Package nextflow.util

Source Code of nextflow.util.ServiceDiscover

/*
* Copyright (c) 2013-2014, Centre for Genomic Regulation (CRG).
* Copyright (c) 2013-2014, Paolo Di Tommaso and the respective authors.
*
*   This file is part of 'Nextflow'.
*
*   Nextflow is free software: you can redistribute it and/or modify
*   it under the terms of the GNU General Public License as published by
*   the Free Software Foundation, either version 3 of the License, or
*   (at your option) any later version.
*
*   Nextflow 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 General Public License for more details.
*
*   You should have received a copy of the GNU General Public License
*   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
*/

package nextflow.util;

/**
* Same as Java {@code ServiceLoader} but return service classes instead of instances
*
* @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
*/

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.ServiceConfigurationError;


/**
* A simple service-provider loading facility.
*
* <p> A <i>service</i> is a well-known set of interfaces and (usually
* abstract) classes.  A <i>service provider</i> is a specific implementation
* of a service.  The classes in a provider typically implement the interfaces
* and subclass the classes defined in the service itself.  Service providers
* can be installed in an implementation of the Java platform in the form of
* extensions, that is, jar files placed into any of the usual extension
* directories.  Providers can also be made available by adding them to the
* application's class path or by some other platform-specific means.
*
* <p> For the purpose of loading, a service is represented by a single type,
* that is, a single interface or abstract class.  (A concrete class can be
* used, but this is not recommended.)  A provider of a given service contains
* one or more concrete classes that extend this <i>service type</i> with data
* and code specific to the provider.  The <i>provider class</i> is typically
* not the entire provider itself but rather a proxy which contains enough
* information to decide whether the provider is able to satisfy a particular
* request together with code that can create the actual provider on demand.
* The details of provider classes tend to be highly service-specific; no
* single class or interface could possibly unify them, so no such type is
* defined here.  The only requirement enforced by this facility is that
* provider classes must have a zero-argument constructor so that they can be
* instantiated during loading.
*
* <p><a name="format"> A service provider is identified by placing a
* <i>provider-configuration file</i> in the resource directory
* <tt>META-INF/services</tt>.  The file's name is the fully-qualified <a
* href="../lang/ClassLoader.html#name">binary name</a> of the service's type.
* The file contains a list of fully-qualified binary names of concrete
* provider classes, one per line.  Space and tab characters surrounding each
* name, as well as blank lines, are ignored.  The comment character is
* <tt>'#'</tt> (<tt>'&#92;u0023'</tt>, <font size="-1">NUMBER SIGN</font>); on
* each line all characters following the first comment character are ignored.
* The file must be encoded in UTF-8.
*
* <p> If a particular concrete provider class is named in more than one
* configuration file, or is named in the same configuration file more than
* once, then the duplicates are ignored.  The configuration file naming a
* particular provider need not be in the same jar file or other distribution
* unit as the provider itself.  The provider must be accessible from the same
* class loader that was initially queried to locate the configuration file;
* note that this is not necessarily the class loader from which the file was
* actually loaded.
*
* <p> Providers are located and instantiated lazily, that is, on demand.  A
* service loader maintains a cache of the providers that have been loaded so
* far.  Each invocation of the {@link #iterator iterator} method returns an
* iterator that first yields all of the elements of the cache, in
* instantiation order, and then lazily locates and instantiates any remaining
* providers, adding each one to the cache in turn.  The cache can be cleared
* via the {@link #reload reload} method.
*
* <p> Service loaders always execute in the security context of the caller.
* Trusted system code should typically invoke the methods in this class, and
* the methods of the iterators which they return, from within a privileged
* security context.
*
* <p> Instances of this class are not safe for use by multiple concurrent
* threads.
*
* <p> Unless otherwise specified, passing a <tt>null</tt> argument to any
* method in this class will cause a {@link NullPointerException} to be thrown.
*
*
* <p><span style="font-weight: bold; padding-right: 1em">Example</span>
* Suppose we have a service type <tt>com.example.CodecSet</tt> which is
* intended to represent sets of encoder/decoder pairs for some protocol.  In
* this case it is an abstract class with two abstract methods:
*
* <blockquote><pre>
* public abstract Encoder getEncoder(String encodingName);
* public abstract Decoder getDecoder(String encodingName);</pre></blockquote>
*
* Each method returns an appropriate object or <tt>null</tt> if the provider
* does not support the given encoding.  Typical providers support more than
* one encoding.
*
* <p> If <tt>com.example.impl.StandardCodecs</tt> is an implementation of the
* <tt>CodecSet</tt> service then its jar file also contains a file named
*
* <blockquote><pre>
* META-INF/services/com.example.CodecSet</pre></blockquote>
*
* <p> This file contains the single line:
*
* <blockquote><pre>
* com.example.impl.StandardCodecs    # Standard codecs</pre></blockquote>
*
* <p> The <tt>CodecSet</tt> class creates and saves a single service instance
* at initialization:
*
* <blockquote><pre>
* private static ServiceLoader&lt;CodecSet&gt; codecSetLoader
*     = ServiceLoader.load(CodecSet.class);</pre></blockquote>
*
* <p> To locate an encoder for a given encoding name it defines a static
* factory method which iterates through the known and available providers,
* returning only when it has located a suitable encoder or has run out of
* providers.
*
* <blockquote><pre>
* public static Encoder getEncoder(String encodingName) {
*     for (CodecSet cp : codecSetLoader) {
*         Encoder enc = cp.getEncoder(encodingName);
*         if (enc != null)
*             return enc;
*     }
*     return null;
* }</pre></blockquote>
*
* <p> A <tt>getDecoder</tt> method is defined similarly.
*
*
* <p><span style="font-weight: bold; padding-right: 1em">Usage Note</span> If
* the class path of a class loader that is used for provider loading includes
* remote network URLs then those URLs will be dereferenced in the process of
* searching for provider-configuration files.
*
* <p> This activity is normal, although it may cause puzzling entries to be
* created in web-server logs.  If a web server is not configured correctly,
* however, then this activity may cause the provider-loading algorithm to fail
* spuriously.
*
* <p> A web server should return an HTTP 404 (Not Found) response when a
* requested resource does not exist.  Sometimes, however, web servers are
* erroneously configured to return an HTTP 200 (OK) response along with a
* helpful HTML error page in such cases.  This will cause a {@link
* ServiceConfigurationError} to be thrown when this class attempts to parse
* the HTML page as a provider-configuration file.  The best solution to this
* problem is to fix the misconfigured web server to return the correct
* response code (HTTP 404) along with the HTML error page.
*
* @param  <S>
*         The type of the service to be loaded by this loader
*
* @author Mark Reinhold
* @since 1.6
*/

public final class ServiceDiscover<S> implements Iterable<Class<S>>
{

    private static final String PREFIX = "META-INF/services/";

    // The class or interface representing the service being loaded
    private Class<S> service;

    // The class loader used to locate, load, and instantiate providers
    private ClassLoader loader;

    // Cached providers, in instantiation order
    private LinkedHashMap<String,Class<S>> providers = new LinkedHashMap<>();

    // The current lazy-lookup iterator
    private LazyIterator lookupIterator;

    /**
     * Clear this loader's provider cache so that all providers will be
     * reloaded.
     *
     * <p> After invoking this method, subsequent invocations of the {@link
     * #iterator() iterator} method will lazily look up and instantiate
     * providers from scratch, just as is done by a newly-created loader.
     *
     * <p> This method is intended for use in situations in which new providers
     * can be installed into a running Java virtual machine.
     */
    public void reload() {
        providers.clear();
        lookupIterator = new LazyIterator(service, loader);
    }

    private ServiceDiscover(Class<S> svc, ClassLoader cl) {
        service = svc;
        loader = cl;
        reload();
    }

    private static void fail(Class service, String msg, Throwable cause)
            throws ServiceConfigurationError
    {
        throw new ServiceConfigurationError(service.getName() + ": " + msg,
                cause);
    }

    private static void fail(Class service, String msg)
            throws ServiceConfigurationError
    {
        throw new ServiceConfigurationError(service.getName() + ": " + msg);
    }

    private static void fail(Class service, URL u, int line, String msg)
            throws ServiceConfigurationError
    {
        fail(service, u + ":" + line + ": " + msg);
    }

    // Parse a single line from the given configuration file, adding the name
    // on the line to the names list.
    //
    private int parseLine(Class service, URL u, BufferedReader r, int lc, List<String> names)
            throws IOException, ServiceConfigurationError
    {
        String ln = r.readLine();
        if (ln == null) {
            return -1;
        }
        int ci = ln.indexOf('#');
        if (ci >= 0) ln = ln.substring(0, ci);
        ln = ln.trim();
        int n = ln.length();
        if (n != 0) {
            if ((ln.indexOf(' ') >= 0) || (ln.indexOf('\t') >= 0))
                fail(service, u, lc, "Illegal configuration-file syntax");
            int cp = ln.codePointAt(0);
            if (!Character.isJavaIdentifierStart(cp))
                fail(service, u, lc, "Illegal provider-class name: " + ln);
            for (int i = Character.charCount(cp); i < n; i += Character.charCount(cp)) {
                cp = ln.codePointAt(i);
                if (!Character.isJavaIdentifierPart(cp) && (cp != '.'))
                    fail(service, u, lc, "Illegal provider-class name: " + ln);
            }
            if (!providers.containsKey(ln) && !names.contains(ln))
                names.add(ln);
        }
        return lc + 1;
    }

    // Parse the content of the given URL as a provider-configuration file.
    //
    // @param  service
    //         The service type for which providers are being sought;
    //         used to construct error detail strings
    //
    // @param  u
    //         The URL naming the configuration file to be parsed
    //
    // @return A (possibly empty) iterator that will yield the provider-class
    //         names in the given configuration file that are not yet members
    //         of the returned set
    //
    // @throws ServiceConfigurationError
    //         If an I/O error occurs while reading from the given URL, or
    //         if a configuration-file format error is detected
    //
    private Iterator<String> parse(Class service, URL u)
            throws ServiceConfigurationError
    {
        InputStream in = null;
        BufferedReader r = null;
        ArrayList<String> names = new ArrayList<>();
        try {
            in = u.openStream();
            r = new BufferedReader(new InputStreamReader(in, "utf-8"));
            int lc = 1;
            while ((lc = parseLine(service, u, r, lc, names)) >= 0);
        } catch (IOException x) {
            fail(service, "Error reading configuration file", x);
        } finally {
            try {
                if (r != null) r.close();
                if (in != null) in.close();
            } catch (IOException y) {
                fail(service, "Error closing configuration file", y);
            }
        }
        return names.iterator();
    }

    // Private inner class implementing fully-lazy provider lookup
    //
    private class LazyIterator
            implements Iterator<Class<S>>
    {

        Class<S> service;
        ClassLoader loader;
        Enumeration<URL> configs = null;
        Iterator<String> pending = null;
        String nextName = null;

        private LazyIterator(Class<S> service, ClassLoader loader) {
            this.service = service;
            this.loader = loader;
        }

        public boolean hasNext() {
            if (nextName != null) {
                return true;
            }
            if (configs == null) {
                try {
                    String fullName = PREFIX + service.getName();
                    if (loader == null)
                        configs = ClassLoader.getSystemResources(fullName);
                    else
                        configs = loader.getResources(fullName);
                } catch (IOException x) {
                    fail(service, "Error locating configuration files", x);
                }
            }
            while ((pending == null) || !pending.hasNext()) {
                if (!configs.hasMoreElements()) {
                    return false;
                }
                pending = parse(service, configs.nextElement());
            }
            nextName = pending.next();
            return true;
        }

        public Class<S> next() {
            if (!hasNext()) {
                throw new NoSuchElementException();
            }
            String cn = nextName;
            nextName = null;
            Class<?> c = null;
            try {
                c = Class.forName(cn, false, loader);
            } catch (ClassNotFoundException x) {
                fail(service, "Provider " + cn + " not found");
            }
            if (!service.isAssignableFrom(c)) {
                fail(service, "Provider " + cn  + " not a subtype");
            }
            try {
                providers.put(cn, (Class<S>)c);
                return (Class<S>)c;
            }
            catch (Throwable x) {
                fail(service, "Provider " + cn + " could not be instantiated: " + x, x);
            }
            throw new Error();          // This cannot happen
        }

        public void remove() {
            throw new UnsupportedOperationException();
        }

    }

    /**
     * Lazily loads the available providers of this loader's service.
     *
     * <p> The iterator returned by this method first yields all of the
     * elements of the provider cache, in instantiation order.  It then lazily
     * loads and instantiates any remaining providers, adding each one to the
     * cache in turn.
     *
     * <p> To achieve laziness the actual work of parsing the available
     * provider-configuration files and instantiating providers must be done by
     * the iterator itself.  Its {@link java.util.Iterator#hasNext hasNext} and
     * {@link java.util.Iterator#next next} methods can therefore throw a
     * {@link ServiceConfigurationError} if a provider-configuration file
     * violates the specified format, or if it names a provider class that
     * cannot be found and instantiated, or if the result of instantiating the
     * class is not assignable to the service type, or if any other kind of
     * exception or error is thrown as the next provider is located and
     * instantiated.  To write robust code it is only necessary to catch {@link
     * ServiceConfigurationError} when using a service iterator.
     *
     * <p> If such an error is thrown then subsequent invocations of the
     * iterator will make a best effort to locate and instantiate the next
     * available provider, but in general such recovery cannot be guaranteed.
     *
     * <blockquote style="font-size: smaller; line-height: 1.2"><span
     * style="padding-right: 1em; font-weight: bold">Design Note</span>
     * Throwing an error in these cases may seem extreme.  The rationale for
     * this behavior is that a malformed provider-configuration file, like a
     * malformed class file, indicates a serious problem with the way the Java
     * virtual machine is configured or is being used.  As such it is
     * preferable to throw an error rather than try to recover or, even worse,
     * fail silently.</blockquote>
     *
     * <p> The iterator returned by this method does not support removal.
     * Invoking its {@link java.util.Iterator#remove() remove} method will
     * cause an {@link UnsupportedOperationException} to be thrown.
     *
     * @return  An iterator that lazily loads providers for this loader's
     *          service
     */
    public Iterator<Class<S>> iterator() {
        return new Iterator<Class<S>>() {

            Iterator<Map.Entry<String,Class<S>>> knownProviders
                    = providers.entrySet().iterator();

            public boolean hasNext() {
                if (knownProviders.hasNext())
                    return true;
                return lookupIterator.hasNext();
            }

            public Class<S> next() {
                if (knownProviders.hasNext())
                    return knownProviders.next().getValue();
                return lookupIterator.next();
            }

            public void remove() {
                throw new UnsupportedOperationException();
            }

        };
    }

    /**
     * Creates a new service loader for the given service type and class
     * loader.
     *
     * @param  service
     *         The interface or abstract class representing the service
     *
     * @param  loader
     *         The class loader to be used to load provider-configuration files
     *         and provider classes, or <tt>null</tt> if the system class
     *         loader (or, failing that, the bootstrap class loader) is to be
     *         used
     *
     * @return A new service loader
     */
    public static <S> ServiceDiscover<S> load(Class<S> service, ClassLoader loader)
    {
        return new ServiceDiscover<>(service, loader);
    }

    /**
     * Creates a new service loader for the given service type, using the
     * current thread's {@linkplain java.lang.Thread#getContextClassLoader
     * context class loader}.
     *
     * <p> An invocation of this convenience method of the form
     *
     * <blockquote><pre>
     * ServiceLoader.load(<i>service</i>)</pre></blockquote>
     *
     * is equivalent to
     *
     * <blockquote><pre>
     * ServiceLoader.load(<i>service</i>,
     *                    Thread.currentThread().getContextClassLoader())</pre></blockquote>
     *
     * @param  service
     *         The interface or abstract class representing the service
     *
     * @return A new service loader
     */
    public static <S> ServiceDiscover<S> load(Class<S> service) {
        ClassLoader cl = Thread.currentThread().getContextClassLoader();
        return ServiceDiscover.load(service, cl);
    }

    /**
     * Creates a new service loader for the given service type, using the
     * extension class loader.
     *
     * <p> This convenience method simply locates the extension class loader,
     * call it <tt><i>extClassLoader</i></tt>, and then returns
     *
     * <blockquote><pre>
     * ServiceDiscover.load(<i>service</i>, <i>extClassLoader</i>)</pre></blockquote>
     *
     * <p> If the extension class loader cannot be found then the system class
     * loader is used; if there is no system class loader then the bootstrap
     * class loader is used.
     *
     * <p> This method is intended for use when only installed providers are
     * desired.  The resulting service will only find and load providers that
     * have been installed into the current Java virtual machine; providers on
     * the application's class path will be ignored.
     *
     * @param  service
     *         The interface or abstract class representing the service
     *
     * @return A new service loader
     */
    public static <S> ServiceDiscover<S> loadInstalled(Class<S> service) {
        ClassLoader cl = ClassLoader.getSystemClassLoader();
        ClassLoader prev = null;
        while (cl != null) {
            prev = cl;
            cl = cl.getParent();
        }
        return ServiceDiscover.load(service, prev);
    }

    /**
     * Returns a string describing this service.
     *
     * @return  A descriptive string
     */
    public String toString() {
        return "java.util.ServiceDiscover[" + service.getName() + "]";
    }

}
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