Merge pull request #639 from molgenis/revert-563-feat/M10506-views

Revert "Feat: add views on tables"

armadillo/src/main/java/org/molgenis/armadillo/audit/AuditEventPublisher.java

@@ -69,7 +69,6 @@ public class AuditEventPublisher implements ApplicationEventPublisherAware {
   public static final String LIST_OBJECTS = "LIST_OBJECTS";
   public static final String UPLOAD_OBJECT = "UPLOAD_OBJECT";
   public static final String COPY_OBJECT = "COPY_OBJECT";
-  public static final String CREATE_LINKED_OBJECT = "CREATE_LINKED_OBJECT";
   public static final String MOVE_OBJECT = "MOVE_OBJECT";
   public static final String GET_OBJECT = "GET_OBJECT";
   public static final String PREVIEW_OBJECT = "PREVIEW_OBJECT";

armadillo/src/main/java/org/molgenis/armadillo/controller/DataController.java

@@ -6,9 +6,6 @@
 import static java.util.concurrent.CompletableFuture.completedFuture;
 import static org.molgenis.armadillo.audit.AuditEventPublisher.*;
 import static org.molgenis.armadillo.controller.ArmadilloUtils.getLastCommandLocation;
-import static org.molgenis.armadillo.security.RunAs.runAsSystem;
-import static org.molgenis.armadillo.storage.ArmadilloStorageService.LINK_FILE;
-import static org.molgenis.armadillo.storage.ArmadilloStorageService.PARQUET;
 import static org.obiba.datashield.core.DSMethodType.AGGREGATE;
 import static org.obiba.datashield.core.DSMethodType.ASSIGN;
 import static org.springframework.http.HttpStatus.*;
@@ -18,15 +15,12 @@
 
 import io.swagger.v3.oas.annotations.Operation;
 import io.swagger.v3.oas.annotations.Parameter;
-import io.swagger.v3.oas.annotations.media.Content;
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
-import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import io.swagger.v3.oas.annotations.security.SecurityRequirement;
 import io.swagger.v3.oas.annotations.tags.Tag;
 import jakarta.validation.Valid;
 import jakarta.validation.constraints.NotBlank;
 import jakarta.validation.constraints.Pattern;
-import java.io.InputStream;
 import java.security.Principal;
 import java.util.*;
 import java.util.concurrent.CompletableFuture;
@@ -35,12 +29,9 @@
 import org.molgenis.armadillo.command.ArmadilloCommandDTO;
 import org.molgenis.armadillo.command.Commands;
 import org.molgenis.armadillo.exceptions.ExpressionException;
-import org.molgenis.armadillo.exceptions.UnknownObjectException;
-import org.molgenis.armadillo.exceptions.UnknownVariableException;
 import org.molgenis.armadillo.model.Workspace;
 import org.molgenis.armadillo.service.DSEnvironmentCache;
 import org.molgenis.armadillo.service.ExpressionRewriter;
-import org.molgenis.armadillo.storage.ArmadilloLinkFile;
 import org.molgenis.armadillo.storage.ArmadilloStorageService;
 import org.molgenis.r.RServerResult;
 import org.molgenis.r.model.RPackage;
@@ -50,7 +41,6 @@
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.validation.annotation.Validated;
 import org.springframework.web.bind.annotation.*;
-import org.springframework.web.server.ResponseStatusException;
 
 @Tag(name = "DataSHIELD", description = "Core API that interacts with the DataSHIELD environments")
 @SecurityRequirement(name = "bearerAuth")
@@ -135,43 +125,39 @@ public ResponseEntity<Void> tableExists(
       summary = "Load table",
       description = "Load a table",
       security = {@SecurityRequirement(name = "jwt")})
-  @ApiResponses(
-      value = {
-        @ApiResponse(responseCode = "200", description = "Object loaded successfully"),
-        @ApiResponse(
-            responseCode = "404",
-            description = "Unknown project or object",
-            content = @Content(mediaType = "application/json")),
-        @ApiResponse(
-            responseCode = "401",
-            description = "Unauthorized",
-            content = @Content(mediaType = "application/json"))
-      })
   @PostMapping(value = "/load-table")
   public CompletableFuture<ResponseEntity<Void>> loadTable(
       Principal principal,
       @Valid @Pattern(regexp = SYMBOL_RE) @RequestParam String symbol,
       @Valid @Pattern(regexp = TABLE_RESOURCE_REGEX) @RequestParam String table,
       @Valid @Pattern(regexp = SYMBOL_CSV_RE) @RequestParam(required = false) String variables,
       @RequestParam(defaultValue = "false") boolean async) {
+
     java.util.regex.Pattern tableResourcePattern =
         java.util.regex.Pattern.compile(TABLE_RESOURCE_REGEX);
     HashMap<String, Object> data = getMatchedData(tableResourcePattern, table, TABLE);
     data.put(SYMBOL, symbol);
-    String project = (String) data.get(PROJECT);
-    String objectName = String.format(PATH_FORMAT, data.get(FOLDER), data.get(TABLE));
-    if (storage.hasObject(project, objectName + LINK_FILE)) {
-      return loadTableFromLinkFile(project, objectName, variables, principal, data, symbol, async);
-    } else if (storage.hasObject(project, objectName + PARQUET)) {
-      var variableList = getVariableList(variables);
-      return doLoadTable(symbol, table, variableList, principal, data, async);
-    } else {
+    if (!storage.tableExists(
+        (String) data.get(PROJECT),
+        String.format(PATH_FORMAT, data.get(FOLDER), data.get(TABLE)))) {
       data = new HashMap<>(data);
       data.put(MESSAGE, "Table not found");
       auditEventPublisher.audit(principal, LOAD_TABLE_FAILURE, data);
-      throw new ResponseStatusException(
-          NOT_FOUND, format("Project '%s' has no object '%s'", project, objectName));
+      return completedFuture(notFound().build());
     }
+    var variableList =
+        Optional.ofNullable(variables).map(it -> it.split(",")).stream()
+            .flatMap(Arrays::stream)
+            .map(String::trim)
+            .toList();
+    var result =
+        auditEventPublisher.audit(
+            commands.loadTable(symbol, table, variableList), principal, LOAD_TABLE, data);
+    return async
+        ? completedFuture(created(getLastCommandLocation()).body(null))
+        : result
+            .thenApply(ResponseEntity::ok)
+            .exceptionally(t -> status(INTERNAL_SERVER_ERROR).build());
   }
 
   @Operation(
@@ -474,75 +460,4 @@ HashMap<String, Object> getMatchedData(
     groups.put(resource, matcher.group(3));
     return groups;
   }
-
-  public List<String> getVariableList(String variables) {
-    return Optional.ofNullable(variables).map(it -> it.split(",")).stream()
-        .flatMap(Arrays::stream)
-        .map(String::trim)
-        .toList();
-  }
-
-  private CompletableFuture<ResponseEntity<Void>> doLoadTable(
-      String symbol,
-      String table,
-      List<String> variableList,
-      Principal principal,
-      Map<String, Object> data,
-      Boolean async) {
-    var result =
-        auditEventPublisher.audit(
-            commands.loadTable(symbol, table, variableList), principal, LOAD_TABLE, data);
-    return async
-        ? completedFuture(created(getLastCommandLocation()).body(null))
-        : result
-            .thenApply(ResponseEntity::ok)
-            .exceptionally(t -> status(INTERNAL_SERVER_ERROR).build());
-  }
-
-  protected List<String> getLinkedVariables(ArmadilloLinkFile linkFile, String variables) {
-    List<String> allowedVariables = List.of(linkFile.getVariables().split(","));
-    List<String> variableList = getVariableList(variables);
-    var invalidVariables =
-        variableList.stream().filter(element -> !allowedVariables.contains(element)).toList();
-    if (invalidVariables.size() > 0) {
-      String invalid = invalidVariables.toString();
-      throw new UnknownVariableException(linkFile.getProject(), linkFile.getLinkObject(), invalid);
-    }
-    return variableList.size() == 0
-        ? allowedVariables
-        : variableList.stream().filter(allowedVariables::contains).toList();
-  }
-
-  private CompletableFuture<ResponseEntity<Void>> loadTableFromLinkFile(
-      String project,
-      String objectName,
-      String variables,
-      Principal principal,
-      HashMap<String, Object> data,
-      String symbol,
-      Boolean async) {
-    InputStream armadilloLinkFileStream = storage.loadObject(project, objectName + LINK_FILE);
-    ArmadilloLinkFile linkFile =
-        storage.createArmadilloLinkFileFromStream(armadilloLinkFileStream, project, objectName);
-    String sourceProject = linkFile.getSourceProject();
-    String sourceObject = linkFile.getSourceObject();
-    if (runAsSystem(() -> storage.hasObject(sourceProject, sourceObject + PARQUET))) {
-      List<String> variableList = getLinkedVariables(linkFile, variables);
-      HashMap<String, Object> finalData = data;
-      return runAsSystem(
-          () ->
-              doLoadTable(
-                  symbol,
-                  sourceProject + "/" + sourceObject,
-                  variableList,
-                  principal,
-                  finalData,
-                  async));
-    } else {
-      data = new HashMap<>(data);
-      data.put(MESSAGE, "Object not found");
-      auditEventPublisher.audit(principal, LOAD_TABLE_FAILURE, data);
-      throw new UnknownObjectException(sourceProject, sourceObject);
-    }
-  }
 }

armadillo/src/main/java/org/molgenis/armadillo/controller/StorageController.java

@@ -1,8 +1,6 @@
 package org.molgenis.armadillo.controller;
 
-import static org.apache.logging.log4j.util.Strings.concat;
 import static org.molgenis.armadillo.audit.AuditEventPublisher.*;
-import static org.molgenis.armadillo.storage.ArmadilloStorageService.LINK_FILE;
 import static org.springframework.http.HttpStatus.NO_CONTENT;
 import static org.springframework.http.HttpStatus.OK;
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -24,10 +22,8 @@
 import jakarta.validation.constraints.NotEmpty;
 import java.io.IOException;
 import java.security.Principal;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 import org.molgenis.armadillo.audit.AuditEventPublisher;
 import org.molgenis.armadillo.exceptions.FileProcessingException;
 import org.molgenis.armadillo.exceptions.UnknownObjectException;
@@ -151,57 +147,6 @@ public void copyObject(
         Map.of(PROJECT, project, "from", object, "to", requestBody.name()));
   }
 
-  @Operation(
-      summary = "Create a view from an existing table in another project",
-      description =
-          "The view you're creating will be a symbolic link to selected variables of an existing table. It will"
-              + "look and respond like a table, but it will not take up duplicated resources")
-  @ApiResponses(
-      value = {
-        @ApiResponse(responseCode = "204", description = "Link successfully created"),
-        @ApiResponse(responseCode = "404", description = "Unknown project or object"),
-        @ApiResponse(responseCode = "409", description = "Object already exists"),
-        @ApiResponse(responseCode = "401", description = "Unauthorized")
-      })
-  @PostMapping(
-      value = "/projects/{project}/objects/link",
-      consumes = {APPLICATION_JSON_VALUE})
-  @ResponseStatus(NO_CONTENT)
-  public void createLinkedObject(
-      Principal principal,
-      @PathVariable String project,
-      @RequestBody LinkedObjectRequestBody requestBody) {
-    var variableList =
-        Optional.ofNullable(requestBody.variables()).map(it -> it.split(",")).stream()
-            .flatMap(Arrays::stream)
-            .map(String::trim)
-            .toList();
-    auditor.audit(
-        () -> {
-          try {
-            storage.createLinkedObject(
-                requestBody.sourceProject(),
-                requestBody.sourceObjectName(),
-                requestBody.linkedObject(),
-                project,
-                requestBody.variables());
-          } catch (IOException e) {
-            throw new RuntimeException(e);
-          }
-        },
-        principal,
-        CREATE_LINKED_OBJECT,
-        Map.of(
-            PROJECT,
-            project,
-            OBJECT,
-            requestBody.linkedObject() + LINK_FILE,
-            "source",
-            concat(concat(project, "/"), requestBody.linkedObject()),
-            "columns",
-            variableList));
-  }
-
   @Operation(
       summary = "Move an object within a project",
       description =