21885081110

Committed 10 Feb 2026 10:36PM UTC coverage: 65.419% (+0.1%) from 65.317%

Build # 21885081110

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github

Committed by

dkayiwa

Commit Message

TRUNK-6542 Editing observations should copy reference ranges

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59.82

/api/src/main/java/org/openmrs/module/ModuleUtil.java

/**
 * This Source Code Form is subject to the terms of the Mozilla Public License,
 * v. 2.0. If a copy of the MPL was not distributed with this file, You can
 * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
 * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
 *
 * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
 * graphic logo is a trademark of OpenMRS Inc.
 */
package org.openmrs.module;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Properties;
import java.util.Set;
import java.util.jar.JarEntry;
import java.util.jar.JarFile;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.ZipEntry;

import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.openmrs.GlobalProperty;
import org.openmrs.api.AdministrationService;
import org.openmrs.api.context.Context;
import org.openmrs.api.context.ServiceContext;
import org.openmrs.scheduler.SchedulerUtil;
import org.openmrs.util.OpenmrsClassLoader;
import org.openmrs.util.OpenmrsConstants;
import org.openmrs.util.OpenmrsUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.support.AbstractRefreshableApplicationContext;

/**
 * Utility methods for working and manipulating modules
 */
public class ModuleUtil {

        private ModuleUtil() {
        }
        
        private static final Logger log = LoggerFactory.getLogger(ModuleUtil.class);
        
        /**
         * Start up the module system with the given properties.
         *
         * @param props Properties (OpenMRS runtime properties)
         */
        public static void startup(Properties props) throws ModuleMustStartException {
                
                String moduleListString = props.getProperty(ModuleConstants.RUNTIMEPROPERTY_MODULE_LIST_TO_LOAD);
                
                if (moduleListString == null || moduleListString.isEmpty()) {
                        // Attempt to get all of the modules from the modules folder
                        // and store them in the modules list
                        log.debug("Starting all modules");
                        ModuleFactory.loadModules();
                } else {
                        // use the list of modules and load only those
                        log.debug("Starting all modules in this list: " + moduleListString);
                        
                        String[] moduleArray = moduleListString.split(" ");
                        List<File> modulesToLoad = new ArrayList<>();
                        
                        for (String modulePath : moduleArray) {
                                if (modulePath != null && modulePath.length() > 0) {
                                        File file = new File(modulePath);
                                        if (file.exists()) {
                                                modulesToLoad.add(file);
                                        } else {
                                                // try to load the file from the classpath
                                                InputStream stream = ModuleUtil.class.getClassLoader().getResourceAsStream(modulePath);
                                                
                                                // expand the classpath-found file to a temporary location
                                                if (stream != null) {
                                                        try {
                                                                // get and make a temp directory if necessary
                                                                String tmpDir = System.getProperty("java.io.tmpdir");
                                                                File expandedFile = File.createTempFile(file.getName() + "-", ".omod", new File(tmpDir));
                                                                
                                                                // pull the name from the absolute path load attempt
                                                                FileOutputStream outStream = new FileOutputStream(expandedFile, false);
                                                                
                                                                // do the actual file copying
                                                                OpenmrsUtil.copyFile(stream, outStream);
                                                                
                                                                // add the freshly expanded file to the list of modules we're going to start up
                                                                modulesToLoad.add(expandedFile);
                                                                expandedFile.deleteOnExit();
                                                        }
                                                        catch (IOException io) {
                                                                log.error("Unable to expand classpath found module: " + modulePath, io);
                                                        }
                                                } else {
                                                        log
                                                                .error("Unable to load module at path: "
                                                                        + modulePath
                                                                        + " because no file exists there and it is not found on the classpath. (absolute path tried: "
                                                                        + file.getAbsolutePath() + ")");
                                                }
                                        }
                                }
                        }
                        
                        ModuleFactory.loadModules(modulesToLoad);
                }
                
                // start all of the modules we just loaded
                ModuleFactory.startModules();
                
                // some debugging info
                if (log.isDebugEnabled()) {
                        Collection<Module> modules = ModuleFactory.getStartedModules();
                        if (modules == null || modules.isEmpty()) {
                                log.debug("No modules loaded");
                        } else {
                                log.debug("Found and loaded {} module(s)", modules.size());
                        }
                }
                
                // make sure all mandatory modules are loaded and started
                checkMandatoryModulesStarted();
        }
        
        /**
         * Stops the module system by calling stopModule for all modules that are currently started
         */
        public static void shutdown() {

                List<Module> modules = new ArrayList<>(ModuleFactory.getStartedModules());
                
                for (Module mod : modules) {
                        log.debug("stopping module: {}", mod.getModuleId());
                        
                        if (mod.isStarted()) {
                                ModuleFactory.stopModule(mod, true, true);
                        }
                }
                
                log.debug("done shutting down modules");
                
                // clean up the static variables just in case they weren't done before
                ModuleFactory.extensionMap.clear();
                ModuleFactory.loadedModules.invalidateAll();
                ModuleFactory.moduleClassLoaders.invalidateAll();
                ModuleFactory.startedModules.invalidateAll();
        }
        
        /**
         * Add the <code>inputStream</code> as a file in the modules repository
         *
         * @param inputStream <code>InputStream</code> to load
         * @return filename String of the file's name of the stream
         */
        public static File insertModuleFile(InputStream inputStream, String filename) {
                File folder = getModuleRepository();
                
                // check if module filename is already loaded
                if (OpenmrsUtil.folderContains(folder, filename)) {
                        throw new ModuleException(filename + " is already associated with a loaded module.");
                }
                
                File file = new File(folder.getAbsolutePath(), filename);
                
                try (FileOutputStream outputStream = new FileOutputStream(file)) {
                        OpenmrsUtil.copyFile(inputStream, outputStream);
                }
                catch (IOException e) {
                        throw new ModuleException("Can't create module file for " + filename, e);
                }
                finally {
                        try {
                                inputStream.close();
                        }
                        catch (Exception e) { /* pass */}
                }
                
                return file;
        }

        /**
         * Checks if the current OpenMRS version is in an array of versions.
         * <p>
         * This method calls {@link ModuleUtil#matchRequiredVersions(String, String)} internally.
         * </p>
         *
         * @param versions the openmrs versions to be checked against the current openmrs version
         * @return true if the current openmrs version is in versions otherwise false
         * <strong>Should</strong> return false when versions is null
         * <strong>Should</strong> return false when versions is empty
         * <strong>Should</strong> return true if current openmrs version matches one element in versions
         * <strong>Should</strong> return false if current openmrs version does not match any element in versions
         */
        public static boolean isOpenmrsVersionInVersions(String ...versions) {
                return isVersionInVersions(OpenmrsConstants.OPENMRS_VERSION_SHORT, versions);
        }

        /**
         * For testing of {@link #isOpenmrsVersionInVersions(String...)} only.
         * 
         * @param version the version
         * @param versions versions to match
         * @return true if version matches any value from versions
         */
        static boolean isVersionInVersions(String version, String ...versions) {
                if (versions == null || versions.length == 0) {
                        return false;
                }

                boolean result = false;
                for (String candidateVersion : versions) {
                        if (matchRequiredVersions(version, candidateVersion)) {
                                result = true;
                                break;
                        }
                }
                return result;
        }
        
        /**
         * This method is an enhancement of {@link #compareVersion(String, String)} and adds support for
         * wildcard characters and upperbounds. <br>
         * <br>
         * This method calls {@link ModuleUtil#checkRequiredVersion(String, String)} internally. <br>
         * <br>
         * The require version number in the config file can be in the following format:
         * <ul>
         * <li>1.2.3</li>
         * <li>1.2.*</li>
         * <li>1.2.2 - 1.2.3</li>
         * <li>1.2.* - 1.3.*</li>
         * </ul>
         * <p>
         * Again the possible require version number formats with their interpretation:
         * <ul>
         * <li>1.2.3 means 1.2.3 and above</li>
         * <li>1.2.* means any version of the 1.2.x branch. That is 1.2.0, 1.2.1, 1.2.2,... but not 1.3.0, 1.4.0</li>
         * <li>1.2.2 - 1.2.3 means 1.2.2 and 1.2.3 (inclusive)</li>
         * <li>1.2.* - 1.3.* means any version of the 1.2.x and 1.3.x branch</li>
         * </ul>
         * </p>
         *
         * @param version openmrs version number to be compared
         * @param versionRange value in the config file for required openmrs version
         * @return true if the <code>version</code> is within the <code>value</code>
         * <strong>Should</strong> allow ranged required version
         * <strong>Should</strong> allow ranged required version with wild card
         * <strong>Should</strong> allow ranged required version with wild card on one end
         * <strong>Should</strong> allow single entry for required version
         * <strong>Should</strong> allow required version with wild card
         * <strong>Should</strong> allow non numeric character required version
         * <strong>Should</strong> allow ranged non numeric character required version
         * <strong>Should</strong> allow ranged non numeric character with wild card
         * <strong>Should</strong> allow ranged non numeric character with wild card on one end
         * <strong>Should</strong> return false when openmrs version beyond wild card range
         * <strong>Should</strong> return false when required version beyond openmrs version
         * <strong>Should</strong> return false when required version with wild card beyond openmrs version
         * <strong>Should</strong> return false when required version with wild card on one end beyond openmrs version
         * <strong>Should</strong> return false when single entry required version beyond openmrs version
         * <strong>Should</strong> allow release type in the version
         * <strong>Should</strong> match when revision number is below maximum revision number
         * <strong>Should</strong> not match when revision number is above maximum revision number
         * <strong>Should</strong> correctly set upper and lower limit for versionRange with qualifiers and wild card
         * <strong>Should</strong> match when version has wild card plus qualifier and is within boundary
         * <strong>Should</strong> not match when version has wild card plus qualifier and is outside boundary
         * <strong>Should</strong> match when version has wild card and is within boundary
         * <strong>Should</strong> not match when version has wild card and is outside boundary
         * <strong>Should</strong> return true when required version is empty
         */
        public static boolean matchRequiredVersions(String version, String versionRange) {
                // There is a null check so no risk in keeping the literal on the right side
                if (StringUtils.isNotEmpty(versionRange)) {
                        String[] ranges = versionRange.split(",");
                        for (String range : ranges) {
                                // need to externalize this string
                                String separator = "-";
                                if (range.indexOf("*") > 0 || range.indexOf(separator) > 0 && (!isVersionWithQualifier(range))) {
                                        // if it contains "*" or "-" then we must separate those two
                                        // assume it's always going to be two part
                                        // assign the upper and lower bound
                                        // if there's no "-" to split lower and upper bound
                                        // then assign the same value for the lower and upper
                                        String lowerBound = range;
                                        String upperBound = range;
                                        
                                        int indexOfSeparator = range.indexOf(separator);
                                        while (indexOfSeparator > 0) {
                                                lowerBound = range.substring(0, indexOfSeparator);
                                                upperBound = range.substring(indexOfSeparator + 1);
                                                if (upperBound.matches("^\\s?\\d+.*")) {
                                                        break;
                                                }
                                                indexOfSeparator = range.indexOf(separator, indexOfSeparator + 1);
                                        }
                                        
                                        // only preserve part of the string that match the following format:
                                        // - xx.yy.*
                                        // - xx.yy.zz*
                                        lowerBound = StringUtils.remove(lowerBound, lowerBound.replaceAll("^\\s?\\d+[\\.\\d+\\*?|\\.\\*]+", ""));
                                        upperBound = StringUtils.remove(upperBound, upperBound.replaceAll("^\\s?\\d+[\\.\\d+\\*?|\\.\\*]+", ""));
                                        
                                        // if the lower contains "*" then change it to zero
                                        if (lowerBound.indexOf("*") > 0) {
                                                lowerBound = lowerBound.replaceAll("\\*", "0");
                                        }
                                        
                                        // if the upper contains "*" then change it to maxRevisionNumber
                                        if (upperBound.indexOf("*") > 0) {
                                                upperBound = upperBound.replaceAll("\\*", Integer.toString(Integer.MAX_VALUE));
                                        }
                                        
                                        int lowerReturn = compareVersionIgnoringQualifier(version, lowerBound);
                                        
                                        int upperReturn = compareVersionIgnoringQualifier(version, upperBound);
                                        
                                        if (lowerReturn < 0 || upperReturn > 0) {
                                                log.debug("Version " + version + " is not between " + lowerBound + " and " + upperBound);
                                        } else {
                                                return true;
                                        }
                                } else {
                                        if (compareVersionIgnoringQualifier(version, range) < 0) {
                                                log.debug("Version " + version + " is below " + range);
                                        } else {
                                                return true;
                                        }
                                }
                        }
                }
                else {
                        //no version checking if required version is not specified
                        return true;
                }
                
                return false;
        }
        
        /**
         * This method is an enhancement of {@link #compareVersion(String, String)} and adds support for
         * wildcard characters and upperbounds. <br>
         * <br>
         * <br>
         * The require version number in the config file can be in the following format:
         * <ul>
         * <li>1.2.3</li>
         * <li>1.2.*</li>
         * <li>1.2.2 - 1.2.3</li>
         * <li>1.2.* - 1.3.*</li>
         * </ul>
         * <p>
         * Again the possible require version number formats with their interpretation:
         * <ul>
         * <li>1.2.3 means 1.2.3 and above</li>
         * <li>1.2.* means any version of the 1.2.x branch. That is 1.2.0, 1.2.1, 1.2.2,... but not 1.3.0, 1.4.0</li>
         * <li>1.2.2 - 1.2.3 means 1.2.2 and 1.2.3 (inclusive)</li>
         * <li>1.2.* - 1.3.* means any version of the 1.2.x and 1.3.x branch</li>
         * </ul>
         * </p>
         *
         * @param version openmrs version number to be compared
         * @param versionRange value in the config file for required openmrs version
         * @throws ModuleException if the <code>version</code> is not within the <code>value</code>
         * <strong>Should</strong> throw ModuleException if openmrs version beyond wild card range
         * <strong>Should</strong> throw ModuleException if required version beyond openmrs version
         * <strong>Should</strong> throw ModuleException if required version with wild card beyond openmrs version
         * <strong>Should</strong> throw ModuleException if required version with wild card on one end beyond openmrs
         *         version
         * <strong>Should</strong> throw ModuleException if single entry required version beyond openmrs version
         * <strong>Should</strong> throw ModuleException if SNAPSHOT not handled correctly
         * <strong>Should</strong> handle SNAPSHOT versions
         * <strong>Should</strong> handle ALPHA versions
         */
        public static void checkRequiredVersion(String version, String versionRange) throws ModuleException {
                if (!matchRequiredVersions(version, versionRange)) {
                        String ms = Context.getMessageSourceService().getMessage("Module.requireVersion.outOfBounds",
                            new String[] { versionRange, version }, Context.getLocale());
                        throw new ModuleException(ms);
                }
        }
        
        /**
         * Compare two version strings.
         *
         * @param versionA String like 1.9.2.0, may include a qualifier like "-SNAPSHOT", may be null
         * @param versionB String like 1.9.2.0, may include a qualifier like "-SNAPSHOT", may be null
         * @return the value <code>0</code> if versions are equal; a value less than <code>0</code> if first version is
         *                    before the second one; a value greater than <code>0</code> if first version is after the second one.
         *                    If version numbers are equal and only one of them has a qualifier, the version without the qualifier is
         *                    considered greater.
         */
        public static int compareVersion(String versionA, String versionB) {
                return compareVersion(versionA, versionB, false);
        }

        /**
         * Compare two version strings. Any version qualifiers are ignored in the comparison.
         *
         * @param versionA String like 1.9.2.0, may include a qualifier like "-SNAPSHOT", may be null
         * @param versionB String like 1.9.2.0, may include a qualifier like "-SNAPSHOT", may be null
         * @return the value <code>0</code> if versions are equal; a value less than <code>0</code> if first version is
         *                    before the second one; a value greater than <code>0</code> if first version is after the second one.
         */
        public static int compareVersionIgnoringQualifier(String versionA, String versionB) {
                return compareVersion(versionA, versionB, true);
        }

        private static int compareVersion(String versionA, String versionB, boolean ignoreQualifier) {
                try {
                        if (versionA == null || versionB == null) {
                                return 0;
                        }

                        List<String> versionANumbers = new ArrayList<>();
                        List<String> versionBNumbers = new ArrayList<>();
                        String qualifierSeparator = "-";

                        // strip off any qualifier e.g. "-SNAPSHOT"
                        int qualifierIndexA = versionA.indexOf(qualifierSeparator);
                        if (qualifierIndexA != -1) {
                                versionA = versionA.substring(0, qualifierIndexA);
                        }

                        // strip off any qualifier e.g. "-SNAPSHOT"
                        int qualifierIndexB = versionB.indexOf(qualifierSeparator);
                        if (qualifierIndexB != -1) {
                                versionB = versionB.substring(0, qualifierIndexB);
                        }

                        Collections.addAll(versionANumbers, versionA.split("\\."));
                        Collections.addAll(versionBNumbers, versionB.split("\\."));

                        // match the sizes of the lists
                        while (versionANumbers.size() < versionBNumbers.size()) {
                                versionANumbers.add("0");
                        }
                        while (versionBNumbers.size() < versionANumbers.size()) {
                                versionBNumbers.add("0");
                        }

                        for (int x = 0; x < versionANumbers.size(); x++) {
                                String verAPartString = versionANumbers.get(x).trim();
                                String verBPartString = versionBNumbers.get(x).trim();
                                Long verAPart = NumberUtils.toLong(verAPartString, 0);
                                Long verBPart = NumberUtils.toLong(verBPartString, 0);

                                int ret = verAPart.compareTo(verBPart);
                                if (ret != 0) {
                                        return ret;
                                }
                        }
                        
                        // At this point the version numbers are equal.
                        if (!ignoreQualifier) {
                                if (qualifierIndexA >= 0 && qualifierIndexB < 0) {
                                        return -1;
                                } else if (qualifierIndexA < 0 && qualifierIndexB >= 0) {
                                        return 1;
                                }
                        }
                }
                catch (NumberFormatException e) {
                        log.error("Error while converting a version/value to an integer: " + versionA + "/" + versionB, e);
                }
                
                // default return value if an error occurs or elements are equal
                return 0;
        }
        
        /**
         * Checks for qualifier version (i.e "-SNAPSHOT", "-ALPHA" etc. after maven version conventions)
         *
         * @param version String like 1.9.2-SNAPSHOT
         * @return true if version contains qualifier
         */
        public static boolean isVersionWithQualifier(String version) {
                Matcher matcher = Pattern.compile("(\\d+)\\.(\\d+)(\\.(\\d+))?(\\-([A-Za-z]+))").matcher(version);
                return matcher.matches();
        }
        
        /**
         * Gets the folder where modules are stored. ModuleExceptions are thrown on errors
         *
         * @return folder containing modules
         * <strong>Should</strong> use the runtime property as the first choice if specified
         * <strong>Should</strong> return the correct file if the runtime property is an absolute path
         */
        public static File getModuleRepository() {
                
                String folderName = Context.getRuntimeProperties().getProperty(ModuleConstants.REPOSITORY_FOLDER_RUNTIME_PROPERTY);
                if (StringUtils.isBlank(folderName)) {
                        AdministrationService as = Context.getAdministrationService();
                        folderName = as.getGlobalProperty(ModuleConstants.REPOSITORY_FOLDER_PROPERTY,
                            ModuleConstants.REPOSITORY_FOLDER_PROPERTY_DEFAULT);
                }
                // try to load the repository folder straight away.
                File folder = new File(folderName);
                
                // if the property wasn't a full path already, assume it was intended to be a folder in the
                // application directory
                if (!folder.exists()) {
                        folder = new File(OpenmrsUtil.getApplicationDataDirectory(), folderName);
                }
                
                // now create the modules folder if it doesn't exist
                if (!folder.exists()) {
                        log.warn("Module repository " + folder.getAbsolutePath() + " doesn't exist.  Creating directories now.");
                        folder.mkdirs();
                }
                
                if (!folder.isDirectory()) {
                        throw new ModuleException("Module repository is not a directory at: " + folder.getAbsolutePath());
                }
                
                return folder;
        }
        
        /**
         * Utility method to convert a {@link File} object to a local URL.
         *
         * @param file a file object
         * @return absolute URL that points to the given file
         * @throws MalformedURLException if file can't be represented as URL for some reason
         */
        public static URL file2url(final File file) throws MalformedURLException {
                if (file == null) {
                        return null;
                }
                try {
                        return file.getCanonicalFile().toURI().toURL();
                }
                catch (IOException | NoSuchMethodError ioe) {
                        throw new MalformedURLException("Cannot convert: " + file.getName() + " to url");
                }
        }
        
        /**
         * Expand the given <code>fileToExpand</code> jar to the <code>tmpModuleFile</code> directory
         *
         * If <code>name</code> is null, the entire jar is expanded. If<code>name</code> is not null,
         * then only that path/file is expanded.
         *
         * @param fileToExpand file pointing at a .jar
         * @param tmpModuleDir directory in which to place the files
         * @param name filename inside of the jar to look for and expand
         * @param keepFullPath if true, will recreate entire directory structure in tmpModuleDir
         *            relating to <code>name</code>. if false will start directory structure at
         *            <code>name</code>
         * @throws UnsupportedOperationException if an entry would be extracted outside of tmpModuleDir (Zip slip attack)
         * <strong>Should</strong> expand entire jar if name is null
         * <strong>Should</strong> expand entire jar if name is empty string
         * <strong>Should</strong> expand directory with parent tree if name is directory and keepFullPath is true
         * <strong>Should</strong> expand directory without parent tree if name is directory and keepFullPath is false
         * <strong>Should</strong> expand file with parent tree if name is file and keepFullPath is true
         * <strong>Should</strong> throw exception for Zip slip attack
         */
        public static void expandJar(File fileToExpand, File tmpModuleDir, String name, boolean keepFullPath) throws IOException {
                String docBase = tmpModuleDir.getAbsolutePath();
                try (JarFile jarFile = new JarFile(fileToExpand)) {
                        Enumeration<JarEntry> jarEntries = jarFile.entries();
                        boolean foundName = (name == null);
                        
                        // loop over all of the elements looking for the match to 'name'
                        while (jarEntries.hasMoreElements()) {
                                JarEntry jarEntry = jarEntries.nextElement();
                                if (name == null || jarEntry.getName().startsWith(name)) {
                                        String entryName = jarEntry.getName();
                                        // trim out the name path from the name of the new file
                                        if (!keepFullPath && name != null) {
                                                entryName = entryName.replaceFirst(name, "");
                                        }
                                        
                                        // if it has a slash, it's in a directory
                                        int last = entryName.lastIndexOf('/');
                                        if (last >= 0) {
                                                File parent = new File(docBase, entryName.substring(0, last));
                                                if (!parent.toPath().normalize().startsWith(docBase)) {
                                                        throw new UnsupportedOperationException("Attempted to create directory '" + entryName + "' rejected as it attempts to write outside the chosen directory. This may be the result of a zip-slip style attack.");
                                                }
                                                parent.mkdirs();
                                                log.debug("Creating parent dirs: " + parent.getAbsolutePath());
                                        }
                                        // we don't want to "expand" directories or empty names
                                        if (entryName.endsWith("/") || "".equals(entryName)) {
                                                continue;
                                        }
                                        try(InputStream input = jarFile.getInputStream(jarEntry)) {
                                                expand(input, docBase, entryName);
                                        }
                                        foundName = true;
                                }
                        }
                        if (!foundName) {
                                log.debug("Unable to find: " + name + " in file " + fileToExpand.getAbsolutePath());
                        }
                        
                }
                catch (IOException e) {
                        log.warn("Unable to delete tmpModuleFile on error", e);
                        throw e;
                }
        }
        
        /**
         * Expand the given file in the given stream to a location (fileDir/name) The <code>input</code>
         * InputStream is not closed in this method
         *
         * @param input stream to read from
         * @param fileDir directory to copy to
         * @param name file/directory within the <code>fileDir</code> to which we expand
         *            <code>input</code>
         * @return File the file created by the expansion.
         * @throws IOException if an error occurred while copying
         */
        private static void expand(InputStream input, String fileDir, String name) throws IOException {
                log.debug("expanding: {}", name);

                File file = new File(fileDir, name);

                if (!file.toPath().normalize().startsWith(fileDir)) {
                        throw new UnsupportedOperationException("Attempted to write file '" + name + "' rejected as it attempts to write outside the chosen directory. This may be the result of a zip-slip style attack.");
                }
                
                try (FileOutputStream outStream = new FileOutputStream(file)) {
                        OpenmrsUtil.copyFile(input, outStream);
                }
        }
        
        /**
         * Downloads the contents of a URL and copies them to a string (Borrowed from oreilly)
         *
         * @param url
         * @return InputStream of contents
         * <strong>Should</strong> return a valid input stream for old module urls
         */
        public static InputStream getURLStream(URL url) {
                InputStream in = null;
                try {
                        URLConnection uc = url.openConnection();
                        uc.setDefaultUseCaches(false);
                        uc.setUseCaches(false);
                        uc.setRequestProperty("Cache-Control", "max-age=0,no-cache");
                        uc.setRequestProperty("Pragma", "no-cache");
                        
                        log.debug("Logging an attempt to connect to: " + url);
                        
                        in = openConnectionCheckRedirects(uc);
                }
                catch (IOException io) {
                        log.warn("io while reading: " + url, io);
                }
                
                return in;
        }
        
        /**
         * Convenience method to follow http to https redirects. Will follow a total of 5 redirects,
         * then fail out due to foolishness on the url's part.
         *
         * @param c the {@link URLConnection} to open
         * @return an {@link InputStream} that is not necessarily at the same url, possibly at a 403
         *         redirect.
         * @throws IOException
         * @see #getURLStream(URL)
         */
        protected static InputStream openConnectionCheckRedirects(URLConnection c) throws IOException {
                boolean redir;
                int redirects = 0;
                InputStream in;
                do {
                        if (c instanceof HttpURLConnection) {
                                ((HttpURLConnection) c).setInstanceFollowRedirects(false);
                        }
                        // We want to open the input stream before getting headers
                        // because getHeaderField() et al swallow IOExceptions.
                        in = c.getInputStream();
                        redir = false;
                        if (c instanceof HttpURLConnection) {
                                HttpURLConnection http = (HttpURLConnection) c;
                                int stat = http.getResponseCode();
                                if (stat == 300 || stat == 301 || stat == 302 || stat == 303 || stat == 305 || stat == 307) {
                                        URL base = http.getURL();
                                        String loc = http.getHeaderField("Location");
                                        URL target = null;
                                        if (loc != null) {
                                                target = new URL(base, loc);
                                        }
                                        http.disconnect();
                                        // Redirection should be allowed only for HTTP and HTTPS
                                        // and should be limited to 5 redirects at most.
                                        if (target == null || !("http".equals(target.getProtocol()) || "https".equals(target.getProtocol()))
                                                || redirects >= 5) {
                                                throw new SecurityException("illegal URL redirect");
                                        }
                                        redir = true;
                                        c = target.openConnection();
                                        redirects++;
                                }
                        }
                } while (redir);
                return in;
        }
        
        /**
         * Downloads the contents of a URL and copies them to a string (Borrowed from oreilly)
         *
         * @param url
         * @return String contents of the URL
         * <strong>Should</strong> return an update rdf page for old https dev urls
         * <strong>Should</strong> return an update rdf page for old https module urls
         * <strong>Should</strong> return an update rdf page for module urls
         */
        public static String getURL(URL url) {
                InputStream in = null;
                ByteArrayOutputStream out = null;
                String output = "";
                try {
                        in = getURLStream(url);
                        if (in == null) {
                                // skip this module if updateURL is not defined
                                return "";
                        }
                        
                        out = new ByteArrayOutputStream();
                        OpenmrsUtil.copyFile(in, out);
                        output = out.toString(StandardCharsets.UTF_8.name());
                }
                catch (IOException io) {
                        log.warn("io while reading: " + url, io);
                }
                finally {
                        try {
                                in.close();
                        }
                        catch (Exception e) { /* pass */}
                        try {
                                out.close();
                        }
                        catch (Exception e) { /* pass */}
                }
                
                return output;
        }
        
        /**
         * Iterates over the modules and checks each update.rdf file for an update
         *
         * @return True if an update was found for one of the modules, false if none were found
         * @throws ModuleException
         */
        public static Boolean checkForModuleUpdates() throws ModuleException {
                
                Boolean updateFound = false;
                
                for (Module mod : ModuleFactory.getLoadedModules()) {
                        String updateURL = mod.getUpdateURL();
                        if (StringUtils.isNotEmpty(updateURL)) {
                                try {
                                        // get the contents pointed to by the url
                                        URL url = new URL(updateURL);
                                        if (!url.toString().endsWith(ModuleConstants.UPDATE_FILE_NAME)) {
                                                log.warn("Illegal url: " + url);
                                                continue;
                                        }
                                        String content = getURL(url);
                                        
                                        // skip empty or invalid updates
                                        if ("".equals(content)) {
                                                continue;
                                        }
                                        
                                        // process and parse the contents
                                        UpdateFileParser parser = new UpdateFileParser(content);
                                        parser.parse();
                                        
                                        log.debug("Update for mod: " + mod.getModuleId() + " compareVersion result: "
                                                + compareVersion(mod.getVersion(), parser.getCurrentVersion()));
                                        
                                        // check the update.rdf version against the installed version
                                        if (compareVersion(mod.getVersion(), parser.getCurrentVersion()) < 0) {
                                                if (mod.getModuleId().equals(parser.getModuleId())) {
                                                        mod.setDownloadURL(parser.getDownloadURL());
                                                        mod.setUpdateVersion(parser.getCurrentVersion());
                                                        updateFound = true;
                                                } else {
                                                        log.warn("Module id does not match in update.rdf:" + parser.getModuleId());
                                                }
                                        } else {
                                                mod.setDownloadURL(null);
                                                mod.setUpdateVersion(null);
                                        }
                                }
                                catch (ModuleException e) {
                                        log.warn("Unable to get updates from update.xml", e);
                                }
                                catch (MalformedURLException e) {
                                        log.warn("Unable to form a URL object out of: " + updateURL, e);
                                }
                        }
                }
                
                return updateFound;
        }
        
        /**
         * @return true/false whether the 'allow upload' or 'allow web admin' property has been turned
         *         on
         */
        public static Boolean allowAdmin() {
                
                Properties properties = Context.getRuntimeProperties();
                String prop = properties.getProperty(ModuleConstants.RUNTIMEPROPERTY_ALLOW_UPLOAD, null);
                if (prop == null) {
                        prop = properties.getProperty(ModuleConstants.RUNTIMEPROPERTY_ALLOW_ADMIN, "false");
                }
                
                return "true".equals(prop);
        }
        
        /**
         * @see ModuleUtil#refreshApplicationContext(AbstractRefreshableApplicationContext, boolean, Module)
         */
        public static AbstractRefreshableApplicationContext refreshApplicationContext(AbstractRefreshableApplicationContext ctx) {
                return refreshApplicationContext(ctx, false, null);
        }
        
        /**
         * Refreshes the given application context "properly" in OpenMRS. Will first shut down the
         * Context and destroy the classloader, then will refresh and set everything back up again.
         *
         * @param ctx Spring application context that needs refreshing.
         * @param isOpenmrsStartup if this refresh is being done at application startup.
         * @param startedModule the module that was just started and waiting on the context refresh.
         * @return AbstractRefreshableApplicationContext The newly refreshed application context.
         */
        public static AbstractRefreshableApplicationContext refreshApplicationContext(AbstractRefreshableApplicationContext ctx,
                boolean isOpenmrsStartup, Module startedModule) {
                //notify all started modules that we are about to refresh the context
                Set<Module> startedModules = new LinkedHashSet<>(ModuleFactory.getStartedModulesInOrder());
                for (Module module : startedModules) {
                        try {
                                if (module.getModuleActivator() != null) {
                                        log.debug("Run module willRefreshContext: {}", module.getModuleId());
                                        Thread.currentThread().setContextClassLoader(ModuleFactory.getModuleClassLoader(module));
                                        module.getModuleActivator().willRefreshContext();
                                }
                        }
                        catch (Error e) {
                                log.warn("Unable to call willRefreshContext() method in the module's activator", e);
                        }
                }
                
                OpenmrsClassLoader.saveState();
                SchedulerUtil.shutdown();
                ServiceContext.destroyInstance();
                
                try {
                        ctx.stop();
                        ctx.close();
                }
                catch (Exception e) {
                        log.warn("Exception while stopping and closing context: ", e);
                        // Spring seems to be trying to refresh the context instead of /just/ stopping
                        // pass
                }
                OpenmrsClassLoader.destroyInstance();
                ctx.setClassLoader(OpenmrsClassLoader.getInstance());
                Thread.currentThread().setContextClassLoader(OpenmrsClassLoader.getInstance());
                
                log.debug("Refreshing context");
                ServiceContext.getInstance().startRefreshingContext();
                try {
                        ctx.refresh();
                }
                finally {
                        ServiceContext.getInstance().doneRefreshingContext();
                }
                log.debug("Done refreshing context");
                
                ctx.setClassLoader(OpenmrsClassLoader.getInstance());
                Thread.currentThread().setContextClassLoader(OpenmrsClassLoader.getInstance());
                
                OpenmrsClassLoader.restoreState();
                log.debug("Startup scheduler");
                SchedulerUtil.startup(Context.getRuntimeProperties());
                
                OpenmrsClassLoader.setThreadsToNewClassLoader();
                
                // reload the advice points that were lost when refreshing Spring
                log.debug("Reloading advice for all started modules: {}", startedModules.size());
                
                try {
                        //The call backs in this block may need lazy loading of objects
                        //which will fail because we use an OpenSessionInViewFilter whose opened session
                        //was closed when the application context was refreshed as above.
                        //So we need to open another session now. TRUNK-3739
                        Context.openSessionWithCurrentUser();
                        for (Module module : startedModules) {
                                if (!module.isStarted()) {
                                        continue;
                                }
                                
                                ModuleFactory.loadAdvice(module);
                                try {
                                        ModuleFactory.passDaemonToken(module);
                                        
                                        if (module.getModuleActivator() != null) {
                                                log.debug("Run module contextRefreshed: {}", module.getModuleId());
                                                module.getModuleActivator().contextRefreshed();
                                                try {
                                                        //if it is system start up, call the started method for all started modules
                                                        if (isOpenmrsStartup) {
                                                                log.debug("Run module started: {}", module.getModuleId());
                                                                module.getModuleActivator().started();
                                                        }
                                                        //if refreshing the context after a user started or uploaded a new module
                                                        else if (!isOpenmrsStartup && module.equals(startedModule)) {
                                                                log.debug("Run module started: {}", module.getModuleId());
                                                                module.getModuleActivator().started();
                                                        }
                                                        log.debug("Done running module started: {}", module.getModuleId());
                                                }
                                                catch (Error e) {
                                                        log.warn("Unable to invoke started() method on the module's activator", e);
                                                        ModuleFactory.stopModule(module, true, true);
                                                }
                                        }
                                        
                                }
                                catch (Error e) {
                                        log.warn("Unable to invoke method on the module's activator ", e);
                                }
                        }
                }
                finally {
                        Context.closeSessionWithCurrentUser();
                }
                
                return ctx;
        }
        
        /**
         * Looks at the &lt;moduleid&gt;.mandatory properties and at the currently started modules to make
         * sure that all mandatory modules have been started successfully.
         *
         * @throws ModuleException if a mandatory module isn't started
         * <strong>Should</strong> throw ModuleException if a mandatory module is not started
         */
        protected static void checkMandatoryModulesStarted() throws ModuleException {
                
                List<String> mandatoryModuleIds = getMandatoryModules();
                Set<String> startedModuleIds = ModuleFactory.getStartedModulesMap().keySet();
                
                mandatoryModuleIds.removeAll(startedModuleIds);
                
                // any module ids left in the list are not started
                if (!mandatoryModuleIds.isEmpty()) {
                        throw new MandatoryModuleException(mandatoryModuleIds);
                }
        }
        
        /**
         * Returns all modules that are marked as mandatory. Currently this means there is a
         * &lt;moduleid&gt;.mandatory=true global property.
         *
         * @return list of modules ids for mandatory modules
         * <strong>Should</strong> return mandatory module ids
         */
        public static List<String> getMandatoryModules() {
                
                List<String> mandatoryModuleIds = new ArrayList<>();
                
                try {
                        List<GlobalProperty> props = Context.getAdministrationService().getGlobalPropertiesBySuffix(".mandatory");
                        
                        for (GlobalProperty prop : props) {
                                if ("true".equalsIgnoreCase(prop.getPropertyValue())) {
                                        mandatoryModuleIds.add(prop.getProperty().replace(".mandatory", ""));
                                }
                        }
                }
                catch (Exception e) {
                        log.warn("Unable to get the mandatory module list", e);
                }
                
                return mandatoryModuleIds;
        }
        
        /**
         * <pre>
         * Gets the module that should handle a path. The path you pass in should be a module id (in
         * path format, i.e. /ui/springmvc, not ui.springmvc) followed by a resource. Something like
         * the following:
         *   /ui/springmvc/css/ui.css
         *
         * The first running module out of the following would be returned:
         *   ui.springmvc.css
         *   ui.springmvc
         *   ui
         * </pre>
         *
         * @param path
         * @return the running module that matches the most of the given path
         * <strong>Should</strong> handle ui springmvc css ui dot css when ui dot springmvc module is running
         * <strong>Should</strong> handle ui springmvc css ui dot css when ui module is running
         * <strong>Should</strong> return null for ui springmvc css ui dot css when no relevant module is running
         */
        public static Module getModuleForPath(String path) {
                int ind = path.lastIndexOf('/');
                if (ind <= 0) {
                        throw new IllegalArgumentException(
                                "Input must be /moduleId/resource. Input needs a / after the first character: " + path);
                }
                String moduleId = path.startsWith("/") ? path.substring(1, ind) : path.substring(0, ind);
                moduleId = moduleId.replace('/', '.');
                // iterate over progressively shorter module ids
                while (true) {
                        Module mod = ModuleFactory.getStartedModuleById(moduleId);
                        if (mod != null) {
                                return mod;
                        }
                        // try the next shorter module id
                        ind = moduleId.lastIndexOf('.');
                        if (ind < 0) {
                                break;
                        }
                        moduleId = moduleId.substring(0, ind);
                }
                return null;
        }
        
        /**
         * Takes a global path and returns the local path within the specified module. For example
         * calling this method with the path "/ui/springmvc/css/ui.css" and the ui.springmvc module, you
         * would get "/css/ui.css".
         *
         * @param module
         * @param path
         * @return local path
         * <strong>Should</strong> handle ui springmvc css ui dot css example
         */
        public static String getPathForResource(Module module, String path) {
                if (path.startsWith("/")) {
                        path = path.substring(1);
                }
                return path.substring(module.getModuleIdAsPath().length());
        }
        
        /**
         * This loops over all FILES in this jar to get the package names. If there is an empty
         * directory in this jar it is not returned as a providedPackage.
         *
         * @param file jar file to look into
         * @return list of strings of package names in this jar
         */
        public static Collection<String> getPackagesFromFile(File file) {
                
                // End early if we're given a non jar file
                if (!file.getName().endsWith(".jar")) {
                        return Collections.emptySet();
                }
                
                Set<String> packagesProvided = new HashSet<>();
                
                JarFile jar = null;
                try {
                        jar = new JarFile(file);
                        
                        Enumeration<JarEntry> jarEntries = jar.entries();
                        while (jarEntries.hasMoreElements()) {
                                JarEntry jarEntry = jarEntries.nextElement();
                                if (jarEntry.isDirectory()) {
                                        // skip over directory entries, we only care about files
                                        continue;
                                }
                                String name = jarEntry.getName();
                                
                                // Skip over some folders in the jar/omod
                                if (name.startsWith("lib") || name.startsWith("META-INF") || name.startsWith("web/module")) {
                                        continue;
                                }
                                
                                Integer indexOfLastSlash = name.lastIndexOf("/");
                                if (indexOfLastSlash <= 0) {
                                        continue;
                                }
                                String packageName = name.substring(0, indexOfLastSlash);
                                
                                packageName = packageName.replaceAll("/", ".");
                                
                                if (packagesProvided.add(packageName) && log.isTraceEnabled()) {
                                        log.trace("Adding module's jarentry with package: " + packageName);
                                }
                        }
                        
                        jar.close();
                }
                catch (IOException e) {
                        log.error("Error while reading file: " + file.getAbsolutePath(), e);
                }
                finally {
                        if (jar != null) {
                                try {
                                        jar.close();
                                }
                                catch (IOException e) {
                                        // Ignore quietly
                                }
                        }
                }
                
                return packagesProvided;
        }
        
        /**
         * Get a resource as from the module's api jar. Api jar should be in the omod's lib folder.
         * 
         * @param jarFile omod file loaded as jar
         * @param moduleId id of the module
         * @param version version of the module
         * @param resource name of a resource from the api jar
         * @return resource as an input stream or <code>null</code> if resource cannot be loaded
         * <strong>Should</strong> load file from api as input stream
         * <strong>Should</strong> return null if api is not found
         * <strong>Should</strong> return null if file is not found in api
         */
        public static InputStream getResourceFromApi(JarFile jarFile, String moduleId, String version, String resource) {
                String apiLocation = "lib/" + moduleId + "-api-" + version + ".jar";
                return getResourceFromInnerJar(jarFile, apiLocation, resource);
        }
        
        /**
         * Load resource from a jar inside a jar.
         * 
         * @param outerJarFile jar file that contains a jar file
         * @param innerJarFileLocation inner jar file location relative to the outer jar
         * @param resource path to a resource relative to the inner jar
         * @return resource from the inner jar as an input stream or <code>null</code> if resource cannot be loaded
         */
        private static InputStream getResourceFromInnerJar(JarFile outerJarFile, String innerJarFileLocation, String resource) {
                File tempFile = null;
                FileOutputStream tempOut = null;
                JarFile innerJarFile = null;
                InputStream innerInputStream = null;
                try {
                        tempFile = File.createTempFile("tempFile", "jar");
                        tempOut = new FileOutputStream(tempFile);
                        ZipEntry innerJarFileEntry = outerJarFile.getEntry(innerJarFileLocation);
                        if (innerJarFileEntry != null) {
                                IOUtils.copy(outerJarFile.getInputStream(innerJarFileEntry), tempOut);
                                innerJarFile = new JarFile(tempFile);
                                ZipEntry targetEntry = innerJarFile.getEntry(resource);
                                if (targetEntry != null) {
                                        // clone InputStream to make it work after the innerJarFile is closed
                                        innerInputStream = innerJarFile.getInputStream(targetEntry);
                                        byte[] byteArray = IOUtils.toByteArray(innerInputStream);
                                        return new ByteArrayInputStream(byteArray);
                                }
                        }
                }
                catch (IOException e) {
                        log.error("Unable to get '" + resource + "' from '" + innerJarFileLocation + "' of '" + outerJarFile.getName()
                                + "'", e);
                }
                finally {
                        IOUtils.closeQuietly(tempOut);
                        IOUtils.closeQuietly(innerInputStream);

                        // close inner jar file before attempting to delete temporary file
                        try {
                                if (innerJarFile != null) {
                                        innerJarFile.close();
                                }
                        }
                        catch (IOException e) {
                                log.warn("Unable to close inner jarfile: " + innerJarFile, e);
                        }

                        // delete temporary file
                        if (tempFile != null && !tempFile.delete()) {
                                log.warn("Could not delete temporary jarfile: " + tempFile);
                        }
                }
                return null;
        }
        
        /**
         * Gets the root folder of a module's sources during development
         * 
         * @param moduleId the module id
         * @return the module's development folder is specified, else null
         */
        public static File getDevelopmentDirectory(String moduleId) {
                String directory = System.getProperty(moduleId + ".development.directory");
                if (StringUtils.isNotBlank(directory)) {
                        return new File(directory);
                }
                
                return null;
        }
}

openmrs / openmrs-core / 21885081110

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