def install(destDir=None, downloadDir=None, redownload=False, compile=True, updateLocalSettings=False): print >> sys.stderr, "Installing SVM-Multiclass" if compile: url = Settings.URL["SVM_MULTICLASS_SOURCE"] else: if 8 * struct.calcsize("P") == 32: # check for 32 bit or 64 bit environment (see http://stackoverflow.com/questions/1405913/how-do-i-determine-if-my-python-shell-is-executing-in-32bit-or-64bit-mode-on-os) url = Settings.URL["SVM_MULTICLASS_LINUX_32"] else: url = Settings.URL["SVM_MULTICLASS_LINUX_64"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = Settings.DATAPATH destDir += "/tools/SVMMultiClass" Download.downloadAndExtract(url, destDir, downloadDir, redownload=redownload) if compile: print >> sys.stderr, "Compiling SVM-Multiclass" Tools.Tool.testPrograms("SVM-Multiclass", ["make"]) subprocess.call("cd " + destDir + "; make", shell=True) Tools.Tool.finalizeInstall(["svm_multiclass_learn", "svm_multiclass_classify"], {"svm_multiclass_learn":"echo | ./svm_multiclass_learn -? > /dev/null", "svm_multiclass_classify":"echo | ./svm_multiclass_classify -? > /dev/null"}, destDir, {"SVM_MULTICLASS_DIR":destDir}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False, updateLocalSettings=False): url = Settings.URL["BLLIP_SOURCE"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH) + "/tools/download" if destDir == None: destDir = Settings.DATAPATH + "/tools/BLLIP" items = Download.downloadAndExtract(url, destDir, downloadDir + "/bllip.zip", None, False) print >> sys.stderr, "Installing BLLIP parser" Tool.testPrograms("BLLIP parser", ["make", "flex"], {"flex":"flex --version"}) parserPath = Download.getTopDir(destDir, items) cwd = os.getcwd() os.chdir(parserPath) print >> sys.stderr, "Compiling first-stage parser" subprocess.call("make", shell=True) print >> sys.stderr, "Compiling second-stage parser" subprocess.call("make reranker", shell=True) os.chdir(cwd) print >> sys.stderr, "Installing the McClosky biomedical parsing model" url = "http://bllip.cs.brown.edu/download/bioparsingmodel-rel1.tar.gz" Download.downloadAndExtract(url, destDir, downloadDir, None) bioModelDir = os.path.abspath(destDir + "/biomodel") # Check that everything works Tool.finalizeInstall(["first-stage/PARSE/parseIt", "second-stage/programs/features/best-parses"], {"first-stage/PARSE/parseIt":"first-stage/PARSE/parseIt " + bioModelDir + "/parser/ < /dev/null", "second-stage/programs/features/best-parses":"second-stage/programs/features/best-parses -l " + bioModelDir + "/reranker/features.gz " + bioModelDir + "/reranker/weights.gz < /dev/null"}, parserPath, {"BLLIP_PARSER_DIR":os.path.abspath(parserPath), "MCCLOSKY_BIOPARSINGMODEL_DIR":bioModelDir}, updateLocalSettings)
def install(self, destDir=None, downloadDir=None, redownload=False, updateLocalSettings=False): url = Settings.URL["BLLIP_SOURCE"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH) + "/tools/download" if destDir == None: destDir = Settings.DATAPATH + "/tools/BLLIP" items = Download.downloadAndExtract(url, destDir, downloadDir + "/bllip.zip", None, False) print >> sys.stderr, "Installing BLLIP parser" Tool.testPrograms("BLLIP parser", ["make", "flex"], {"flex":"flex --version"}) parserPath = Download.getTopDir(destDir, items) cwd = os.getcwd() os.chdir(parserPath) print >> sys.stderr, "Compiling first-stage parser" subprocess.call("make", shell=True) print >> sys.stderr, "Compiling second-stage parser" subprocess.call("make reranker", shell=True) os.chdir(cwd) print >> sys.stderr, "Installing the McClosky biomedical parsing model" url = "http://bllip.cs.brown.edu/download/bioparsingmodel-rel1.tar.gz" Download.downloadAndExtract(url, destDir, downloadDir, None) bioModelDir = os.path.abspath(destDir + "/biomodel") # Check that everything works Tool.finalizeInstall(["first-stage/PARSE/parseIt", "second-stage/programs/features/best-parses"], {"first-stage/PARSE/parseIt":"first-stage/PARSE/parseIt " + bioModelDir + "/parser/ < /dev/null", "second-stage/programs/features/best-parses":"second-stage/programs/features/best-parses -l " + bioModelDir + "/reranker/features.gz " + bioModelDir + "/reranker/weights.gz < /dev/null"}, parserPath, {"BLLIP_PARSER_DIR":os.path.abspath(parserPath), "MCCLOSKY_BIOPARSINGMODEL_DIR":bioModelDir}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False, compile=True, updateLocalSettings=False): print >> sys.stderr, "Installing SVM-Multiclass" if compile: url = Settings.URL["SVM_MULTICLASS_SOURCE"] else: url = Settings.URL["SVM_MULTICLASS_LINUX"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = Settings.DATAPATH destDir += "/tools/SVMMultiClass" Download.downloadAndExtract(url, destDir, downloadDir, redownload=redownload) if compile: print >> sys.stderr, "Compiling SVM-Multiclass" Tools.Tool.testPrograms("SVM-Multiclass", ["make"]) subprocess.call("cd " + destDir + "; make", shell=True) Tools.Tool.finalizeInstall( ["svm_multiclass_learn", "svm_multiclass_classify"], { "svm_multiclass_learn": "echo | ./svm_multiclass_learn -? > /dev/null", "svm_multiclass_classify": "echo | ./svm_multiclass_classify -? > /dev/null" }, destDir, {"SVM_MULTICLASS_DIR": destDir}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False): url = Settings.URL["GENIA_SENTENCE_SPLITTER"] packageName = "geniass" if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = os.path.join(Settings.DATAPATH, "tools/") Download.downloadAndExtract(url, packageName, destDir, downloadDir)
def install(destDir=None, downloadDir=None, redownload=False): print >> sys.stderr, "Installing BANNER" url = Settings.URL["BANNER_SOURCE"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download") if destDir == None: destDir = Settings.DATAPATH Download.downloadAndExtract(url, destDir + "/tools/BANNER", downloadDir + "/banner.tar.gz", "trunk", False, redownload=redownload) print >> sys.stderr, "Compiling BANNER with ANT" subprocess.call("cd " + destDir + "/tools/BANNER; export JAVA_HOME=/usr/lib/jvm/java-6-openjdk; ant -f build_ext.xml", shell=True)
def install(destDir=None, downloadDir=None, redownload=False): print >> sys.stderr, "Installing BioNLP'11 evaluators" settings = {} if downloadDir == None: downloadDir = Settings.DATAPATH if destDir == None: destDir = Settings.DATAPATH for corpus in ["GE", "BB", "BI", "CO"]: print >> sys.stderr, "Installing BioNLP'11", corpus, "evaluator" settings[corpus + "_EVALUATOR"] = Download.getTopDir(destDir + "/tools/evaluators/", Download.downloadAndExtract(Settings.URL[corpus + "_EVALUATOR"], destDir + "/tools/evaluators/", downloadDir + "/tools/download/")) print >> sys.stderr, "Installing BioNLP'11", corpus, "evaluator gold data" Download.downloadAndExtract(Settings.URL[corpus + "_DEVEL"], destDir + "/tools/evaluators/gold/" + corpus + "-devel", downloadDir + "/corpora/BioNLP11-original/corpus/", os.path.basename(Settings.URL[corpus + "_DEVEL"])[:-len(".tar.gz")]) return settings
def install(destDir=None, downloadDir=None, redownload=False, updateLocalSettings=False): print >> sys.stderr, "Installing GENIA Sentence Splitter" if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = os.path.join(Settings.DATAPATH, "tools/geniass") Download.downloadAndExtract(Settings.URL["GENIA_SENTENCE_SPLITTER"], destDir, downloadDir, "geniass") print >> sys.stderr, "Compiling GENIA Sentence Splitter" Tool.testPrograms("Genia Sentence Splitter", ["make", "ruby"]) cwd = os.getcwd() os.chdir(destDir) print >> sys.stderr, "Compiling Genia Sentence Splitter" subprocess.call("make", shell=True) os.chdir(cwd) Tool.finalizeInstall(["./run_geniass.sh"], {"./run_geniass.sh":"./run_geniass.sh README /dev/null " + Settings.RUBY_PATH}, destDir, {"GENIA_SENTENCE_SPLITTER_DIR":destDir}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False, compile=True): print >> sys.stderr, "Installing SVM-Multiclass" if compile: url = Settings.URL["SVM_MULTICLASS_SOURCE"] else: url = Settings.URL["SVM_MULTICLASS_LINUX"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = Settings.DATAPATH destDir += "/tools/SVMMultiClass" Download.downloadAndExtract(url, destDir, downloadDir, redownload=redownload) if compile: print >> sys.stderr, "Compiling SVM-Multiclass" subprocess.call("cd " + destDir + "; make", shell=True) test(destDir)
def install(destDir=None, downloadDir=None, redownload=False, compile=False, javaHome=None, updateLocalSettings=False): print >> sys.stderr, "Installing BANNER" if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download") if destDir == None: destDir = Settings.DATAPATH if compile: Download.downloadAndExtract(Settings.URL["BANNER_SOURCE"], destDir + "/tools/BANNER", downloadDir + "/banner.tar.gz", "trunk", False, redownload=redownload) print >> sys.stderr, "Compiling BANNER with ANT" Tool.testPrograms("BANNER", ["ant"], {"ant":"ant -version"}) #/usr/lib/jvm/java-6-openjdk if javaHome == None or javaHome.strip() == "": subprocess.call("cd " + destDir + "/tools/BANNER; ant -f build_ext.xml", shell=True) else: subprocess.call("cd " + destDir + "/tools/BANNER; export JAVA_HOME=" + javaHome + "; ant -f build_ext.xml", shell=True) else: print >> sys.stderr, "Downloading precompiled BANNER" Download.downloadAndExtract(Settings.URL["BANNER_COMPILED"], destDir + "/tools", downloadDir, redownload=redownload) Tool.finalizeInstall([], None, destDir + "/tools/BANNER", {"BANNER_DIR":destDir + "/tools/BANNER"}, updateLocalSettings)
def install(self, destDir=None, downloadDir=None, redownload=False, updateLocalSettings=False): print >> sys.stderr, "Installing Stanford Parser" if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = os.path.join(Settings.DATAPATH, "tools/") items = Download.downloadAndExtract(Settings.URL["STANFORD_PARSER"], destDir, downloadDir) stanfordPath = Download.getTopDir(destDir, items) Tool.finalizeInstall(["stanford-parser.jar"], {"stanford-parser.jar":"java -cp stanford-parser.jar edu.stanford.nlp.trees.EnglishGrammaticalStructure"}, stanfordPath, {"STANFORD_PARSER_DIR":stanfordPath}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False, updateLocalSettings=False): print >> sys.stderr, "Installing Stanford Parser" if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = os.path.join(Settings.DATAPATH, "tools/") items = Download.downloadAndExtract(Settings.URL["STANFORD_PARSER"], destDir, downloadDir) stanfordPath = Download.getTopDir(destDir, items) Tool.finalizeInstall(["stanford-parser.jar"], {"stanford-parser.jar":"java -cp stanford-parser.jar:slf4j-api.jar edu.stanford.nlp.trees.EnglishGrammaticalStructure"}, stanfordPath, {"STANFORD_PARSER_DIR":stanfordPath}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False, compile=True, updateLocalSettings=False): print >> sys.stderr, "Installing SVM-Multiclass" if compile: url = Settings.URL["SVM_MULTICLASS_SOURCE"] else: url = Settings.URL["SVM_MULTICLASS_LINUX"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = Settings.DATAPATH destDir += "/tools/SVMMultiClass" Download.downloadAndExtract(url, destDir, downloadDir, redownload=redownload) if compile: print >> sys.stderr, "Compiling SVM-Multiclass" Tools.Tool.testPrograms("SVM-Multiclass", ["make"]) subprocess.call("cd " + destDir + "; make", shell=True) Tools.Tool.finalizeInstall(["svm_multiclass_learn", "svm_multiclass_classify"], {"svm_multiclass_learn":"echo | ./svm_multiclass_learn -? > /dev/null", "svm_multiclass_classify":"echo | ./svm_multiclass_classify -? > /dev/null"}, destDir, {"SVM_MULTICLASS_DIR":destDir}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False, compile=False, javaHome=None, updateLocalSettings=False): print >> sys.stderr, "Installing BANNER" if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download") if destDir == None: destDir = Settings.DATAPATH if compile: Download.downloadAndExtract(Settings.URL["BANNER_SOURCE"], destDir + "/tools/BANNER", downloadDir + "/banner.tar.gz", "trunk", False, redownload=redownload) print >> sys.stderr, "Compiling BANNER with ANT" Tool.testPrograms("BANNER", ["ant"], {"ant": "ant -version"}) #/usr/lib/jvm/java-6-openjdk if javaHome == None or javaHome.strip() == "": subprocess.call("cd " + destDir + "/tools/BANNER; ant -f build_ext.xml", shell=True) else: subprocess.call("cd " + destDir + "/tools/BANNER; export JAVA_HOME=" + javaHome + "; ant -f build_ext.xml", shell=True) else: print >> sys.stderr, "Downloading precompiled BANNER" Download.downloadAndExtract(Settings.URL["BANNER_COMPILED"], destDir + "/tools", downloadDir, redownload=redownload) Tool.finalizeInstall([], None, destDir + "/tools/BANNER", {"BANNER_DIR": destDir + "/tools/BANNER"}, updateLocalSettings)
def install(destDir=None, downloadDir=None, redownload=False): print >> sys.stderr, "Installing BioNLP'11 evaluators" settings = {} if downloadDir == None: downloadDir = Settings.DATAPATH if destDir == None: destDir = Settings.DATAPATH for corpus in ["GE11", "BB11", "BI11", "CO11"]: print >> sys.stderr, "Installing BioNLP'11", corpus, "evaluator" settings[corpus + "_EVALUATOR"] = Download.getTopDir( destDir + "/tools/evaluators/", Download.downloadAndExtract(Settings.URL[corpus + "_EVALUATOR"], destDir + "/tools/evaluators/", downloadDir + "/tools/download/")) print >> sys.stderr, "Installing BioNLP'11", corpus, "evaluator gold data" Download.downloadAndExtract( Settings.URL[corpus + "_DEVEL"], destDir + "/tools/evaluators/gold/" + corpus + "-devel", downloadDir + "/corpora/BioNLP11-original/corpus/", os.path.basename(Settings.URL[corpus + "_DEVEL"])[:-len(".tar.gz")]) return settings
def install(destDir=None, downloadDir=None, redownload=False): url = Settings.URL["BLLIP_SOURCE"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH) if destDir == None: destDir = Settings.DATAPATH items = Download.downloadAndExtract( url, destDir + "/tools/BLLIP", downloadDir + "/tools/download/bllip.zip", None, False) # Install the parser # topDirs = [] # for item in items: # if item.endswith("/") and item.count("/") == 1: # topDirs.append(item) # assert len(topDirs) == 1 # parserPath = os.path.join(destDir + "/tools/BLLIP", topDirs[0]) # cwd = os.getcwd() # os.chdir(parserPath) # subprocess.call("make") # os.chdir(cwd) url = "http://bllip.cs.brown.edu/download/bioparsingmodel-rel1.tar.gz" Download.downloadAndExtract(url, destDir + "/tools/BLLIP", downloadDir + "/tools/download/", None)
def install(destDir=None, downloadDir=None, redownload=False, compile=True, updateLocalSettings=False): print >> sys.stderr, "Installing SVM-Multiclass" if compile: url = Settings.URL["SVM_MULTICLASS_SOURCE"] else: if 8 * struct.calcsize( "P" ) == 32: # check for 32 bit or 64 bit environment (see http://stackoverflow.com/questions/1405913/how-do-i-determine-if-my-python-shell-is-executing-in-32bit-or-64bit-mode-on-os) url = Settings.URL["SVM_MULTICLASS_LINUX_32"] else: url = Settings.URL["SVM_MULTICLASS_LINUX_64"] if downloadDir == None: downloadDir = os.path.join(Settings.DATAPATH, "tools/download/") if destDir == None: destDir = Settings.DATAPATH destDir += "/tools/SVMMultiClass" Download.downloadAndExtract(url, destDir, downloadDir, redownload=redownload) if compile: print >> sys.stderr, "Compiling SVM-Multiclass" Tools.Tool.testPrograms("SVM-Multiclass", ["make"]) subprocess.call("cd " + destDir + "; make", shell=True) Tools.Tool.finalizeInstall( ["svm_multiclass_learn", "svm_multiclass_classify"], { "svm_multiclass_learn": "echo | ./svm_multiclass_learn -? > /dev/null", "svm_multiclass_classify": "echo | ./svm_multiclass_classify -? > /dev/null" }, destDir, {"SVM_MULTICLASS_DIR": destDir}, updateLocalSettings)