import jalview.urls.IdOrgSettings;
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
try
{
// props file provided as URL
- fis = new URL(propertiesFile).openStream();
+ fis = HttpUtils.openStream(new URL(propertiesFile));
if (!Jalview.quiet())
{
jalview.bin.Console.outPrintln(
if (authorDetails != null)
{
URL localJarFileURL = new URL(authorDetails);
- InputStream in = localJarFileURL.openStream();
+ InputStream in = HttpUtils.openStream(localJarFileURL);
applicationProperties.load(in);
in.close();
}
URL url = new URL(remoteBuildPropertiesUrl);
BufferedReader in = new BufferedReader(
- new InputStreamReader(url.openStream()));
+ new InputStreamReader(HttpUtils.openStream(url)));
Properties remoteBuildProperties = new Properties();
remoteBuildProperties.load(in);
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null
+ && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
+import jalview.util.HttpUtils;
import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
// return processJsonResponseFor(new
// InputStreamReader(geturl.openStream()));
ArrayList<Reader> readers = new ArrayList<>();
- readers.add(new InputStreamReader(geturl.openStream()));
+ readers.add(new InputStreamReader(HttpUtils.openStream(geturl)));
return readers.iterator();
}
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.bin.Console;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
-import javax.swing.JOptionPane;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
public class UserQuestionnaireCheck implements Runnable
{
// see if we have already responsed to this questionnaire or get a new
// qid/rid pair
BufferedReader br = new BufferedReader(
- new InputStreamReader(qurl.openStream()));
+ new InputStreamReader(HttpUtils.openStream(qurl)));
String qresp;
while ((qresp = br.readLine()) != null)
{
import jalview.gui.OOMWarning;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
public class BioJsHTMLOutput extends HTMLOutput
try
{
URL resourceUrl = new URL(url);
- is = new BufferedInputStream(resourceUrl.openStream());
+ is = new BufferedInputStream(HttpUtils.openStream(resourceUrl));
BufferedReader br = new BufferedReader(new InputStreamReader(is));
responseStrBuilder = new StringBuilder();
String lineContent;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Console;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
URLConnection _conn = url.openConnection();
if (_conn instanceof HttpURLConnection)
{
- HttpURLConnection conn = (HttpURLConnection) _conn;
+ HttpURLConnection conn = HttpUtils
+ .followConnection((HttpURLConnection) _conn);
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- throw new IOException(
- "Response status from " + urlStr + " was " + rc);
+ throw new FileNotFoundException("Response status from " + urlStr
+ + " was " + conn.getResponseCode());
}
+ _conn = conn;
}
else
{
return new BufferedReader(new FileReader((File) file));
case URL:
URL url = new URL(file.toString());
- in = new BufferedReader(new InputStreamReader(url.openStream()));
+ in = new BufferedReader(
+ new InputStreamReader(HttpUtils.openStream(url)));
break;
case RELATIVE_URL: // JalviewJS only
bytes = Platform.getFileAsBytes(file.toString());
import jalview.gui.AlignmentPanel;
import jalview.gui.IProgressIndicator;
import jalview.io.exceptions.ImageOutputException;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
public abstract class HTMLOutput implements Runnable
{
try
{
- isReader = new InputStreamReader(url.openStream());
+ isReader = new InputStreamReader(HttpUtils.openStream(url));
buffReader = new BufferedReader(isReader);
String line;
String lineSeparator = System.getProperty("line.separator");
{
return identify(parser);
}
+ } catch (IOException e)
+ {
+ Console.error("Error whilst trying to read " + file, e);
} catch (Exception e)
{
Console.error("Error whilst identifying " + file, e);
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactMatrix;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.GroupSet;
-import jalview.datamodel.GroupSetI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
// jalview.bin.Console.outPrintln("Jalview2XML: opening url
// jarInputStream for "
// + _url);
- return new JarInputStream(_url.openStream());
+ return new JarInputStream(HttpUtils.openStream(_url));
}
else
{
{
try
{
- InputStream channelPropsIS = channelPropsURL.openStream();
+ InputStream channelPropsIS = HttpUtils.openStream(channelPropsURL);
tryChannelProps.load(channelPropsIS);
channelPropsIS.close();
} catch (IOException e)
InputStream is = null;
try
{
- is = new URL(url).openStream();
+ is = HttpUtils.openStream(new URL(url));
if (is != null)
{
return true;
// jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-
connection.setRequestMethod(HttpMethod.HEAD);
-
connection.setDoInput(true);
-
connection.setUseCaches(false);
connection.setConnectTimeout(300);
connection.setReadTimeout(readTimeout);
- return connection.getResponseCode() == 200;
+
+ // HttpURLConnection doesn't follow redirects from http to https. It should!
+ HttpURLConnection conn = followConnection(connection);
+ return conn.getResponseCode() == 200;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ *
+ * @param URL
+ * url
+ * @return HttpUrlConnection conn
+ */
+ public static HttpURLConnection openConnection(URL url) throws IOException
+ {
+ if (url == null)
+ {
+ return null;
+ }
+ HttpURLConnection conn = null;
+ if (url != null && url.getProtocol().startsWith("http"))
+ {
+ HttpURLConnection conn0 = (HttpURLConnection) url.openConnection();
+ if (conn0 != null)
+ {
+ conn = HttpUtils.followConnection(conn0);
+ }
+ else
+ {
+ conn = conn0;
+ }
+ }
+ return conn;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ *
+ * @param HttpURLConnection
+ * conn0
+ * @return HttpUrlConnection conn
+ */
+ public static HttpURLConnection followConnection(HttpURLConnection conn0)
+ throws IOException
+ {
+ HttpURLConnection newConn = null;
+ URL url = conn0.getURL();
+ if (url == null)
+ {
+ return null;
+ }
+ int response = conn0.getResponseCode();
+ boolean followed = false;
+ if (response >= 300 && response < 400 && conn0.getFollowRedirects())
+ {
+ // we are only checking for a redirect from http to https
+ if ("http".equals(url.getProtocol()))
+ {
+ URL loc = new URL(conn0.getHeaderField("Location"));
+ if (loc != null && "https".equals(loc.getProtocol()))
+ {
+ newConn = (HttpURLConnection) loc.openConnection();
+ newConn.setRequestMethod(conn0.getRequestMethod());
+ newConn.setDoInput(conn0.getDoInput());
+ newConn.setUseCaches(conn0.getUseCaches());
+ newConn.setConnectTimeout(conn0.getConnectTimeout());
+ newConn.setReadTimeout(conn0.getReadTimeout());
+ newConn.setInstanceFollowRedirects(
+ conn0.getInstanceFollowRedirects());
+ followed = true;
+ }
+ }
+ }
+ return followed ? newConn : conn0;
+ }
+
+ /**
+ * wrapper to follow a URL connection ALLOWING redirects from http to https
+ * and return the followed InputStream
+ *
+ * @param URL
+ * url
+ * @return HttpUrlConnection conn
+ */
+ public static InputStream openStream(URL url) throws IOException
+ {
+ InputStream is = null;
+ if (url != null && url.getProtocol().startsWith("http"))
+ {
+ HttpURLConnection conn = HttpUtils
+ .followConnection((HttpURLConnection) url.openConnection());
+ if (conn != null)
+ {
+ is = conn.getInputStream();
+ }
+ }
+ return is;
}
public static String getUserAgent()
try
{
URL localFileURL = new URL(buildDetails);
- InputStream in = localFileURL.openStream();
+ InputStream in = HttpUtils.openStream(localFileURL);
Properties buildProperties = new Properties();
buildProperties.load(in);
in.close();
*/
package jalview.ws.jws1;
-import jalview.datamodel.AlignmentI;
-import jalview.io.FileFormat;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.InputStreamParser;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.net.URLEncoder;
import java.util.Iterator;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.InputStreamParser;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+
public class Annotate3D
{
// protected BufferedReader in;
"http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ content);
BufferedReader is = new BufferedReader(
- new InputStreamReader(url.openStream()));
+ new InputStreamReader(HttpUtils.openStream(url)));
String str4;
while ((str4 = is.readLine()) != null)
{
*/
package jalview.ws.jws2;
-import jalview.bin.Console;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
-
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import compbio.data.msa.JABAService;
import compbio.ws.client.Jws2Client;
import compbio.ws.client.Services;
+import jalview.bin.Console;
+import jalview.util.HttpUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
/**
* @author JimP
try
{
URL url = new URL(server);
- url.openStream().close();
+ HttpUtils.openStream(url).close();
result = true;
} catch (MalformedURLException e)
{
package jalview.ws.utils;
-import jalview.util.Platform;
-
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
+import jalview.util.HttpUtils;
+import jalview.util.Platform;
+
public class UrlDownloadClient
{
/**
temp = Files.createTempFile(".jalview_", ".tmp");
URL url = new URL(urlstring);
- rbc = Channels.newChannel(url.openStream());
+ rbc = Channels.newChannel(HttpUtils.openStream(url));
fos = new FileOutputStream(temp.toString());
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+++ /dev/null
-#!/usr/bin/env perl
-
-use strict;
-
-my $i4jversion = 8;
-if ($ARGV[0] eq "-v") {
- shift @ARGV;
- $i4jversion = shift @ARGV;
- die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
-}
-
-my $fileformats = $ARGV[0];
-$fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
-
-# default mimetype will be text/x-$shortname
-# TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
-# TODO: look up standard mime type used for BLASTfmt matrices, etc
-my $mimetypes = {
- rnaml => "application/rnaml+xml",
- biojson => "application/x-jalview-biojson+json",
- jnet => "application/x-jalview-jnet+text",
- features => "application/x-jalview-features+text",
- scorematrix => "application/x-jalview-scorematrix+text",
- pdb => "chemical/x-pdb",
- mmcif => "chemical/x-cif",
- mmcif2 => "chemical/x-mmcif",
- jalview => "application/x-jalview+xml+zip",
- jvl => "application/x-jalview-jvl+text",
- annotations => "application/x-jalview-annotations+text",
-};
-
-my @dontaddshortname = qw(features json);
-my @dontaddextension = qw(html xml json jar mfa fastq);
-my $add_associations = {
- biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
- gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
- gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
- features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
- annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
- mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
- mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
- jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
- jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
- scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
-};
-my $add_extensions = {
- blc => ["blc"],
-};
-my @put_first = qw(jalview jvl);
-
-my @non_primary = qw(mmcif mmcif2 pdb);
-
-my $v = ($i4jversion >= 8)?$i4jversion:"";
-my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
-my $i4jtemplate;
-my $mactemplatefile = "file_associations_template-Info_plist.xml";
-my $mactemplate;
-
-open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
-while(<MT>){
- $mactemplate .= $_;
-}
-close(MT);
-open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
-while(<IT>){
- $i4jtemplate .= $_;
-}
-close(IT);
-my $macauto;
-my $i4jauto;
-
-my $macautofile = $mactemplatefile;
-$macautofile =~ s/template/auto$1/;
-
-my $i4jautofile = $i4jtemplatefile;
-$i4jautofile =~ s/template/auto$1/;
-
-for my $key (sort keys %$add_associations) {
- my $a = $add_associations->{$key};
- warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
-}
-
-open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
-print MA "<key>CFBundleDocumentTypes</key>\n<array>\n\n";
-
-open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
-
-open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
-my $id = 10000;
-my $file_associations = {};
-while(my $line = <IN>) {
- $line =~ s/\s+/ /g;
- $line =~ s/(^ | $)//g;
- if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
- my $shortname = lc($1);
- next if (grep($_ eq $shortname, @dontaddshortname));
- my $name = $2;
- my $extensions = $3;
- $extensions =~ s/\s+//g;
- my @possextensions = map(lc($_),split(m/,/,$extensions));
- my @extensions;
- my $addext = $add_extensions->{$shortname};
- if (ref($addext) eq "ARRAY") {
- push(@possextensions, @$addext);
- }
- for my $possext (@possextensions) {
- next if grep($_ eq $possext, @extensions);
- next if grep($_ eq $possext, @dontaddextension);
- push(@extensions,$possext);
- }
- next unless scalar(@extensions);
- $file_associations->{$shortname} = {
- shortname => $shortname,
- name => $name,
- extensions => \@extensions
- };
- warn("Reading file association for $shortname (".join(",",@extensions).")\n");
- }
-}
-close(IN);
-
-my %all_associations = (%$file_associations, %$add_associations);
-
-my @ordered = (@put_first, @non_primary);
-for my $key (sort keys %all_associations) {
- next if grep($_ eq $key, @ordered);
- push(@ordered, $key);
-}
-my $num = $#ordered + 1;
-
-warn("--\n");
-
-my $i4jcount = 0;
-for my $shortname (@ordered) {
- my $a = $all_associations{$shortname};
- next if (ref($a) ne "HASH");
-
- my $name = $a->{name};
- my $extensions = $a->{extensions};
- my $mimetype = $mimetypes->{$shortname};
- $mimetype = "application/x-$shortname+txt" unless $mimetype;
-
- my $iconfile = $a->{iconfile};
- $iconfile = "Jalview-File" unless $iconfile;
-
- my $primary = (! grep($_ eq $shortname, @non_primary));
- my $primarystring = $primary?"true":"false";
- my $role = $primary?"Editor":"Viewer";
-
- my @extensions = @$extensions;
-
- my $xname = xml_escape($name);
- my $xmimetype = xml_escape($mimetype);
- my $xshortname = xml_escape($shortname);
- my $xiconfile = xml_escape($iconfile);
- my $xrole = xml_escape($role);
- my $xROLE = xml_escape(uc($role));
- my $xprimarystring = xml_escape($primarystring);
-
- my $macentry = $mactemplate;
- $macentry =~ s/\$\$NAME\$\$/$xname/g;
- $macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
- $macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
- $macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
- $macentry =~ s/\$\$ROLE\$\$/$xrole/g;
- $macentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
- while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
- my $pre = $1;
- my $post = $2;
- my $macextensions;
- for my $ext (@extensions) {
- my $xext = xml_escape($ext);
- $macextensions .= $pre.$xext.$post;
- }
- $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
- }
- print MA $macentry;
-
- my $i4jentry = $i4jtemplate;
- $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
- $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
- $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
- $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
- $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
- $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
-
- my $ext = join(",",sort(@extensions));
- my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
- my $progresspercent = int(($i4jcount/$num)*100);
- $progresspercent = 100 if $progresspercent > 100;
- $i4jcount++;
- my $xext = xml_escape($ext);
- my $addunixextension = "true";
-
- $i4jentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
- $i4jentry =~ s/\$\$EXTENSION\$\$/$xext/g;
- $i4jentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
- $i4jentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
- $i4jentry =~ s/\$\$ID\$\$/$id/g;
- $id++;
- $i4jentry =~ s/\$\$ID1\$\$/$id/g;
- $id++;
- $i4jentry =~ s/\$\$ID2\$\$/$id/g;
- $id++;
-
- print IA $i4jentry;
-
- delete $all_associations{$shortname};
- warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
-}
-
-close(IA);
-print MA "</array>\n";
-close(MA);
-
-sub xml_escape {
- my $x = shift;
- # stolen from Pod::Simple::XMLOutStream in base distro
- $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
- return $x;
-}
git://source.jalview.org / jalview.git / commitdiff