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package org.broadinstitute.hellbender.engine;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.Utils;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.Serializable;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.*;
import java.nio.file.spi.FileSystemProvider;
/**
* Default implementation for PathURI.
*
* This class takes a raw string that is to be interpreted as a path specifier, and converts it internally to a
* URI and/or Path object. If no scheme is provided as part of the raw string used in the constructor(s), the
* input is assumed to represent a file on the local file system, and will be backed by a URI with a "file:/"
* scheme and a path part that is automatically encoded/escaped to ensure it is a valid URI. If the raw string
* contains a scheme, it will be backed by a URI formed from the raw string as presented, with no further
* encoding/escaping.
*
* For example, a URI that contains a scheme and has an embedded "#" in the path will be treated as a URI
* having a fragment delimiter. If the URI contains an scheme, the "#" will be escaped and the encoded "#"
* will be interpreted as part of the URI path.
*
* There are 3 succeeding levels of input validation/conversion:
*
* 1) PathSpecifier constructor: requires a syntactically valid URI, possibly containing a scheme (if no scheme
* is present the path part will be escaped/encoded), or a valid local file reference
* 2) hasFileSystemProvider: true if the input string is an identifier that is syntactically valid, and is backed by
* an installed {@code java.nio} file system provider that matches the URI scheme
* 3) isPath: syntactically valid URI that can be resolved to a java.io.Path by the associated provider
*
* Definitions taken from RFC 2396 "Uniform Resource Identifiers (URI): Generic Syntax"
* (https://www.ietf.org/rfc/rfc2396.txt):
*
* "absolute" URI - specifies a scheme
* "relative" URI - does not specify a scheme
* "opaque" URI - an "absolute" URI whose scheme-specific part does not begin with a slash character
* "hierarchical" URI - either an "absolute" URI whose scheme-specific part begins with a slash character,
* or a "relative" URI (no scheme)
*
* URIs that do not make use of the slash "/" character for separating hierarchical components are
* considered "opaque" by the generic URI parser.
*
* General syntax for an "absolute" URI:
*
* :
*
* Many "hierarchical" URI schemes use this syntax:
*
* ://?
*
* More specifically:
*
* absoluteURI = scheme ":" ( hier_part | opaque_part )
* hier_part = ( net_path | abs_path ) [ "?" query ]
* net_path = "//" authority [ abs_path ]
* abs_path = "/" path_segments
* opaque_part = uric_no_slash *uric
* uric_no_slash = unreserved | escaped | ";" | "?" | ":" | "@" | "&" | "=" | "+" | "$" | ","
*/
public class PathSpecifier implements PathURI, Serializable {
private static final long serialVersionUID = 1L;
private final String rawInputString; // raw input string provided by th user; may or may not have a scheme
private final URI uri; // working URI; always has a scheme (assume "file" if not provided)
private transient String pathFailureReason; // cache the reason for "toPath" conversion failure
private transient Path cachedPath; // cache the Path associated with this URI if its "Path-able"
/**
* If the raw input string already contains a scheme (including a "file" scheme), assume its already
* properly escape/encoded. If no scheme component is present, assume it referencess a raw path on the
* local file system, so try to get a Path first, and then retrieve the URI from the resulting Path.
* This ensures that input strings that are local file references without a scheme component and contain
* embedded characters are valid in file names, but which would otherwise be interpreted as excluded
* URI characters (such as the URI fragment delimiter "#") are properly escape/encoded.
* @param rawInputString
*/
public PathSpecifier(final String rawInputString) {
Utils.nonNull(rawInputString);
this.rawInputString = rawInputString;
URI tempURI;
try {
tempURI = new URI(rawInputString);
if (!tempURI.isAbsolute()) {
// if the URI has no scheme, assume its a local (non-URI) file reference, and resolve
// it to a Path and retrieve the URI from the Path to ensure proper escape/encoding
setCachedPath(Paths.get(rawInputString));
tempURI = getCachedPath().toUri();
}
} catch (URISyntaxException uriException) {
// the input string isn't a valid URI; assume its a local (non-URI) file reference, and
// use the URI resulting from the corresponding Path
try {
setCachedPath(Paths.get(rawInputString));
tempURI = getCachedPath().toUri();
} catch (InvalidPathException | UnsupportedOperationException | SecurityException pathException) {
// we have two exceptions, each of which might be relevant since we can't tell whether
// the user intended to provide a local file reference or a URI, so preserve both
final String errorMessage = String.format(
"%s can't be interpreted as a local file (%s) or as a URI (%s).",
rawInputString,
pathException.getMessage(),
uriException.getMessage());
throw new IllegalArgumentException(errorMessage, pathException);
}
}
if (!tempURI.isAbsolute()) {
// assert the invariant that every URI we create has a scheme, even if the raw input string does not
throw new UserException("URI has no scheme");
}
uri = tempURI;
}
@Override
public URI getURI() {
return uri;
}
@Override
public String getURIString() {
return getURI().toString();
}
/**
* Return the raw input string provided to the constructor.
*/
@Override
public String getRawInputString() { return rawInputString; }
@Override
public boolean hasFileSystemProvider() {
// try to find a provider; assume that our URI always has a scheme
for (FileSystemProvider provider: FileSystemProvider.installedProviders()) {
if (provider.getScheme().equalsIgnoreCase(uri.getScheme())) {
return true;
}
}
return false;
}
@Override
public boolean isPath() {
try {
return getCachedPath() != null || toPath() != null;
} catch (ProviderNotFoundException |
FileSystemNotFoundException |
IllegalArgumentException |
UserException |
AssertionError e) {
// jimfs throws an AssertionError that wraps a URISyntaxException when trying to create path where
// the scheme-specific part is missing or incorrect
pathFailureReason = e.getMessage();
return false;
}
}
/**
* Resolve the URI to a {@link Path} object.
*
* @return the resulting {@code Path}
* @throws UserException if an I/O error occurs when creating the file system
*/
@Override
public Path toPath() {
if (getCachedPath() != null) {
return getCachedPath();
} else {
final Path tmpPath = Paths.get(getURI());
setCachedPath(tmpPath);
return tmpPath;
}
}
@Override
public String getToPathFailureReason() {
if (pathFailureReason == null) {
try {
toPath();
return String.format("'%s' appears to be a valid Path", rawInputString);
} catch (ProviderNotFoundException e) {
return String.format("ProviderNotFoundException: %s", e.getMessage());
} catch (FileSystemNotFoundException e) {
return String.format("FileSystemNotFoundException: %s", e.getMessage());
} catch (IllegalArgumentException e) {
return String.format("IllegalArgumentException: %s", e.getMessage());
} catch (UserException e) {
return String.format("UserException: %s", e.getMessage());
}
}
return pathFailureReason;
}
@Override
public InputStream getInputStream() {
if (!isPath()) {
throw new UserException(getToPathFailureReason());
}
final Path resourcePath = toPath();
try {
return Files.newInputStream(resourcePath);
} catch (IOException e) {
throw new UserException(
String.format("Could not create open input stream for %s (as URI %s)", getRawInputString(), getURIString()), e);
}
}
@Override
public OutputStream getOutputStream() {
if (!isPath()) {
throw new UserException(getToPathFailureReason());
}
final Path resourcePath = toPath();
try {
return Files.newOutputStream(resourcePath);
} catch (IOException e) {
throw new UserException(String.format("Could not open output stream for %s (as URI %s)", getRawInputString(), getURIString()), e);
}
}
// get the cached path associated with this URI if its already been created
protected Path getCachedPath() { return cachedPath; }
protected void setCachedPath(Path path) {
this.cachedPath = path;
}
@Override
public String toString() {
return rawInputString;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof PathSpecifier)) return false;
PathSpecifier that = (PathSpecifier) o;
if (!getRawInputString().equals(that.getRawInputString())) return false;
if (!getURI().equals(that.getURI())) return false;
return true;
}
@Override
public int hashCode() {
int result = getRawInputString().hashCode();
result = 31 * result + getURI().hashCode();
return result;
}
}
