentVarData);
- }
- }
-
- return data;
- }
-
- public JsonObject getDataFromVariables(List<String> vars)
- {
- return getDataFromVariables(vars);
- }
-
- @Cacheable("colscount")
- public long countVariables()
- {
- // Dirty
- return jdbcTemplate.queryForObject(
- "SELECT COUNT(*) FROM INFORMATION_SCHEMA.COLUMNS " +
- "WHERE table_name = '"+featuresMainTable+"'", Long.class);
- }
-
- @Cacheable("rowscount")
- public long countDatasetRows()
- {
- // Dirty
- return jdbcTemplate.queryForObject(
- "SELECT COUNT(*) FROM "+featuresMainTable, Long.class);
- }
-
-}