// plasmaCRProcess.java // ----------------------- // part of YaCy // (C) by Michael Peter Christen; mc@anomic.de // first published on http://www.anomic.de // Frankfurt, Germany, 2005 // Created 15.11.2005 // // $LastChangedDate$ // $LastChangedRevision$ // $LastChangedBy$ // // This program 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 2 of the License, or // (at your option) any later version. // // This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA // // Using this software in any meaning (reading, learning, copying, compiling, // running) means that you agree that the Author(s) is (are) not responsible // for cost, loss of data or any harm that may be caused directly or indirectly // by usage of this softare or this documentation. The usage of this software // is on your own risk. The installation and usage (starting/running) of this // software may allow other people or application to access your computer and // any attached devices and is highly dependent on the configuration of the // software which must be done by the user of the software; the author(s) is // (are) also not responsible for proper configuration and usage of the // software, even if provoked by documentation provided together with // the software. // // Any changes to this file according to the GPL as documented in the file // gpl.txt aside this file in the shipment you received can be done to the // lines that follows this copyright notice here, but changes must not be // done inside the copyright notive above. A re-distribution must contain // the intact and unchanged copyright notice. // Contributions and changes to the program code must be marked as such. package de.anomic.plasma; import java.io.File; import java.io.IOException; import java.util.Iterator; import de.anomic.kelondro.kelondroAttrSeq; import de.anomic.kelondro.kelondroBase64Order; import de.anomic.kelondro.kelondroBitfield; import de.anomic.kelondro.kelondroCollectionIndex; import de.anomic.kelondro.kelondroFlexTable; import de.anomic.kelondro.kelondroIndex; import de.anomic.kelondro.kelondroRow; import de.anomic.kelondro.kelondroRowSet; import de.anomic.server.serverDate; import de.anomic.server.serverFileUtils; import de.anomic.server.serverMemory; public class plasmaRankingCRProcess { /* header.append("# Name=YaCy " + ((type.equals("crl")) ? "Local" : "Global") + " Citation Reference Ticket"); header.append((char) 13); header.append((char) 10); header.append("# Created=" + System.currentTimeMillis()); header.append((char) 13); header.append((char) 10); header.append("# Structure=,'=',,,,,,,,,,,'|',*"); header.append((char) 13); header.append((char) 10); header.append("# ---"); header.append((char) 13); header.append((char) 10); */ public static final kelondroRow CRG_accrow = new kelondroRow( "byte[] Referee-12," + "Cardinal UDate-3 {b64e}, Cardinal VDate-3 {b64e}, " + "Cardinal LCount-2 {b64e}, Cardinal GCount-2 {b64e}, Cardinal ICount-2 {b64e}, Cardinal DCount-2 {b64e}, Cardinal TLength-3 {b64e}, " + "Cardinal WACount-3 {b64e}, Cardinal WUCount-3 {b64e}, Cardinal Flags-1 {b64e}, " + "Cardinal FUDate-3 {b64e}, Cardinal FDDate-3 {b64e}, Cardinal LUDate-3 {b64e}, " + "Cardinal UCount-2 {b64e}, Cardinal PCount-2 {b64e}, Cardinal ACount-2 {b64e}, Cardinal VCount-2 {b64e}, Cardinal Vita-2 {b64e}", kelondroBase64Order.enhancedCoder, 0); public static final kelondroRow CRG_colrow = new kelondroRow("byte[] Anchor-12", kelondroBase64Order.enhancedCoder, 0); public static final String CRG_accname = "CRG-a-attr"; public static final String CRG_seqname = "CRG-a-coli"; public static final kelondroRow RCI_coli = new kelondroRow("byte[] RefereeDom-6", kelondroBase64Order.enhancedCoder, 0); public static final String RCI_colname = "RCI-a-coli"; private static boolean accumulate_upd(File f, kelondroAttrSeq acc) { // open file kelondroAttrSeq source_cr = null; try { source_cr = new kelondroAttrSeq(f, false); } catch (IOException e) { return false; } // put elements in accumulator file Iterator el = source_cr.keys(); String key; kelondroAttrSeq.Entry new_entry, acc_entry; int FUDate, FDDate, LUDate, UCount, PCount, ACount, VCount, Vita; kelondroBitfield acc_flags, new_flags; while (el.hasNext()) { key = (String) el.next(); new_entry = source_cr.getEntry(key); new_flags = new kelondroBitfield(kelondroBase64Order.enhancedCoder.encodeLong((long) new_entry.getAttr("Flags", 0), 1).getBytes()); // enrich information with additional values if ((acc_entry = acc.getEntry(key)) != null) { FUDate = (int) acc_entry.getAttr("FUDate", 0); FDDate = (int) acc_entry.getAttr("FDDate", 0); LUDate = (int) acc_entry.getAttr("LUDate", 0); UCount = (int) acc_entry.getAttr("UCount", 0); PCount = (int) acc_entry.getAttr("PCount", 0); ACount = (int) acc_entry.getAttr("ACount", 0); VCount = (int) acc_entry.getAttr("VCount", 0); Vita = (int) acc_entry.getAttr("Vita", 0); // update counters and dates acc_entry.setSeq(new_entry.getSeqSet()); // need to be checked UCount++; // increase update counter PCount += (new_flags.get(1)) ? 1 : 0; ACount += (new_flags.get(2)) ? 1 : 0; VCount += (new_flags.get(3)) ? 1 : 0; // 'OR' the flags acc_flags = new kelondroBitfield(kelondroBase64Order.enhancedCoder.encodeLong((long) acc_entry.getAttr("Flags", 0), 1).getBytes()); for (int i = 0; i < 6; i++) { if (new_flags.get(i)) acc_flags.set(i, true); } acc_entry.setAttr("Flags", (int) kelondroBase64Order.enhancedCoder.decodeLong(acc_flags.exportB64())); } else { // initialize counters and dates acc_entry = acc.newEntry(key, new_entry.getAttrs(), new_entry.getSeqSet()); FUDate = plasmaWordIndex.microDateHoursInt(System.currentTimeMillis()); // first update date FDDate = plasmaWordIndex.microDateHoursInt(System.currentTimeMillis()); // very difficult to compute; this is only a quick-hack LUDate = (int) new_entry.getAttr("VDate", 0); UCount = 0; PCount = (new_flags.get(1)) ? 1 : 0; ACount = (new_flags.get(2)) ? 1 : 0; VCount = (new_flags.get(3)) ? 1 : 0; Vita = 0; } // make plausibility check? // insert into accumulator acc_entry.setAttr("FUDate", (long) FUDate); acc_entry.setAttr("FDDate", (long) FDDate); acc_entry.setAttr("LUDate", (long) LUDate); acc_entry.setAttr("UCount", (long) UCount); acc_entry.setAttr("PCount", (long) PCount); acc_entry.setAttr("ACount", (long) ACount); acc_entry.setAttr("VCount", (long) VCount); acc_entry.setAttr("Vita", (long) Vita); acc.putEntrySmall(acc_entry); } return true; } private static boolean accumulate_upd(File f, kelondroIndex acc, kelondroCollectionIndex seq) throws IOException { // open file kelondroAttrSeq source_cr = null; try { source_cr = new kelondroAttrSeq(f, false); } catch (IOException e) { return false; } // put elements in accumulator file Iterator el = source_cr.keys(); String key; kelondroAttrSeq.Entry new_entry; kelondroRow.Entry acc_entry; int FUDate, FDDate, LUDate, UCount, PCount, ACount, VCount, Vita; kelondroBitfield acc_flags, new_flags; while (el.hasNext()) { key = (String) el.next(); new_entry = source_cr.getEntry(key); new_flags = new kelondroBitfield(kelondroBase64Order.enhancedCoder.encodeLong((long) new_entry.getAttr("Flags", 0), 1).getBytes()); // enrich information with additional values if ((acc_entry = acc.get(key.getBytes())) != null) { FUDate = (int) acc_entry.getColLong("FUDate", 0); FDDate = (int) acc_entry.getColLong("FDDate", 0); LUDate = (int) acc_entry.getColLong("LUDate", 0); UCount = (int) acc_entry.getColLong("UCount", 0); PCount = (int) acc_entry.getColLong("PCount", 0); ACount = (int) acc_entry.getColLong("ACount", 0); VCount = (int) acc_entry.getColLong("VCount", 0); Vita = (int) acc_entry.getColLong("Vita", 0); // update counters and dates seq.put(key.getBytes(), new_entry.getSeqCollection()); // FIXME: old and new collection must be joined UCount++; // increase update counter PCount += (new_flags.get(1)) ? 1 : 0; ACount += (new_flags.get(2)) ? 1 : 0; VCount += (new_flags.get(3)) ? 1 : 0; // 'OR' the flags acc_flags = new kelondroBitfield(kelondroBase64Order.enhancedCoder.encodeLong(acc_entry.getColLong("Flags", 0), 1).getBytes()); for (int i = 0; i < 6; i++) { if (new_flags.get(i)) acc_flags.set(i, true); } acc_entry.setCol("Flags", (int) kelondroBase64Order.enhancedCoder.decodeLong(acc_flags.exportB64())); } else { // initialize counters and dates acc_entry = acc.row().newEntry(); acc_entry.setCol("Referee", key, null); for (int i = 1; i < acc.row().columns(); i++) { acc_entry.setCol(i, new_entry.getAttr(acc.row().column(i).nickname, 0)); } seq.put(key.getBytes(), new_entry.getSeqCollection()); FUDate = plasmaWordIndex.microDateHoursInt(System.currentTimeMillis()); // first update date FDDate = plasmaWordIndex.microDateHoursInt(System.currentTimeMillis()); // very difficult to compute; this is only a quick-hack LUDate = (int) new_entry.getAttr("VDate", 0); UCount = 0; PCount = (new_flags.get(1)) ? 1 : 0; ACount = (new_flags.get(2)) ? 1 : 0; VCount = (new_flags.get(3)) ? 1 : 0; Vita = 0; } // make plausibility check? // insert into accumulator acc_entry.setCol("FUDate", (long) FUDate); acc_entry.setCol("FDDate", (long) FDDate); acc_entry.setCol("LUDate", (long) LUDate); acc_entry.setCol("UCount", (long) UCount); acc_entry.setCol("PCount", (long) PCount); acc_entry.setCol("ACount", (long) ACount); acc_entry.setCol("VCount", (long) VCount); acc_entry.setCol("Vita", (long) Vita); acc.put(acc_entry); } return true; } public static void accumulate(File from_dir, File tmp_dir, File err_dir, File bkp_dir, File to_file, int max_files, boolean newdb) throws IOException { if (!(from_dir.isDirectory())) { System.out.println("source path " + from_dir + " is not a directory."); return; } if (!(tmp_dir.isDirectory())) { System.out.println("temporary path " + tmp_dir + " is not a directory."); return; } if (!(err_dir.isDirectory())) { System.out.println("error path " + err_dir + " is not a directory."); return; } if (!(bkp_dir.isDirectory())) { System.out.println("back-up path " + bkp_dir + " is not a directory."); return; } // open target file kelondroAttrSeq acc = null; kelondroIndex newacc = null; kelondroCollectionIndex newseq = null; if (newdb) { File path = to_file.getParentFile(); // path to storage place newacc = new kelondroFlexTable(path, CRG_accname, CRG_accrow, 0, false); newseq = new kelondroCollectionIndex(path, CRG_seqname, 12, kelondroBase64Order.enhancedCoder, 2, 9, CRG_colrow); } else { if (!(to_file.exists())) { acc = new kelondroAttrSeq("Global Ranking Accumulator File", ",'='," + ",,,,,,,,,," + ",,,,,,,," + "'|',*", false); acc.toFile(to_file); } acc = new kelondroAttrSeq(to_file, false); } // collect source files File source_file = null; String[] files = from_dir.list(); if (files.length < max_files) max_files = files.length; for (int i = 0; i < max_files; i++) { // open file source_file = new File(from_dir, files[i]); if (newdb) { if (accumulate_upd(source_file, newacc, newseq)) { // move CR file to temporary folder source_file.renameTo(new File(tmp_dir, files[i])); } else { // error case: the CR-file is not valid; move to error path source_file.renameTo(new File(err_dir, files[i])); } } else { if (accumulate_upd(source_file, acc)) { // move CR file to temporary folder source_file.renameTo(new File(tmp_dir, files[i])); } else { // error case: the CR-file is not valid; move to error path source_file.renameTo(new File(err_dir, files[i])); } } } try { if (newdb) { newacc.close(); newseq.close(); } else { // save accumulator to temporary file File tmp_file; if (to_file.toString().endsWith(".gz")) { tmp_file = new File(to_file.toString() + "." + (System.currentTimeMillis() % 1000) + ".tmp.gz"); } else { tmp_file = new File(to_file.toString() + "." + (System.currentTimeMillis() % 1000) + ".tmp"); } // store the file acc.toFile(tmp_file); // since this was successful, we remove the old file and move the new file to it to_file.delete(); tmp_file.renameTo(to_file); } serverFileUtils.moveAll(tmp_dir, bkp_dir); } catch (IOException e) { // move previously processed files back e.printStackTrace(); serverFileUtils.moveAll(tmp_dir, from_dir); } } public static int genrci(File cr_in, File rci_out) throws IOException { if (!(cr_in.exists())) return 0; kelondroAttrSeq cr = new kelondroAttrSeq(cr_in, false); //if (rci_out.exists()) rci_out.delete(); // we want only fresh rci here (during testing) if (!(rci_out.exists())) { kelondroAttrSeq rcix = new kelondroAttrSeq("Global Ranking Reverse Citation Index", ",'='," + "," + "'|',*", false); rcix.toFile(rci_out); } final kelondroAttrSeq rci = new kelondroAttrSeq(rci_out, false); // loop over all referees int count = 0; int size = cr.size(); long start = System.currentTimeMillis(); long l; final Iterator i = cr.keys(); String referee, anchor, anchorDom; kelondroAttrSeq.Entry cr_entry, rci_entry; long cr_UDate, rci_UDate; while (i.hasNext()) { referee = i.next(); cr_entry = cr.getEntry(referee); cr_UDate = cr_entry.getAttr("UDate", 0); // loop over all anchors Iterator j = cr_entry.getSeqSet().iterator(); while (j.hasNext()) { // get domain of anchors anchor = j.next(); if (anchor.length() == 6) anchorDom = anchor; else anchorDom = anchor.substring(6); // update domain-specific entry rci_entry = rci.getEntry(anchorDom); if (rci_entry == null) rci_entry = rci.newEntry(anchorDom, false); rci_entry.addSeq(referee); // update Update-Date rci_UDate = rci_entry.getAttr("UDate", 0); if (cr_UDate > rci_UDate) rci_entry.setAttr("UDate", cr_UDate); // insert entry rci.putEntry(rci_entry); } count++; if ((count % 1000) == 0) { l = java.lang.Math.max(1, (System.currentTimeMillis() - start) / 1000); System.out.println("processed " + count + " citations, " + (count / l) + " per second, rci.size = " + rci.size() + ", " + ((size - count) / (count / l)) + " seconds remaining; mem = " + serverMemory.available()); } i.remove(); } // finished. write to file cr = null; cr_in = null; serverMemory.gc(1000, "plasmaRankingCRProcess.genrci(...)"); // thq rci.toFile(rci_out); return count; } public static int genrcix(File cr_path_in, File rci_path_out) throws IOException { //kelondroFlexTable acc = new kelondroFlexTable(cr_path_in, CRG_accname, kelondroBase64Order.enhancedCoder, 128 * 1024 * 1024, -1, CRG_accrow, true); kelondroCollectionIndex seq = new kelondroCollectionIndex(cr_path_in, CRG_seqname, 12, kelondroBase64Order.enhancedCoder, 2, 9, CRG_colrow); kelondroCollectionIndex rci = new kelondroCollectionIndex(rci_path_out, RCI_colname, 6, kelondroBase64Order.enhancedCoder, 2, 9, RCI_coli); // loop over all referees int count = 0; int size = seq.size(); long start = System.currentTimeMillis(); long l; final Iterator i = seq.keycollections(null, null, false); Object[] keycollection; String referee, refereeDom, anchor, anchorDom; kelondroRowSet cr_entry, rci_entry; while (i.hasNext()) { keycollection = i.next(); referee = new String((byte[]) keycollection[0]); if (referee.length() == 6) refereeDom = referee; else refereeDom = referee.substring(6); cr_entry = (kelondroRowSet) keycollection[1]; // loop over all anchors Iterator j = cr_entry.rows(); kelondroRow.Entry entry; while (j.hasNext()) { // get domain of anchors entry = j.next(); anchor = (String) entry.getColString(0, null); if (anchor.length() == 6) anchorDom = anchor; else anchorDom = anchor.substring(6); // update domain-specific entry rci_entry = rci.get(anchorDom.getBytes()); if (rci_entry == null) rci_entry = new kelondroRowSet(RCI_coli, 0); rci_entry.add(refereeDom.getBytes()); // insert entry rci.put(anchorDom.getBytes(), rci_entry); } count++; if ((count % 1000) == 0) { l = java.lang.Math.max(1, (System.currentTimeMillis() - start) / 1000); System.out.println("processed " + count + " citations, " + (count / l) + " per second, rci.size = " + rci.size() + ", " + ((size - count) / (count / l) / 60) + " minutes remaining; mem = " + serverMemory.free()); } } // finished. write to file seq.close(); rci.close(); return count; } public static void main(String[] args) { // java -classpath source de.anomic.plasma.kelondroPropFile -transcode DATA/RANKING/GLOBAL/CRG-test-unsorted-original.cr DATA/RANKING/GLOBAL/CRG-test-generated.cr try { if ((args.length == 5) && (args[0].equals("-accumulate"))) { accumulate(new File(args[1]), new File(args[2]), new File(args[3]), new File(args[4]), new File(args[5]), Integer.parseInt(args[6]), true); } if ((args.length == 2) && (args[0].equals("-accumulate"))) { File root_path = new File(args[1]); File from_dir = new File(root_path, "DATA/RANKING/GLOBAL/014_othercr"); File ready_dir = new File(root_path, "DATA/RANKING/GLOBAL/015_ready"); File tmp_dir = new File(root_path, "DATA/RANKING/GLOBAL/016_tmp"); File err_dir = new File(root_path, "DATA/RANKING/GLOBAL/017_err"); File acc_dir = new File(root_path, "DATA/RANKING/GLOBAL/018_acc"); String filename = "CRG-a-" + new serverDate().toShortString(true) + ".cr.gz"; File to_file = new File(root_path, "DATA/RANKING/GLOBAL/020_con0/" + filename); if (!(ready_dir.exists())) ready_dir.mkdirs(); if (!(tmp_dir.exists())) tmp_dir.mkdirs(); if (!(err_dir.exists())) err_dir.mkdirs(); if (!(acc_dir.exists())) acc_dir.mkdirs(); if (!(to_file.getParentFile().exists())) to_file.getParentFile().mkdirs(); serverFileUtils.moveAll(from_dir, ready_dir); long start = System.currentTimeMillis(); int files = ready_dir.list().length; accumulate(ready_dir, tmp_dir, err_dir, acc_dir, to_file, 1000, true); long seconds = java.lang.Math.max(1, (System.currentTimeMillis() - start) / 1000); System.out.println("Finished accumulate for " + files + " files in " + seconds + " seconds (" + (files / seconds) + " files/second)"); } if ((args.length == 3) && (args[0].equals("-recycle"))) { File root_path = new File(args[1]); int max_age_hours = Integer.parseInt(args[2]); File own_dir = new File(root_path, "DATA/RANKING/GLOBAL/010_owncr"); File acc_dir = new File(root_path, "DATA/RANKING/GLOBAL/018_acc"); File bkp_dir = new File(root_path, "DATA/RANKING/GLOBAL/019_bkp"); if (!(own_dir.exists())) return; if (!(acc_dir.exists())) return; if (!(bkp_dir.exists())) bkp_dir.mkdirs(); String[] list = acc_dir.list(); long start = System.currentTimeMillis(); int files = list.length; long d; File f; for (int i = 0; i < list.length; i++) { f = new File(acc_dir, list[i]); try { d = (System.currentTimeMillis() - (new kelondroAttrSeq(f, false)).created()) / 3600000; if (d > max_age_hours) { // file is considered to be too old, it is not recycled System.out.println("file " + f.getName() + " is old (" + d + " hours) and not recycled, only moved to backup"); f.renameTo(new File(bkp_dir, list[i])); } else { // file is fresh, it is duplicated and moved to be transferred to other peers again System.out.println("file " + f.getName() + " is fresh (" + d + " hours old), recycled and moved to backup"); serverFileUtils.copy(f, new File(own_dir, list[i])); f.renameTo(new File(bkp_dir, list[i])); } } catch (IOException e) { // there is something wrong with this file; delete it System.out.println("file " + f.getName() + " is corrupted and deleted"); f.delete(); } } long seconds = java.lang.Math.max(1, (System.currentTimeMillis() - start) / 1000); System.out.println("Finished recycling of " + files + " files in " + seconds + " seconds (" + (files / seconds) + " files/second)"); } if ((args.length == 2) && (args[0].equals("-genrci"))) { File root_path = new File(args[1]); File cr_filedir = new File(root_path, "DATA/RANKING/GLOBAL/020_con0"); File rci_filedir = new File(root_path, "DATA/RANKING/GLOBAL/030_rci0"); rci_filedir.mkdirs(); long start = System.currentTimeMillis(); int count = genrcix(cr_filedir, rci_filedir); long seconds = java.lang.Math.max(1, (System.currentTimeMillis() - start) / 1000); System.out.println("Completed RCI generation: " + count + " citation references in " + seconds + " seconds (" + (count / seconds) + " CR-records/second)"); } /* if ((args.length == 2) && (args[0].equals("-genrci"))) { File root_path = new File(args[1]); File cr_filedir = new File(root_path, "DATA/RANKING/GLOBAL/020_con0"); File rci_file = new File(root_path, "DATA/RANKING/GLOBAL/030_rci0/RCI-0.rci.gz"); rci_file.getParentFile().mkdirs(); String[] cr_filenames = cr_filedir.list(); for (int i = 0; i < cr_filenames.length; i++) { long start = System.currentTimeMillis(); int count = genrci(new File(cr_filedir, cr_filenames[i]), rci_file); long seconds = java.lang.Math.max(1, (System.currentTimeMillis() - start) / 1000); System.out.println("Completed RCI generation for input file " + cr_filenames[i] + ": " + count + " citation references in " + seconds + " seconds (" + (count / seconds) + " CR-records/second)"); } } */ } catch (IOException e) { e.printStackTrace(); } } /* Class-A File format: UDate : latest update timestamp of the URL (as virtual date, hours since epoch) VDate : last visit timestamp of the URL (as virtual date, hours since epoch) LCount : count of links to local resources GCount : count of links to global resources ICount : count of links to images (in document) DCount : count of links to other documents TLength: length of the plain text content (bytes) WACount: total number of all words in content WUCount: number of unique words in content (removed doubles) Flags : Flags (0=update, 1=popularity, 2=attention, 3=vote) Class-a File format is an extension of Class-A plus the following attributes FUDate : first update timestamp of the URL FDDate : first update timestamp of the domain LUDate : latest update timestamp of the URL UCount : Update Counter (of 'latest update timestamp') PCount : Popularity Counter (proxy clicks) ACount : Attention Counter (search result clicks) VCount : Votes Vita : Vitality (normed number of updates per time) */ }