From ecafbe6e252e13d40c5971c5d60217003fd7b84b Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Tue, 30 Jun 2020 11:56:23 +0200
Subject: [PATCH] MAINT: remove SQLite and AWI related stuff
---
.../server/datatype/SQLiteDatatype.java | 26 -
.../server/jobs/extension/AWIBoxLoan.java | 562 ------------------
.../extension/AWIBoxLoanCuratorEmail.java | 92 ---
.../jobs/extension/AWIBoxLoanModel.java | 154 -----
.../AWIBoxLoanRequestLoanCuratorEmail.java | 24 -
.../AWIBoxLoanRequestReturnCuratorEmail.java | 22 -
.../server/jobs/extension/JobException.java | 42 --
.../jobs/extension/SQLiteTransaction.java | 172 ------
.../server/jobs/extension/TestAWIBoxLoan.java | 277 ---------
9 files changed, 1371 deletions(-)
delete mode 100644 src/main/java/caosdb/server/datatype/SQLiteDatatype.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/AWIBoxLoan.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/AWIBoxLoanCuratorEmail.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestLoanCuratorEmail.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestReturnCuratorEmail.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/JobException.java
delete mode 100644 src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java
delete mode 100644 src/test/java/caosdb/server/jobs/extension/TestAWIBoxLoan.java
diff --git a/src/main/java/caosdb/server/datatype/SQLiteDatatype.java b/src/main/java/caosdb/server/datatype/SQLiteDatatype.java
deleted file mode 100644
index 9a7c2f1c..00000000
--- a/src/main/java/caosdb/server/datatype/SQLiteDatatype.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package caosdb.server.datatype;
-
-@DatatypeDefinition(name = "SQLite")
-public class SQLiteDatatype extends ReferenceDatatype {}
diff --git a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoan.java b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoan.java
deleted file mode 100644
index 30dd77e0..00000000
--- a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoan.java
+++ /dev/null
@@ -1,562 +0,0 @@
-package caosdb.server.jobs.extension;
-
-import static caosdb.server.permissions.Role.ANONYMOUS_ROLE;
-
-import caosdb.server.accessControl.UserSources;
-import caosdb.server.database.exceptions.EntityDoesNotExistException;
-import caosdb.server.datatype.SingleValue;
-import caosdb.server.entity.EntityInterface;
-import caosdb.server.entity.Message;
-import caosdb.server.entity.Message.MessageType;
-import caosdb.server.entity.wrapper.Property;
-import caosdb.server.jobs.JobAnnotation;
-import caosdb.server.jobs.core.CheckPropValid;
-import caosdb.server.permissions.EntityACL;
-import caosdb.server.permissions.EntityACLFactory;
-import caosdb.server.permissions.EntityPermission;
-import caosdb.server.query.Query;
-import caosdb.server.transaction.Delete;
-import caosdb.server.transaction.Insert;
-import caosdb.server.transaction.Update;
-import caosdb.server.utils.EntityStatus;
-import caosdb.server.utils.ServerMessages;
-import caosdb.server.utils.Utils;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Objects;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-@JobAnnotation(transaction = caosdb.server.transaction.WriteTransaction.class, loadAlways = true)
-public class AWIBoxLoan extends AWIBoxLoanModel {
-
- public Logger logger = LoggerFactory.getLogger(getClass());
- private static final Message UNIQUE_USER =
- new Message("The user must have a unique combination of first name and last name!");
- private static final Message BOX_HAS_LOAN =
- new Message(
- "This box cannot be be requested right now because it appears to have a Loan property attached to it. This usually means, that the box is already requested or borrowed by someone.");
-
- @Override
- protected void run() {
- try {
- if (isAnonymous()
- && (getTransaction() instanceof Delete
- || isAcceptBorrowUpdateLoan()
- || isConfirmLoanUpdateLoan()
- || isRejectReturnUpdateLoan()
- || isAcceptReturnUpdateLoan()
- || isManualReturnUpdateBox()
- || isManualReturnUpdateLoan()
- || !(isRequestLoanSetUser()
- || isRequestLoanInsertLoan()
- || isRequestLoanUpdateBox()
- || isRequestReturnSetUser()
- || isRequestReturnUpdateLoan()))) {
- addError(ServerMessages.AUTHORIZATION_ERROR);
- getContainer()
- .addMessage(
- new Message(MessageType.Info, 0, "Anonymous users have restricted permissions."));
- return;
- }
- } catch (EntityDoesNotExistException exc) {
- addError(ServerMessages.AUTHORIZATION_ERROR);
- getContainer()
- .addMessage(
- new Message(MessageType.Info, 0, "Anonymous users have restricted permissions."));
- return;
- }
-
- try {
- if (!(getTransaction() instanceof Delete
- || isRequestLoanSetUser()
- || isRequestLoanInsertLoan()
- || isManualReturnUpdateLoan()
- || isManualReturnUpdateBox()
- || isRequestLoanUpdateBox()
- || isAcceptBorrowUpdateLoan()
- || isConfirmLoanUpdateLoan()
- || isRequestReturnSetUser()
- || isRequestReturnUpdateLoan()
- || isRejectReturnUpdateLoan())) {
- isAcceptReturnUpdateLoan();
- }
- } catch (EntityDoesNotExistException exc) {
- // ignore
- }
-
- // special ACL for boxes, loans and persons
- try {
- if (getTransaction() instanceof Insert) {
- for (EntityInterface e : getContainer()) {
- if (isBoxRecord(e)) {
- e.setEntityACL(EntityACL.combine(e.getEntityACL(), getBoxACL()));
- } else if (isLoanRecord(e)) {
- e.setEntityACL(EntityACL.combine(e.getEntityACL(), getLoanACL()));
- } else if (isPersonRecord(e)) {
- e.setEntityACL(EntityACL.combine(e.getEntityACL(), getPersonACL()));
- }
- }
- }
- } catch (EntityDoesNotExistException e) {
- }
- }
-
- boolean isManualReturnUpdateLoan() {
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e) || !hasManualReturnLoanProperties(e)) {
- logger.trace("isManualReturnUpdateLoan: false");
- return false;
- }
- }
- for (EntityInterface e : getContainer()) {
- removeAnonymousPermissions(e);
- }
- logger.trace("isManualReturnUpdateLoan: true");
- return true;
- }
-
- boolean hasManualReturnLoanProperties(EntityInterface e) {
- for (Property p : e.getProperties()) {
- if (isReturnedProperty(p)) {
- return true;
- }
- }
- return false;
- }
-
- boolean isReturnedProperty(Property p) {
- return Objects.equals(p.getId(), getReturnedId());
- }
-
- void removeAnonymousPermissions(EntityInterface e) {
- EntityACLFactory f = new EntityACLFactory();
- f.deny(ANONYMOUS_ROLE, false, EntityPermission.UPDATE_ADD_PROPERTY);
- f.deny(ANONYMOUS_ROLE, false, EntityPermission.UPDATE_REMOVE_PROPERTY);
- e.setEntityACL(EntityACL.combine(e.getEntityACL(), f.create()));
- }
-
- boolean isManualReturnUpdateBox() {
- for (EntityInterface e : getContainer()) {
- if (!isBoxRecord(e) || !hasManualReturnBoxProperties(e)) {
- logger.trace("isManualReturnUpdateBox: false");
- return false;
- }
- }
- logger.trace("isManualReturnUpdateBox: true");
- return true;
- }
-
- boolean hasManualReturnBoxProperties(EntityInterface e) {
- return validBoxHasLoanProperty(e) && boxLoanHasReturnedProperty(e);
- }
-
- boolean boxLoanHasReturnedProperty(EntityInterface e) {
- try {
- EntityInterface validBox = retrieveValidEntity(e.getId());
-
- for (Property p : validBox.getProperties()) {
- if (isLoanProperty(p)) {
- return validLoanHasReturnedProperty(p.getId());
- }
- }
- } catch (EntityDoesNotExistException exc) {
- return false;
- }
- return false;
- }
-
- boolean validLoanHasReturnedProperty(Integer id) {
- try {
- EntityInterface validLoan = retrieveValidEntity(id);
- for (Property p : validLoan.getProperties()) {
- if (isReturnedProperty(p)) {
- return true;
- }
- }
- } catch (EntityDoesNotExistException exc) {
- return false;
- }
- return false;
- }
-
- boolean isLoanProperty(Property p) {
- return Objects.equals(p.getId(), getLoanId());
- }
-
- private boolean isRejectReturnUpdateLoan() {
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e) || !hasRejectReturnProperties(e)) {
- logger.trace("isRejectReturnUpdateLoan: false");
- return false;
- }
- }
- for (EntityInterface e : getContainer()) {
- removeDestinationProperty(e);
- }
- logger.trace("isRejectReturnUpdateLoan: true");
- return true;
- }
-
- void removeDestinationProperty(EntityInterface e) {
- Iterator<Property> iterator = e.getProperties().iterator();
- while (iterator.hasNext()) {
- Property p = iterator.next();
- if (isDestinationProperty(p)) {
- iterator.remove();
- }
- }
- }
-
- boolean hasRejectReturnProperties(EntityInterface e) {
- boolean found = false;
- for (Property p : e.getProperties()) {
- if (isDestinationProperty(p)) {
- found = true;
- } else if (isReturnAcceptedProperty(p) || isReturnRequestProperty(p)) {
- logger.trace("hasRejectReturnProperties: false");
- return false;
- }
- }
- logger.trace("hasRejectReturnProperties found: {}", found);
- return found;
- }
-
- boolean isDestinationProperty(Property p) {
- return Objects.equals(p.getId(), getDestinationId());
- }
-
- boolean isAcceptReturnUpdateLoan() {
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e) || !hasAcceptReturnProperties(e)) {
- logger.trace("isAcceptReturnUpdateLoan: false");
- return false;
- }
- }
- logger.trace("isAcceptReturnUpdateLoan: true");
- return true;
- }
-
- boolean hasAcceptReturnProperties(EntityInterface e) {
- boolean found = false;
- for (Property p : e.getProperties()) {
- if (isReturnAcceptedProperty(p)) {
- found = true;
- }
- }
- return found;
- }
-
- boolean isConfirmLoanUpdateLoan() {
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e) || !hasConfirmLoanProperties(e)) {
- logger.trace("isConfirmLoanUpdateLoan: false");
- return false;
- }
- }
- // switch from destination to location
- for (EntityInterface e : getContainer()) {
- switchDestinationToLocation(e);
- }
- logger.trace("isConfirmLoanUpdateLoan: true");
- return true;
- }
-
- void switchDestinationToLocation(EntityInterface e) {
- Iterator<Property> iterator = e.getProperties().iterator();
- EntityInterface p = retrieveValidEntity(getLocationId());
- while (iterator.hasNext()) {
- Property next = iterator.next();
- if (isDestinationProperty(next)) {
- iterator.remove();
- p.setValue(next.getValue());
- e.addProperty(new Property(p));
- break;
- }
- }
- }
-
- boolean hasConfirmLoanProperties(EntityInterface e) {
- boolean found = false;
- for (Property p : e.getProperties()) {
- if (isLentProperty(p)) {
- found = true;
- } else if (isReturnAcceptedProperty(p) || isDestinationProperty(p)) {
- logger.trace("hasConfirmLoanProperties: false");
- return false;
- }
- }
- logger.trace("hasConfirmLoanProperties found: {}", found);
- return found;
- }
-
- boolean isAcceptBorrowUpdateLoan() {
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e) || !hasLoanAcceptProperties(e)) {
- logger.trace("isAcceptBorrowUpdateLoan: false");
- return false;
- }
- }
- logger.trace("isAcceptBorrowUpdateLoan: true");
- return true;
- }
-
- boolean hasLoanAcceptProperties(EntityInterface e) {
- boolean found = false;
- for (Property p : e.getProperties()) {
- if (isLoanAcceptProperty(p)) {
- found = true;
- } else if (isLentProperty(p) || isReturnAcceptedProperty(p)) {
- logger.trace("hasLoanAcceptProperties: false");
- return false;
- }
- }
- logger.trace("hasLoanAcceptProperties found: {}", found);
- return found;
- }
-
- boolean isReturnAcceptedProperty(Property p) {
- return Objects.equals(p.getId(), getReturnAcceptedId());
- }
-
- boolean isLentProperty(Property p) {
- return Objects.equals(p.getId(), getLentId());
- }
-
- boolean isLoanAcceptProperty(Property p) {
- return Objects.equals(p.getId(), getLoanAcceptedId());
- }
-
- EntityACL getPersonACL() {
- // same as loan acl - property updates are allowed for anonymous.
- return getLoanACL();
- }
-
- EntityACL getLoanACL() {
- EntityACLFactory f = new EntityACLFactory();
- f.grant(ANONYMOUS_ROLE, false, EntityPermission.UPDATE_ADD_PROPERTY);
- f.grant(ANONYMOUS_ROLE, false, EntityPermission.UPDATE_REMOVE_PROPERTY);
- return f.create();
- }
-
- EntityACL getBoxACL() {
- EntityACLFactory f = new EntityACLFactory();
- f.grant(ANONYMOUS_ROLE, false, EntityPermission.UPDATE_ADD_PROPERTY);
- f.grant(ANONYMOUS_ROLE, false, EntityPermission.UPDATE_REMOVE_PROPERTY);
- return f.create();
- }
-
- boolean isAnonymous() {
- boolean ret = getUser().hasRole(UserSources.ANONYMOUS_ROLE);
- logger.trace("is Anonymous: {}", ret);
- return ret;
- }
-
- boolean isRequestReturnUpdateLoan() {
- // is UPDATE transaction
- if (getTransaction() instanceof Update) {
- // Container has only loan elements with special properties
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e) || !hasOnlyAllowedLoanProperties4RequestReturn(e)) {
- logger.trace("isRequestReturnUpdateLoan: false");
- return false;
- }
- setReturnRequestedDate(e);
- }
- appendJob(AWIBoxLoanRequestReturnCuratorEmail.class);
- logger.trace("isRequestReturnUpdateLoan: true");
- return true;
- }
- logger.trace("isRequestReturnUpdateLoan: false");
- return false;
- }
-
- boolean isRequestReturnSetUser() {
- // same as request_loan.set_user
- logger.trace("isRequestReturnSetUser: ->");
- return isRequestLoanSetUser();
- }
-
- boolean isRequestLoanUpdateBox() {
- // is UPDATE transaction
- if (getTransaction() instanceof Update) {
- // Container has only box elements
- for (EntityInterface e : getContainer()) {
- if (validBoxHasLoanProperty(e)) {
- e.addError(BOX_HAS_LOAN);
- return false;
- }
- if (!isBoxRecord(e) || !hasOnlyAllowedBoxProperties4RequestLoan(e)) {
- return false;
- }
- // TODO this breaks the box loan functionality if any other prior changes have been made to
- // the box
- // appendJob(e, CheckNoAdditionalPropertiesPresent.class);
- }
- return true;
- }
- return false;
- }
-
- boolean validBoxHasLoanProperty(EntityInterface e) {
- try {
- EntityInterface validBox = retrieveValidEntity(e.getId());
- for (Property p : validBox.getProperties()) {
- if (isLoanProperty(p)) {
- return true;
- }
- }
- } catch (EntityDoesNotExistException exc) {
- return false;
- }
- return false;
- }
-
- /** Has only one new property -> Loan. */
- boolean hasOnlyAllowedBoxProperties4RequestLoan(EntityInterface e) {
- int count = 0;
- for (Property p : e.getProperties()) {
- if (p.getEntityStatus() == EntityStatus.QUALIFIED && Objects.equals(p.getId(), getLoanId())) {
- count++;
- }
- }
-
- // Box has only one update, a loan property
- return count == 1;
- }
-
- boolean isRequestLoanInsertLoan() {
- // is INSERT transaction
- if (getTransaction() instanceof Insert) {
- // Container has only loan elements
- for (EntityInterface e : getContainer()) {
- if (!isLoanRecord(e)) {
- return false;
- }
- }
- for (EntityInterface e : getContainer()) {
- if (isAnonymous()) {
- setCuratorAsOwner(e);
- }
- setLoanRequestDate(e);
- // TODO this check breaks the box loan functionality if any other changes have been made to
- // the box entity
- // appendJob(e, CheckNoAdditionalPropertiesPresent.class);
- // appendJob(e, CheckNoOverridesPresent.class);
- }
- appendJob(AWIBoxLoanRequestLoanCuratorEmail.class);
- return true;
- }
- return false;
- }
-
- void setCuratorAsOwner(EntityInterface e) {
- e.setEntityACL(EntityACL.getOwnerACLFor(caosdb.server.permissions.Role.create("curator")));
- }
-
- void setReturnRequestedDate(EntityInterface e) {
- // TODO setDateProperty(e, getReturnRequestedId());
- }
-
- private void setDateProperty(EntityInterface e, Integer propertyId) {
- // TODO
- EntityInterface p = retrieveValidEntity(propertyId);
- p.setValue(getTransaction().getTimestamp());
- e.addProperty(new Property(p));
- }
-
- void setLoanRequestDate(EntityInterface e) {
- // TODO setDateProperty(e, getLoanRequestedId());
- }
-
- boolean isRequestLoanSetUser() {
- // is INSERT/UPDATE transaction
- // Container has only one element, user
- if ((getTransaction() instanceof Update || getTransaction() instanceof Insert)
- && getContainer().size() == 1
- && isPersonRecord(getContainer().get(0))
- && checkUniqueName(getContainer().get(0))
- && checkEmail(getContainer().get(0))) {
- // TODO this check breaks the box loan functionality if any other changes have been made to
- // the box entity
- // appendJob(getContainer().get(0), CheckNoAdditionalPropertiesPresent.class);
- // appendJob(getContainer().get(0), CheckNoOverridesPresent.class);
- logger.trace("isRequestReturnSetUser: true");
- return true;
- }
- logger.trace("isRequestReturnSetUser: false");
- return false;
- }
-
- boolean checkEmail(EntityInterface entity) {
- runJobFromSchedule(entity, CheckPropValid.class);
- for (Property p : entity.getProperties()) {
- if (Objects.equals(p.getId(), getEmailID()) && p.getValue() instanceof SingleValue) {
- if (!Utils.isRFC822Compliant(((SingleValue) p.getValue()).toDatabaseString())) {
- p.addError(ServerMessages.EMAIL_NOT_WELL_FORMED);
- } else {
- p.setName("email"); // TODO fix webinterface to use lower-case email
- p.setNameOverride(false);
- }
- return true;
- }
- }
- return false;
- }
-
- private boolean checkUniqueName(EntityInterface entity) {
- String firstName = null;
- String lastName = null;
- Query q =
- new Query(
- "FIND "
- + getPersonID().toString()
- + " WITH "
- + getFirstNameId().toString()
- + "='"
- + firstName
- + "' AND "
- + getLastNameId().toString()
- + "='"
- + lastName
- + "'",
- getUser())
- .execute(getTransaction().getAccess());
- List<Integer> resultSet = q.getResultSet();
- if (resultSet.isEmpty()
- || (resultSet.size() == 1 && Objects.equals(resultSet.get(0), entity.getId()))) {
- return true;
- }
- entity.addError(UNIQUE_USER);
- return false;
- }
-
- /**
- * Has only 5/6 new/updated properties: content, returnRequested, destination, Borrower, comment
- * (optional), location
- *
- * @throws Message
- */
- boolean hasOnlyAllowedLoanProperties4RequestReturn(EntityInterface e) {
- runJobFromSchedule(e, CheckPropValid.class);
- // appendJob(e, CheckNoOverridesPresent.class);
-
- boolean foundReturnRequested = false;
- for (Property p : e.getProperties()) {
- if (p.getEntityStatus() == EntityStatus.QUALIFIED) { // this means update
- if (isReturnRequestProperty(p)) {
- foundReturnRequested = true;
- } else if (isReturnAcceptedProperty(p) || isReturnedProperty(p)) {
- logger.trace("hasOnlyAllowedLoanProperties4RequestReturn: false");
- return false; // this is not a returnRequest, return has already been accepted
- }
- }
- }
- logger.trace("hasOnlyAllowedLoanProperties4RequestReturn found: {}", foundReturnRequested);
- return foundReturnRequested;
- }
-
- boolean isReturnRequestProperty(Property p) {
- return Objects.equals(p.getId(), getReturnRequestedId());
- }
-}
diff --git a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanCuratorEmail.java b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanCuratorEmail.java
deleted file mode 100644
index 2bf51e76..00000000
--- a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanCuratorEmail.java
+++ /dev/null
@@ -1,92 +0,0 @@
-package caosdb.server.jobs.extension;
-
-import caosdb.datetime.DateTimeInterface;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
-import caosdb.server.datatype.ReferenceValue;
-import caosdb.server.datatype.SingleValue;
-import caosdb.server.datatype.Value;
-import caosdb.server.entity.EntityInterface;
-import caosdb.server.entity.wrapper.Property;
-import caosdb.server.utils.mail.Mail;
-import java.util.TimeZone;
-
-public abstract class AWIBoxLoanCuratorEmail extends AWIBoxLoanModel {
-
- public static final String KEY_EXT_AWI_CURATOR_EMAIL = "EXT_AWI_BOX_CURATOR_EMAIL";
- protected static final String FROM_EMAIL =
- CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_EMAIL);
- protected static final String FROM_NAME =
- CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_NAME);
- protected static final String CURATOR_EMAIL =
- CaosDBServer.getServerProperty(KEY_EXT_AWI_CURATOR_EMAIL);
-
- protected String loanToString(EntityInterface e) {
- StringBuilder s = new StringBuilder();
- for (Property p : e.getProperties()) {
- s.append("\n");
- s.append(p.getName());
- s.append(": ");
- if (p.getValue() instanceof ReferenceValue) {
- Integer id = ((ReferenceValue) p.getValue()).getId();
- if (isBorrowerProperty(p)) {
- s.append(borrowerToString(id));
- } else if (isBoxProperty(p)) {
- s.append(boxToString(id));
- } else {
- s.append(valueToString(p.getValue()));
- }
- } else {
- s.append(valueToString(p.getValue()));
- }
- }
- return s.toString();
- }
-
- private String valueToString(Value value) {
- if (value == null) {
- return "";
- }
- if (value instanceof DateTimeInterface) {
- return ((DateTimeInterface) value).toDateTimeString(TimeZone.getDefault());
- }
- if (value instanceof SingleValue) {
- return ((SingleValue) value).toDatabaseString();
- } else {
- return value.toString();
- }
- }
-
- private String boxToString(Integer id) {
- StringBuilder s = new StringBuilder();
- EntityInterface box = retrieveValidEntity(id);
- for (Property sp : box.getProperties()) {
- if (isNumberProperty(sp) || isContentProperty(sp) || isLocationProperty(sp)) {
- s.append("\n ");
- s.append(sp.getName());
- s.append(": ");
- s.append(valueToString(sp.getValue()));
- }
- }
- return s.toString();
- }
-
- private String borrowerToString(Integer id) {
- StringBuilder s = new StringBuilder();
- EntityInterface borrower = retrieveValidEntity(id);
- for (Property sp : borrower.getProperties()) {
- s.append("\n ");
- s.append(sp.getName());
- s.append(": ");
- s.append(valueToString(sp.getValue()));
- }
- return s.toString();
- }
-
- protected void sendCuratorEmail(String body, String subject) {
- for (String addr : CURATOR_EMAIL.split(" ")) {
- Mail m = new Mail(FROM_NAME, FROM_EMAIL, null, addr, subject, body);
- m.send();
- }
- }
-}
diff --git a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java
deleted file mode 100644
index 92a8a240..00000000
--- a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanModel.java
+++ /dev/null
@@ -1,154 +0,0 @@
-package caosdb.server.jobs.extension;
-
-import caosdb.server.CaosDBServer;
-import caosdb.server.database.exceptions.EntityDoesNotExistException;
-import caosdb.server.entity.EntityInterface;
-import caosdb.server.entity.Role;
-import caosdb.server.entity.wrapper.Property;
-import caosdb.server.jobs.ContainerJob;
-import caosdb.server.utils.Utils;
-import java.util.Objects;
-
-public abstract class AWIBoxLoanModel extends ContainerJob {
-
- /** Is Record and has single user parent. */
- boolean isPersonRecord(EntityInterface entity) {
- try {
- return entity.getParents().size() == 1
- && Objects.equals(
- retrieveValidIDByName(entity.getParents().get(0).getName()), getPersonID());
- } catch (EntityDoesNotExistException exc) {
- return false;
- }
- }
-
- /** Is Record an has single box parent. */
- boolean isBoxRecord(EntityInterface e) {
- return e.getRole() == Role.Record
- && e.getParents().size() == 1
- && Objects.equals(e.getParents().get(0).getId(), getBoxId());
- }
-
- /** Is Record and has single loan parent */
- boolean isLoanRecord(EntityInterface e) {
- try {
- return e.getRole() == Role.Record
- && e.getParents().size() == 1
- && Objects.equals(retrieveValidIDByName(e.getParents().get(0).getName()), getLoanId());
- } catch (EntityDoesNotExistException exc) {
- return false;
- }
- }
-
- boolean isBoxProperty(Property p) {
- return Objects.equals(p.getId(), getBoxId());
- }
-
- boolean isBorrowerProperty(Property p) {
- return Objects.equals(p.getId(), getBorrowerId());
- }
-
- boolean isLocationProperty(Property p) {
- return Objects.equals(p.getId(), getLocationId());
- }
-
- boolean isContentProperty(Property p) {
- return Objects.equals(p.getId(), getContentId());
- }
-
- boolean isNumberProperty(Property p) {
- return Objects.equals(p.getId(), getNumberId());
- }
-
- Integer getIdOf(String string) {
- String id = CaosDBServer.getServerProperty("EXT_AWI_" + string.toUpperCase() + "_ID");
- if (id != null && Utils.isNonNullInteger(id)) {
- return Integer.parseInt(id);
- }
- String name = CaosDBServer.getServerProperty("EXT_AWI_" + string.toUpperCase() + "_NAME");
- if (name == null || name.isEmpty()) {
- name = string;
- }
- return retrieveValidIDByName(name);
- }
-
- Integer getBorrowerId() {
- return getIdOf("Borrower");
- }
-
- Integer getCommentId() {
- return getIdOf("comment");
- }
-
- Integer getLocationId() {
- return getIdOf("Location");
- }
-
- Integer getDestinationId() {
- return getIdOf("destination");
- }
-
- Integer getContentId() {
- return getIdOf("Content");
- }
-
- Integer getBoxId() {
- return getIdOf("Box");
- }
-
- Integer getLoanId() {
- return getIdOf("Loan");
- }
-
- Integer getPersonID() {
- return getIdOf("Person");
- }
-
- Integer getEmailID() {
- return getIdOf("email");
- }
-
- Integer getLoanAcceptedId() {
- return getIdOf("loanAccepted");
- }
-
- Integer getReturnAcceptedId() {
- return getIdOf("returnAccepted");
- }
-
- Integer getLentId() {
- return getIdOf("lent");
- }
-
- Integer getLoanRequestedId() {
- return getIdOf("loanRequested");
- }
-
- Integer getExhaustContentsId() {
- return getIdOf("exhaustContents");
- }
-
- Integer getExpectedReturnId() {
- return getIdOf("expectedReturn");
- }
-
- Integer getReturnRequestedId() {
- return getIdOf("returnRequested");
- }
-
- Integer getLastNameId() {
- return getIdOf("lastName");
- }
-
- Integer getFirstNameId() {
- return getIdOf("firstName");
- }
-
- Integer getNumberId() {
- return getIdOf("Number");
- }
-
- Integer getReturnedId() {
- return getIdOf("returned");
- }
-}
diff --git a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestLoanCuratorEmail.java b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestLoanCuratorEmail.java
deleted file mode 100644
index ff490e99..00000000
--- a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestLoanCuratorEmail.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package caosdb.server.jobs.extension;
-
-import caosdb.server.entity.EntityInterface;
-import caosdb.server.jobs.JobAnnotation;
-import caosdb.server.jobs.JobExecutionTime;
-
-@JobAnnotation(time = JobExecutionTime.POST_TRANSACTION)
-public class AWIBoxLoanRequestLoanCuratorEmail extends AWIBoxLoanCuratorEmail {
-
- private static final String SUBJECT = "Box Loan Requests";
-
- @Override
- protected void run() {
- StringBuilder body = new StringBuilder("LOAN REQUEST(S):");
-
- if (!getContainer().isEmpty()) {
- for (EntityInterface e : getContainer()) {
- body.append("\n");
- body.append(loanToString(e));
- }
- this.sendCuratorEmail(body.toString(), SUBJECT);
- }
- }
-}
diff --git a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestReturnCuratorEmail.java b/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestReturnCuratorEmail.java
deleted file mode 100644
index 373ce0b8..00000000
--- a/src/main/java/caosdb/server/jobs/extension/AWIBoxLoanRequestReturnCuratorEmail.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package caosdb.server.jobs.extension;
-
-import caosdb.server.entity.EntityInterface;
-import caosdb.server.jobs.JobAnnotation;
-import caosdb.server.jobs.JobExecutionTime;
-
-@JobAnnotation(time = JobExecutionTime.POST_TRANSACTION)
-public class AWIBoxLoanRequestReturnCuratorEmail extends AWIBoxLoanCuratorEmail {
- private static final String SUBJECT = "Box Return Requests";
-
- @Override
- protected void run() {
- if (!getContainer().isEmpty()) {
- StringBuilder body = new StringBuilder("RETURN REQUEST(S):");
- for (EntityInterface e : getContainer()) {
- body.append("\n");
- body.append(loanToString(e));
- }
- this.sendCuratorEmail(body.toString(), SUBJECT);
- }
- }
-}
diff --git a/src/main/java/caosdb/server/jobs/extension/JobException.java b/src/main/java/caosdb/server/jobs/extension/JobException.java
deleted file mode 100644
index e41475bb..00000000
--- a/src/main/java/caosdb/server/jobs/extension/JobException.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package caosdb.server.jobs.extension;
-
-import caosdb.server.jobs.Job;
-
-public class JobException extends RuntimeException {
-
- /** */
- private static final long serialVersionUID = -2802983933079999366L;
-
- private final Job job;
-
- public JobException(final Job job, final Exception e) {
- super(e);
- this.job = job;
- }
-
- public Job getJob() {
- return this.job;
- }
-}
diff --git a/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java b/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java
deleted file mode 100644
index 4882f0af..00000000
--- a/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java
+++ /dev/null
@@ -1,172 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package caosdb.server.jobs.extension;
-
-import caosdb.server.CaosDBException;
-import caosdb.server.entity.FileProperties;
-import caosdb.server.entity.Message;
-import caosdb.server.jobs.EntityJob;
-import caosdb.server.utils.FileUtils;
-import java.io.IOException;
-import java.security.NoSuchAlgorithmException;
-import java.sql.Connection;
-import java.sql.DriverManager;
-import java.sql.ResultSet;
-import java.sql.ResultSetMetaData;
-import java.sql.SQLException;
-import java.sql.Statement;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.concurrent.locks.ReentrantLock;
-
-public class SQLiteTransaction extends EntityJob {
- private static HashMap<String, ReentrantLock> lockedTables = new HashMap<String, ReentrantLock>();
-
- @SuppressWarnings("unlikely-arg-type")
- @Override
- public final void run() {
- Connection con = null;
- try {
- if (getEntity().hasFileProperties()) {
- if (getEntity().getFileProperties().retrieveFromFileSystem() != null) {
-
- if (getEntity().hasMessage("execute")) {
- try {
- if (!lockedTables.containsKey(
- getEntity().getFileProperties().getFile().getCanonicalPath())) {
- synchronized (lockedTables) {
- lockedTables.put(
- getEntity().getFileProperties().getFile().getCanonicalPath(),
- new ReentrantLock());
- }
- }
-
- lockedTables.get(getEntity().getFileProperties().getFile().getCanonicalPath()).lock();
- try {
- con =
- getConnection(
- getEntity()
- .getFileProperties()
- .retrieveFromFileSystem()
- .getCanonicalPath());
- final Statement stmt = con.createStatement();
-
- //
- final List<Message> msgs = getEntity().getMessages("execute");
- Collections.sort(msgs);
- for (final Message m : msgs) {
- getEntity().removeMessage(m);
- stmt.execute(m.getBody());
- final ResultSet rs = stmt.getResultSet();
- final int updateCount = stmt.getUpdateCount();
- if (rs != null) {
- final ResultSetMetaData rsmd = rs.getMetaData();
- final int columns = rsmd.getColumnCount();
- final StringBuilder s = new StringBuilder();
- if (columns > 0) {
- s.append("|");
- for (int i = 1; i <= columns; i++) {
- s.append(rsmd.getColumnName(i));
- s.append("|");
- }
- s.append("\n");
- while (rs.next()) {
- s.append("|");
- for (int i = 1; i <= columns; i++) {
- s.append(rs.getString(i));
- s.append("|");
- }
- s.append("\n");
- }
- } else {
- s.append("");
- }
- final Message mret = new Message("result", m.getCode(), null, s.toString());
- getEntity().addMessage(mret);
-
- } else if (updateCount != -1) {
- final Message mret =
- new Message(
- "result",
- m.getCode(),
- null,
- Integer.toString(updateCount) + " row(s) affected by the query.");
- getEntity().addMessage(mret);
- }
- }
- } finally {
- lockedTables
- .get(getEntity().getFileProperties().getFile().getCanonicalPath())
- .unlock();
- }
- synchronized (
- lockedTables.get(getEntity().getFileProperties().getFile().getCanonicalPath())) {
- if (!lockedTables
- .get(getEntity().getFileProperties().getFile().getCanonicalPath())
- .hasQueuedThreads()) {
- lockedTables.remove(
- lockedTables.get(
- getEntity().getFileProperties().getFile().getCanonicalPath()));
- }
- }
- } finally {
- if (con != null && !con.isClosed()) {
- con.close();
- }
- resetSizeAndChecksum(getEntity().getFileProperties());
- }
- }
- }
- }
- } catch (final NoSuchAlgorithmException e) {
- throw new JobException(this, e);
- } catch (final IOException e) {
- throw new JobException(this, e);
- } catch (final CaosDBException e) {
- throw new JobException(this, e);
- } catch (final ClassNotFoundException e) {
- throw new JobException(this, e);
- } catch (final SQLException e) {
- throw new JobException(this, e);
- }
- }
-
- private static void resetSizeAndChecksum(final FileProperties f)
- throws NoSuchAlgorithmException, IOException {
- f.setSize(f.getFile().length());
- f.setChecksum(FileUtils.getChecksum(f.getFile()));
- }
-
- private static Connection getConnection(final String database)
- throws ClassNotFoundException, SQLException {
- if (!driverLoaded) {
- Class.forName("org.sqlite.JDBC");
- driverLoaded = true;
- }
- final Connection connection = DriverManager.getConnection("jdbc:sqlite:" + database);
- return connection;
- }
-
- private static boolean driverLoaded = false;
-}
diff --git a/src/test/java/caosdb/server/jobs/extension/TestAWIBoxLoan.java b/src/test/java/caosdb/server/jobs/extension/TestAWIBoxLoan.java
deleted file mode 100644
index 08a0e412..00000000
--- a/src/test/java/caosdb/server/jobs/extension/TestAWIBoxLoan.java
+++ /dev/null
@@ -1,277 +0,0 @@
-package caosdb.server.jobs.extension;
-
-import static org.junit.Assert.assertEquals;
-
-import caosdb.server.entity.container.TransactionContainer;
-import caosdb.server.jobs.core.Mode;
-import caosdb.server.transaction.Transaction;
-import caosdb.server.utils.EntityStatus;
-import java.util.Collection;
-import java.util.List;
-import java.util.concurrent.Callable;
-import org.apache.shiro.authc.AuthenticationException;
-import org.apache.shiro.authc.AuthenticationToken;
-import org.apache.shiro.authz.AuthorizationException;
-import org.apache.shiro.authz.Permission;
-import org.apache.shiro.session.Session;
-import org.apache.shiro.subject.ExecutionException;
-import org.apache.shiro.subject.PrincipalCollection;
-import org.apache.shiro.subject.Subject;
-import org.junit.Test;
-
-public class TestAWIBoxLoan {
-
- @Test
- public void testNonAnonymousUser() {
- TransactionContainer container = new TransactionContainer();
- AWIBoxLoan j =
- new AWIBoxLoan() {
-
- @Override
- protected Subject getUser() {
- return new Subject() {
-
- @Override
- public void runAs(PrincipalCollection principals)
- throws NullPointerException, IllegalStateException {}
-
- @Override
- public PrincipalCollection releaseRunAs() {
- return null;
- }
-
- @Override
- public void logout() {}
-
- @Override
- public void login(AuthenticationToken token) throws AuthenticationException {}
-
- @Override
- public boolean isRunAs() {
- return false;
- }
-
- @Override
- public boolean isRemembered() {
- return false;
- }
-
- @Override
- public boolean isPermittedAll(Collection<Permission> permissions) {
- return false;
- }
-
- @Override
- public boolean isPermittedAll(String... permissions) {
- return false;
- }
-
- @Override
- public boolean[] isPermitted(List<Permission> permissions) {
- return null;
- }
-
- @Override
- public boolean[] isPermitted(String... permissions) {
- return null;
- }
-
- @Override
- public boolean isPermitted(Permission permission) {
-
- return false;
- }
-
- @Override
- public boolean isPermitted(String permission) {
-
- return false;
- }
-
- @Override
- public boolean isAuthenticated() {
-
- return false;
- }
-
- @Override
- public boolean[] hasRoles(List<String> roleIdentifiers) {
-
- return null;
- }
-
- @Override
- public boolean hasRole(String roleIdentifier) {
-
- return false;
- }
-
- @Override
- public boolean hasAllRoles(Collection<String> roleIdentifiers) {
-
- return false;
- }
-
- @Override
- public Session getSession(boolean create) {
- return null;
- }
-
- @Override
- public Session getSession() {
- return null;
- }
-
- @Override
- public PrincipalCollection getPrincipals() {
- return null;
- }
-
- @Override
- public Object getPrincipal() {
- return null;
- }
-
- @Override
- public PrincipalCollection getPreviousPrincipals() {
- return null;
- }
-
- @Override
- public void execute(Runnable runnable) {}
-
- @Override
- public <V> V execute(Callable<V> callable) throws ExecutionException {
- return null;
- }
-
- @Override
- public void checkRoles(String... roleIdentifiers) throws AuthorizationException {}
-
- @Override
- public void checkRoles(Collection<String> roleIdentifiers)
- throws AuthorizationException {}
-
- @Override
- public void checkRole(String roleIdentifier) throws AuthorizationException {}
-
- @Override
- public void checkPermissions(Collection<Permission> permissions)
- throws AuthorizationException {}
-
- @Override
- public void checkPermissions(String... permissions) throws AuthorizationException {}
-
- @Override
- public void checkPermission(Permission permission) throws AuthorizationException {}
-
- @Override
- public void checkPermission(String permission) throws AuthorizationException {}
-
- @Override
- public Runnable associateWith(Runnable runnable) {
- return null;
- }
-
- @Override
- public <V> Callable<V> associateWith(Callable<V> callable) {
- return null;
- }
- };
- }
- };
- Transaction<TransactionContainer> t =
- new Transaction<TransactionContainer>(container, null) {
-
- @Override
- protected void transaction() throws Exception {}
-
- @Override
- protected void preTransaction() throws InterruptedException {}
-
- @Override
- protected void preCheck() throws InterruptedException, Exception {}
-
- @Override
- protected void postTransaction() throws Exception {}
-
- @Override
- protected void postCheck() {}
-
- @Override
- public boolean logHistory() {
- return false;
- }
-
- @Override
- protected void init() throws Exception {}
-
- @Override
- protected void cleanUp() {}
- };
-
- j.init(Mode.MUST, null, t);
- assertEquals(0, j.getContainer().getMessages().size());
- assertEquals(EntityStatus.QUALIFIED, j.getContainer().getStatus());
-
- // non-anonymous user
- j.run();
- assertEquals(0, j.getContainer().getMessages().size());
- assertEquals(EntityStatus.QUALIFIED, j.getContainer().getStatus());
- }
-
- @Test
- public void testAnonymousUserUnqualified() {
- TransactionContainer container = new TransactionContainer();
- AWIBoxLoan j =
- new AWIBoxLoan() {
-
- @Override
- protected Subject getUser() {
- return null;
- }
-
- @Override
- boolean isAnonymous() {
- return true;
- }
- };
- Transaction<TransactionContainer> t =
- new Transaction<TransactionContainer>(container, null) {
-
- @Override
- protected void transaction() throws Exception {}
-
- @Override
- protected void preTransaction() throws InterruptedException {}
-
- @Override
- protected void preCheck() throws InterruptedException, Exception {}
-
- @Override
- protected void postTransaction() throws Exception {}
-
- @Override
- protected void postCheck() {}
-
- @Override
- public boolean logHistory() {
- return false;
- }
-
- @Override
- protected void init() throws Exception {}
-
- @Override
- protected void cleanUp() {}
- };
-
- j.init(Mode.MUST, null, t);
- assertEquals(0, j.getContainer().getMessages().size());
- assertEquals(EntityStatus.QUALIFIED, j.getContainer().getStatus());
-
- j.run();
- assertEquals(2, j.getContainer().getMessages().size());
- assertEquals(EntityStatus.UNQUALIFIED, j.getContainer().getStatus());
- }
-}
--
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