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tagger_mamba.py
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tagger_mamba.py
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import os
import re
import sys
import hashlib
import mamba.http
import mamba.setup
import mamba.task
import mamba.util
try:
import blackmamba.database
import blackmamba.html
import blackmamba.xpage
except ImportError:
blackmamba = None
import tagger.tagger
class Setup(mamba.setup.Configuration):
def __init__(self, ini_file):
mamba.setup.Configuration.__init__(self, ini_file)
sys.setcheckinterval(10000)
styles = {}
if "STYLES" in self.sections:
for priority in self.sections["STYLES"]:
styles[int(priority)] = self.sections["STYLES"][priority]
types = {}
if "TYPES" in self.sections:
for priority in self.sections["TYPES"]:
types[int(priority)] = self.sections["TYPES"][priority]
print '[INIT] Loading tagger ...'
self.tagger = tagger.tagger.Tagger()
self.tagger.set_styles(styles, types)
if "java_scripts" in self.globals:
self.tagger.load_headers(self.globals["java_scripts"])
self.tagger.load_names(self.globals["entities_file"], self.globals["names_file"])
if "global_file" in self.globals:
self.tagger.load_global(self.globals["global_file"])
if "local_file" in self.globals:
self.tagger.load_local(self.globals["local_file"])
if "changelog_file" in self.globals:
self.tagger.load_changelog(self.globals["changelog_file"])
class AddName(mamba.task.Request):
def main(self):
rest = mamba.task.RestDecoder(self)
for check in ("name", "document_id", "entity_type", "entity_identifier"):
if check not in rest:
raise mamba.task.SyntaxError, 'Required parameter "%s" missing.' % check
mamba.setup.config().tagger.add_name(mamba.util.string_to_bytes(rest["name"], "utf-8"), int(rest["entity_type"]), mamba.util.string_to_bytes(rest["entity_identifier"], "utf-8"), mamba.util.string_to_bytes(rest["document_id"], "utf-8"))
mamba.http.HTTPResponse(self, "AddName succeeded.").send()
class AllowName(mamba.task.Request):
def main(self):
rest = mamba.task.RestDecoder(self)
for check in ("name", "document_id"):
if check not in rest:
raise mamba.task.SyntaxError, 'Required parameter "%s" missing.' % check
mamba.setup.config().tagger.allow_name(mamba.util.string_to_bytes(rest["name"], "utf-8"), mamba.util.string_to_bytes(rest["document_id"], "utf-8"))
mamba.http.HTTPResponse(self, 'AllowName succeeded.').send()
class BlockName(mamba.task.Request):
def main(self):
rest = mamba.task.RestDecoder(self)
for check in ("name", "document_id"):
if check not in rest:
raise mamba.task.SyntaxError, 'Required parameter "%s" missing.' % check
mamba.setup.config().tagger.block_name(mamba.util.string_to_bytes(rest["name"], "utf-8"), mamba.util.string_to_bytes(rest["document_id"], "utf-8"))
mamba.http.HTTPResponse(self, 'BlockName succeeded.').send()
class GetHead(mamba.task.EmptyRequest):
def main(self):
mamba.http.HTTPResponse(self, mamba.setup.config().globals["java_scripts"]).send()
class GetHeader(GetHead):
pass
class GetPopup(mamba.task.Request):
def main(self):
rest = mamba.task.RestDecoder(self)
entities = mamba.setup.config().tagger.resolve_name(mamba.util.string_to_bytes(rest["name"], self.http.charset))
if len(entities):
url_params = []
show_first = ["9606", "10090"]
for pref_organism in show_first:
for type, id in entities:
if type == pref_organism:
url_params.append(type + "." + id + "+")
for type, id in entities:
if type not in show_first:
url_params.append(type + "." + id + "+")
popup_url = 'http://reflect.ws/popup/fcgi-bin/createPopup.fcgi?' + ''.join(url_params)
popup_url = popup_url[:-1]
reply = mamba.http.HTTPRedirect(self, popup_url)
reply.send()
else:
html = "<html><head><title>No Reflect popup available</title></head><body>The name '%s' was not found in our dictionary.</body></html>" % self.names[0]
mamba.http.HTTPResponse(self, html, content_type="text/html").send()
class ResolveName(mamba.task.Request):
def main(self):
rest = mamba.task.RestDecoder(self)
names = []
if "name" in rest:
names.append(mamba.util.string_to_bytes(rest["name"], self.http.charset))
elif "names" in rest:
names += mamba.util.string_to_bytes(rest["names"], self.http.charset).split("\n")
else:
raise mamba.task.SyntaxError, 'Required parameter "name" or "names" is missing.'
format = "tsv"
if "format" in rest:
format = rest["format"]
if format == "xml":
xml = []
xml.append("""<?xml version="1.0" encoding="UTF-8"?>\n""")
xml.append("""<ResolveNameResponse xmlns="Reflect" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">""")
xml.append("""<items>""")
for name in names:
xml.append("""<item><name xsi:type="xsd:string">%s</name><entities>""" % name)
for entity in mamba.setup.config().tagger.resolve_name(name):
xml.append("""<entity><type xsi:type="xsd:int">%d</type><identifier xsi:type="xsd:string">%s</identifier></entity>""" % (entity[0], entity[1]))
xml.append("""</entities></item>""")
xml.append("</items>")
xml.append("</ResolveNameResponse>")
result = "".join(xml)
content_type = "text/xml"
else:
tsv = []
for name in names:
for entity in mamba.setup.config().tagger.resolve_name(name):
tsv.append("%s\t%d\t%s\n" % (name, entity[0], entity[1]))
result = "".join(tsv)
content_type = "text/plain"
mamba.http.HTTPResponse(self, result, content_type).send()
_taggable_types = ["text/html", "text/plain", "text/xml", "text/tab-separated-values", 'application/msword', 'application/pdf', 'application/vnd.ms-excel']
class TaggingRequest(mamba.task.Request):
def __init__(self, http, action):
mamba.task.Request.__init__(self, http, action, priority=1)
def parse(self, rest):
self.hash = None
if "hash" in rest:
self.hash = rest["hash"]
self.document = None
if "document" in rest:
self.document = rest["document"]
elif "text" in rest:
self.document = rest["text"]
if self.document != None and "content_type" in rest and rest["content_type"].lower() == "text/html" or isinstance(self.document, str):
self.document = unicode(self.document, self.http.charset, errors="replace")
self.document_id = None
self.document_url = None
doi = None
if "doi" in rest:
doi = rest["doi"]
elif "document_identifier" in rest:
doi = rest["document_identifier"]
if doi:
if self.doi.startswith('doi:'):
doi = doi[4:]
self.document_id = doi
self.document_url = "http://dx.doi.org/"+doi
elif "uri" in rest:
if rest["uri"].startswith("http"):
self.document_id = rest["uri"]
self.document_url = rest["uri"]
else:
self.document_id = "http://"+rest["uri"]
self.document_url = "http://"+rest["uri"]
elif "url" in rest:
if rest["url"].startswith("http"):
self.document_id = rest["url"]
self.document_url = rest["url"]
else:
self.document_id = "http://"+rest["url"]
self.document_url = "http://"+rest["url"]
elif "pmid" in rest:
self.document_id = rest["pmid"]
self.document_url = "http://www.ncbi.nlm.nih.gov/pubmed/"+rest["pmid"]
elif self.hash != None:
self.document_id = self.hash
self.auto_detect = 1
if "auto_detect" in rest:
self.auto_detect = int(rest["auto_detect"])
self.auto_detect_doi = 1
if "auto_detect_doi" in rest:
self.auto_detect_doi = int(rest["auto_detect_doi"])
self.ignore_blacklist = 0
if "ignore_blacklist" in rest:
self.ignore_blacklist = int(rest["ignore_blacklist"])
if "entity_types" in rest:
self.entity_types = set()
for type in rest["entity_types"].split():
self.entity_types.add(int(type))
else:
self.entity_types = set()
if hasattr(self, "user_settings"):
if "proteins" in self.user_settings and mamba.setup.config_is_true(self.user_settings["proteins"]):
self.entity_types.add(9606)
if "chemicals" in self.user_settings and mamba.setup.config_is_true(self.user_settings["chemicals"]):
self.entity_types.add(-1)
if "wikipedia" in self.user_settings and mamba.setup.config_is_true(self.user_settings["wikipedia"]):
self.entity_types.add(-11)
def convert(self):
md5 = hashlib.md5()
md5.update(self.document)
key = md5.hexdigest()
if 'bin_dir' in mamba.setup.config().globals:
bin_dir = mamba.setup.config().globals["bin_dir"]
else:
bin_dir = "./bin"
infile = "/dev/shm/"+key
outfile = "/dev/shm/"+key+".html"
f = open(infile, 'w')
f.write(self.document)
f.flush()
f.close()
if self.document.startswith('%PDF'):
os.system("%s/pdf2html %s >& /dev/null" % (bin_dir, infile))
elif os.system("unset DISPLAY; abiword --to=html --exp-props='embed-css: yes; embed-images: yes;' %s" % infile):
os.system("%s/xls2csv %s | %s/csv2html > %s" % (bin_dir, infile, bin_dir, outfile))
f = open(outfile, "r")
html = f.read();
f.close()
os.remove(infile)
os.remove(outfile)
if len(html):
self.document = unicode(html, "utf-8", "replace")
self.queue("main")
else:
mamba.http.HTTPErrorResponse(self, 400, "Request contains an unsupported document type").send()
def download(self):
self.info("Downloading: %s" % self.document_url)
page, status, headers, page_url, charset = mamba.http.Internet().download(self.document_url)
if charset:
page = unicode(page, charset, "replace")
self.http.charset = charset
if status != 200:
mamba.http.HTTPErrorResponse(self, status, page).send()
else:
page_is_text = False
if "Content-Type" in headers:
for accepted in _taggable_types:
if headers["Content-Type"].lower().startswith(accepted):
page_is_text = True
break
if not page_is_text:
mamba.http.Redirect(self, location=page_url).send()
elif page:
self.uri = page_url # URI could have been changed via multiple redirects.
self.document = page
self.queue("main")
else:
mamba.http.HTTPErrorResponse(self, 404, "Unable to download URI: '%s'" % str(fetch_url)).send()
def main(self):
if not hasattr(self, "document"):
self.parse(mamba.task.RestDecoder(self))
if self.http.method == "OPTIONS":
mamba.http.HTTPResponse(self, "").send()
elif isinstance(self.document, unicode):
self.queue("tagging")
elif self.document != None:
self.queue("convert")
elif self.document_url != None:
self.queue("download")
elif self.hash != None:
self.load()
else:
mamba.http.HTTPErrorResponse(self, 400, "Request is missing a document and has no uri, doi or pmid either.").send()
class OpenAnnotation(TaggingRequest):
def __init__(self, http, action = "OpenAnnotation"):
TaggingRequest.__init__(self, http, action)
def parse(self, rest):
TaggingRequest.parse(self, rest)
self.annotation_index = None
if "annotation_index" in rest:
self.annotation_index = int(rest["annotation_index"])
if not "entity_types" in rest:
self.entity_types = set([9606,-1,-2,-22,-25,-26,-27])
def tagging(self):
data = mamba.setup.config().tagger.get_jsonld(document=mamba.util.string_to_bytes(self.document, self.http.charset), document_charset=self.http.charset, document_id=self.document_id, annotation_index=self.annotation_index, entity_types=self.entity_types, auto_detect=self.auto_detect, ignore_blacklist=self.ignore_blacklist)
mamba.http.HTTPResponse(self, data, "application/ld+json").send()
class GetEntities(TaggingRequest):
def __init__(self, http, action = "GetEntities"):
TaggingRequest.__init__(self, http, action)
def parse(self, rest):
TaggingRequest.parse(self, rest)
self.format = "xml"
if "format" in rest:
self.format = rest["format"].lower()
if self.format not in ("xml", "tsv", "csv", "ssv"):
raise mamba.task.SyntaxError, 'In action: %s unknown format: "%s". Supports only: %s' % (self.action, format, ', '.join(supported_formats))
def tagging(self):
data = mamba.setup.config().tagger.get_entities(document=mamba.util.string_to_bytes(self.document, self.http.charset), document_id=self.document_id, entity_types=self.entity_types, auto_detect=self.auto_detect, ignore_blacklist=self.ignore_blacklist, format=self.format)
if format == "xml":
mamba.http.HTTPResponse(self, data, "text/xml").send()
else:
mamba.http.HTTPResponse(self, data, "text/plain").send()
class GetHTML(TaggingRequest):
def __init__(self, http):
TaggingRequest.__init__(self, http, "GetHTML")
def load(self):
try:
f = open(self.worker.params["tmp_dir"]+"/"+self.hash+".html", "r")
self.document = f.read()
f.close()
mamba.http.HTMLResponse(self, self.document).send()
except:
mamba.http.HTTPErrorResponse(self, 404, "Pretagged document not available.").send()
def respond(self):
if self.hash != None:
self.save()
mamba.http.HTMLResponse(self, self.document).send()
def save(self):
if self.hash == None:
hash = hashlib.md5()
hash.update(mamba.util.string_to_bytes(self.document, self.http.charset))
self.hash = hash.hexdigest()
f = open(self.worker.params["tmp_dir"]+"/"+self.hash+".html", "w")
f.write(mamba.util.string_to_bytes(self.document, self.http.charset))
f.close()
def tagging(self):
footer = ['<div class="reflect_user_settings" style="display: none;">']
for key in self.user_settings:
footer.append(' <span name="%s">%s</span>' % (key, self.user_settings[key]))
footer.append('</div>\n')
self.document = mamba.setup.config().tagger.get_html(document=mamba.util.string_to_bytes(self.document, self.http.charset), document_id=self.document_id, entity_types=self.entity_types, auto_detect=self.auto_detect, ignore_blacklist=self.ignore_blacklist, basename='reflect', add_events=True, extra_classes=False, force_important=True, html_footer="\n".join(footer))
self.respond()
class GetURI(GetHTML):
def __init__(self, http):
TaggingRequest.__init__(self, http, "GetURI")
def respond(self):
self.save()
mamba.http.HTTPResponse(self, self.worker.params["tmp_dir"]+"/"+self.hash+".html", "text/plain").send()
class Extract(TaggingRequest):
def __init__(self, http, action = "Extract"):
TaggingRequest.__init__(self, http, action)
def tagging(self):
dictionary = blackmamba.database.Connect("dictionary")
document = mamba.util.string_to_bytes(self.document, self.http.charset)
tagger = mamba.setup.config().tagger
matches = tagger.get_matches(document=document, document_id=self.document_id, entity_types=self.entity_types, auto_detect=self.auto_detect, ignore_blacklist=self.ignore_blacklist)
rows = {}
for match in reversed(matches):
classes = ["extract_match"]
entities = match[2]
if entities != None:
for entity in entities:
classes.append(entity[1])
row = (blackmamba.database.preferred_type_name(entity[0], dictionary), blackmamba.html.xcase(blackmamba.database.preferred_name(entity[0], entity[1], dictionary)), entity[0], entity[1])
if not row in rows:
rows[row] = set()
rows[row].add(document[match[0]:match[1]+1])
document = tagger.create_html(document=document, document_id=None, matches=matches, basename='extract', add_events=False, extra_classes=True, force_important=False, html_footer="")
page = blackmamba.xpage.XPage(self.action)
selection = blackmamba.html.XDiv(page.content, "ajax_table")
blackmamba.html.XH2(selection, "table_title").text = "Selected text"
blackmamba.html.XP(selection).text = document
tsv = []
table = blackmamba.html.XDiv(page.content, "ajax_table")
blackmamba.html.XH2(table, "table_title").text = "Identified terms"
if len(rows):
xtable = blackmamba.html.XDataTable(table)
xtable["width"] = "100%"
xtable.addhead("Type", "Name", "Identifier")
for row in sorted(rows):
tsv.append("%s\t%s\t%s\t%s\t%s\t%s\n" % (row[0], row[1], row[3], ";".join(sorted(rows[row])), self.document_url or "", self.document))
url = blackmamba.database.url(row[2], row[3])
if url:
xtable.addrow(row[0], row[1], blackmamba.html.XLink(None, url, row[3], '_blank'))
else:
xtable.addrow(row[0], row[1], row[3])
form = blackmamba.html.XForm(blackmamba.html.XP(table))
blackmamba.html.XTextArea(form, attr = {"class" : "hidden", "id" : "clipboard"}).text = "".join(tsv)
blackmamba.html.XLink(form, "", "Copy to clipboard", attr = {"class" : "button_link", "id" : "extract_copy_to_clipboard", "onClick" : "extract_copy_to_clipboard('clipboard'); return false;"})
blackmamba.html.XLink(form, "", "Save to file", attr = {"class" : "button_link", "download" : "entities.tsv", "id" : "extract_save_to_file", "onClick" : "extract_save_to_file(this);"})
else:
blackmamba.html.XP(table).text = "No terms were identified in the selected text."
mamba.http.HTMLResponse(self, page.tohtml()).send()
class ExtractPopup(Extract):
def __init__(self, http, action = "ExtractPopup"):
Extract.__init__(self, http, action)