Merge branch 'develop' into feature/executable

Conflicts:
	sourceloader.py

FourmiCrawler/items.py

@@ -1,6 +1,4 @@
-# Define here the models for your scraped items
+# For more information on item definitions, see the Scrapy documentation in:
-#
-# See documentation in:
 # http://doc.scrapy.org/en/latest/topics/items.html
 
 from scrapy.item import Item, Field

FourmiCrawler/pipelines.py

@@ -1,10 +1,25 @@
-# Define your item pipelines here
+# For more information on item pipelines, see the Scrapy documentation in:
-#
+# http://doc.scrapy.org/en/latest/topics/item-pipeline.html
-# Don't forget to add your pipeline to the ITEM_PIPELINES setting
-# See: http://doc.scrapy.org/en/latest/topics/item-pipeline.html
 import re
+
 from scrapy.exceptions import DropItem
 
+class RemoveNonePipeline(object):
+
+    def __init__(self):
+        self.known_values = set()
+
+    def process_item(self, item, spider):
+        """
+        Processing the items so None values are replaced by empty strings
+        :param item: The incoming item
+        :param spider: The spider which scraped the spider
+        :return: :raise DropItem: Returns the item if unique or drops them if it's already known
+        """
+        for key in item:
+            if item[key] is None:
+                item[key] = ""
+        return item
 
 class DuplicatePipeline(object):
 

FourmiCrawler/settings.py

@@ -11,8 +11,9 @@ BOT_NAME = 'FourmiCrawler'
 SPIDER_MODULES = ['FourmiCrawler']
 NEWSPIDER_MODULE = 'FourmiCrawler'
 ITEM_PIPELINES = {
-    'FourmiCrawler.pipelines.AttributeSelectionPipeline': 100,
+    "FourmiCrawler.pipelines.RemoveNonePipeline": 100,
-    'FourmiCrawler.pipelines.DuplicatePipeline': 200,
+    'FourmiCrawler.pipelines.AttributeSelectionPipeline': 200,
+    'FourmiCrawler.pipelines.DuplicatePipeline': 300,
 }
 FEED_URI = 'results.json'
 FEED_FORMAT = 'jsonlines'

FourmiCrawler/sources/NIST.py

@@ -0,0 +1,273 @@
+from source import Source
+from scrapy import log
+from scrapy.http import Request
+from scrapy.selector import Selector
+from FourmiCrawler.items import Result
+import re
+
+# [TODO]: values can be '128.', perhaps remove the dot in that case?
+# [TODO]: properties have references and comments which do not exist in the
+#         Result item, but should be included eventually.
+
+class NIST(Source):
+    """NIST Scraper plugin
+
+    This plugin manages searching for a chemical on the NIST website
+    and parsing the resulting page if the chemical exists on NIST.
+    """
+    website = "http://webbook.nist.gov/*"  
+
+    search = 'cgi/cbook.cgi?Name=%s&Units=SI&cTP=on'
+
+    ignore_list = set()
+
+    def __init__(self):
+        Source.__init__(self)
+
+    def parse(self, response):
+        sel = Selector(response)
+
+        title = sel.xpath('head/title/text()').extract()[0]
+        if title == 'Name Not Found':
+            log.msg('NIST: Chemical not found!', level=log.ERROR)
+            return
+        if title not in self.ignore_list:
+            self.ignore_list.update(title)
+            log.msg('NIST emit synonym: %s' % title, level=log.DEBUG)
+            self._spider.get_synonym_requests(title)
+
+        requests = []
+
+        requests.extend(self.parse_generic_info(sel))
+
+        symbol_table = {}
+        tds = sel.xpath('//table[@class="symbol_table"]/tr/td')
+        for (symbol_td, name_td) in zip(tds[::2], tds[1::2]):
+            symbol = ''.join(symbol_td.xpath('node()').extract())
+            name = name_td.xpath('text()').extract()[0]
+            symbol_table[symbol] = name
+            log.msg('NIST symbol: |%s|, name: |%s|' % (symbol, name),
+                    level=log.DEBUG)
+
+        for table in sel.xpath('//table[@class="data"]'):
+            summary = table.xpath('@summary').extract()[0]
+            if summary == 'One dimensional data':
+                log.msg('NIST table: Aggregrate data', level=log.DEBUG)
+                requests.extend(
+                    self.parse_aggregate_data(table, symbol_table))
+            elif table.xpath('tr/th="Initial Phase"').extract()[0] == '1':
+                log.msg('NIST table; Enthalpy/entropy of phase transition',
+                        level=log.DEBUG)
+                requests.extend(self.parse_transition_data(table, summary))
+            elif table.xpath('tr[1]/td'):
+                log.msg('NIST table: Horizontal table', level=log.DEBUG)
+            elif summary == 'Antoine Equation Parameters':
+                log.msg('NIST table: Antoine Equation Parameters',
+                        level=log.DEBUG)
+                requests.extend(self.parse_antoine_data(table, summary))
+            elif len(table.xpath('tr[1]/th')) == 5:
+                log.msg('NIST table: generic 5 columns', level=log.DEBUG)
+                # Symbol (unit) Temperature (K) Method Reference Comment
+                requests.extend(self.parse_generic_data(table, summary))
+            elif len(table.xpath('tr[1]/th')) == 4:
+                log.msg('NIST table: generic 4 columns', level=log.DEBUG)
+                # Symbol (unit) Temperature (K) Reference Comment
+                requests.extend(self.parse_generic_data(table, summary))
+            else:
+                log.msg('NIST table: NOT SUPPORTED', level=log.WARNING)
+                continue #Assume unsupported
+        return requests
+
+    def parse_generic_info(self, sel):
+        """Parses: synonyms, chemical formula, molecular weight, InChI,
+        InChiKey, CAS number
+        """
+        ul = sel.xpath('body/ul[li/strong="IUPAC Standard InChI:"]')
+        li = ul.xpath('li')
+
+        raw_synonyms = ul.xpath('li[strong="Other names:"]/text()').extract()
+        for synonym in raw_synonyms[0].strip().split(';\n'):
+            log.msg('NIST synonym: %s' % synonym, level=log.DEBUG)
+            self.ignore_list.update(synonym)
+            self._spider.get_synonym_requests(synonym)
+
+        data = {}
+
+        raw_formula = ul.xpath('li[strong/a="Formula"]//text()').extract()
+        data['Chemical formula'] = ''.join(raw_formula[2:]).strip()
+
+        raw_mol_weight = ul.xpath('li[strong/a="Molecular weight"]/text()')
+        data['Molecular weight'] = raw_mol_weight.extract()[0].strip()
+
+        raw_inchi = ul.xpath('li[strong="IUPAC Standard InChI:"]//tt/text()')
+        data['IUPAC Standard InChI'] = raw_inchi.extract()[0]
+
+        raw_inchikey = ul.xpath('li[strong="IUPAC Standard InChIKey:"]'
+                            '/tt/text()')
+        data['IUPAC Standard InChIKey'] = raw_inchikey.extract()[0]
+
+        raw_cas_number = ul.xpath('li[strong="CAS Registry Number:"]/text()')
+        data['CAS Registry Number'] = raw_cas_number.extract()[0].strip()
+
+        requests = []
+        for key, value in data.iteritems():
+            result = Result({
+                'attribute': key,
+                'value': value,
+                'source': 'NIST',
+                'reliability': 'Unknown',
+                'conditions': ''
+            })
+            requests.append(result)
+
+        return requests
+
+    def parse_aggregate_data(self, table, symbol_table):
+        """Parses the table(s) which contain possible links to individual
+        data points
+        """
+        results = []
+        for tr in table.xpath('tr[td]'):
+            extra_data_url = tr.xpath('td[last()][a="Individual data points"]'
+                                '/a/@href').extract()
+            if extra_data_url:
+                request = Request(url=self.website[:-1] + extra_data_url[0],
+                    callback=self.parse_individual_datapoints)
+                results.append(request)
+                continue
+            data = []
+            for td in tr.xpath('td'):
+                data.append(''.join(td.xpath('node()').extract()))
+
+            name = symbol_table[data[0]]
+            condition = ''
+
+            m = re.match(r'(.*) at (.*)', name)
+            if m:
+                name = m.group(1)
+                condition = m.group(2)
+
+            result = Result({
+                'attribute': name,
+                'value': data[1] + ' ' + data[2],
+                'source': 'NIST',
+                'reliability': 'Unknown',
+                'conditions': condition
+            })
+            log.msg('NIST: |%s|' % data, level=log.DEBUG)
+            results.append(result)
+        return results
+
+    @staticmethod
+    def parse_transition_data(table, summary):
+        """Parses the table containing properties regarding phase changes"""
+        results = []
+
+        tr_unit = ''.join(table.xpath('tr[1]/th[1]/node()').extract())
+        m = re.search(r'\((.*)\)', tr_unit)
+        unit = '!'
+        if m:
+            unit = m.group(1)
+
+        for tr in table.xpath('tr[td]'):
+            tds = tr.xpath('td/text()').extract()
+            result = Result({
+                'attribute': summary,
+                'value': tds[0] + ' ' + unit,
+                'source': 'NIST',
+                'reliability': 'Unknown',
+                'conditions': '%s K, (%s -> %s)' % (tds[1], tds[2], tds[3])
+            })
+            results.append(result)
+
+
+        return results
+
+    @staticmethod
+    def parse_generic_data(table, summary):
+        """Parses the common tables of 4 and 5 rows. Assumes they are of the
+        form:
+        Symbol (unit)|Temperature (K)|Method|Reference|Comment
+        Symbol (unit)|Temperature (K)|Reference|Comment
+        """
+        results = []
+
+        tr_unit = ''.join(table.xpath('tr[1]/th[1]/node()').extract())
+        m = re.search(r'\((.*)\)', tr_unit)
+        unit = '!'
+        if m:
+            unit = m.group(1)
+
+        for tr in table.xpath('tr[td]'):
+            tds = tr.xpath('td/text()').extract()
+            result = Result({
+                'attribute': summary,
+                'value': tds[0] + ' ' + unit,
+                'source': 'NIST',
+                'reliability': 'Unknown',
+                'conditions': '%s K' % tds[1]
+            })
+            results.append(result)
+        return results
+
+    @staticmethod
+    def parse_antoine_data(table, summary):
+        """Parse table containing parameters for the Antione equation"""
+        results = []
+
+        for tr in table.xpath('tr[td]'):
+            tds = tr.xpath('td/text()').extract()
+            result = Result({
+                'attribute': summary,
+                'value': 'A=%s, B=%s, C=%s' % (tds[1], tds[2], tds[3]),
+                'source': 'NIST',
+                'reliability': 'Unknown',
+                'conditions': '%s K' % tds[0]
+            })
+            results.append(result)
+
+        return results
+
+    def parse_individual_datapoints(self, response):
+        """Parses the page linked from aggregate data"""
+        sel = Selector(response)
+        table = sel.xpath('//table[@class="data"]')[0]
+
+        results = []
+
+        name = table.xpath('@summary').extract()[0]
+        condition = ''
+        m = re.match(r'(.*) at (.*)', name)
+        if m:
+            name = m.group(1)
+            condition = m.group(2)
+
+        tr_unit = ''.join(table.xpath('tr[1]/th[1]/node()').extract())
+        m = re.search(r'\((.*)\)', tr_unit)
+        unit = '!'
+        if m:
+            unit = m.group(1)
+
+        for tr in table.xpath('tr[td]'):
+            tds = tr.xpath('td/text()').extract()
+            uncertainty = ''
+            m = re.search('Uncertainty assigned by TRC =  (.*?) ', tds[-1])
+            if m:
+                uncertainty = '+- %s ' % m.group(1)
+                # [TODO]: get the plusminus sign working in here
+            result = Result({
+                'attribute': name,
+                'value': '%s %s%s' % (tds[0], uncertainty, unit),
+                'source': 'NIST',
+                'reliability': 'Unknown',
+                'conditions': condition
+            })
+            results.append(result)
+
+        return results
+
+    def new_compound_request(self, compound):
+        if compound not in self.ignore_list:
+            self.ignore_list.update(compound)
+            return Request(url=self.website[:-1] + self.search % compound,
+                           callback=self.parse)

FourmiCrawler/sources/source.py

@@ -7,15 +7,32 @@ class Source:
     _spider = None
 
     def __init__(self):
+        """
+        Initiation of a new Source
+        """
         pass
 
-    def parse(self, reponse):
+    def parse(self, response):
-        log.msg("The parse function of the empty parser was used.", level=log.WARNING)
+        """
+        This function should be able to parse all Scrapy Response objects with a URL matching the website Regex.
+        :param response: A Scrapy Response object
+        :return: A list of Result items and new Scrapy Requests
+        """
+        log.msg("The parse function of the empty source was used.", level=log.WARNING)
         pass
 
     def new_compound_request(self, compound):
+        """
+        This function should return a Scrapy Request for the given compound request.
+        :param compound: A compound name.
+        :return: A new Scrapy Request
+        """
         # return Request(url=self.website[:-1] + compound, callback=self.parse)
         pass
 
     def set_spider(self, spider):
+        """
+        A Function to save the associated spider.
+        :param spider: A FourmiSpider object
+        """
         self._spider = spider

FourmiCrawler/spider.py

@@ -1,43 +1,75 @@
+import re
+
 from scrapy.spider import Spider
 from scrapy import log
-import re
 
 
 class FourmiSpider(Spider):
+    """
+    A spider writen for the Fourmi Project which calls upon all available sources to request and scrape data.
+    """
     name = "FourmiSpider"
-    __parsers = []
+    __sources = []
     synonyms = []
 
     def __init__(self, compound=None, selected_attributes=[".*"], *args, **kwargs):
+        """
+        Initiation of the Spider
+        :param compound: compound that will be searched.
+        :param selected_attributes: A list of regular expressions that the attributes should match.
+        """
         super(FourmiSpider, self).__init__(*args, **kwargs)
         self.synonyms.append(compound)
         self.selected_attributes = selected_attributes;
 
-    def parse(self, reponse):
+    def parse(self, response):
-        for parser in self.__parsers:
+        """
-            if re.match(parser.website, reponse.url):
+        The function that is called when a response to a request is available. This function distributes this to a
-                log.msg("Url: " + reponse.url + " -> Source: " + parser.website, level=log.DEBUG)
+        source which should be able to handle parsing the data.
-                return parser.parse(reponse)
+        :param response: A Scrapy Response object that should be parsed
+        :return: A list of Result items and new Request to be handled by the scrapy core.
+        """
+        for source in self.__sources:
+            if re.match(source.website, response.url):
+                log.msg("Url: " + response.url + " -> Source: " + source.website, level=log.DEBUG)
+                return source.parse(response)
         return None
 
     def get_synonym_requests(self, compound):
+        """
+        A function that generates new Scrapy Request for each source given a new synonym of a compound.
+        :param compound: A compound name
+        :return: A list of Scrapy Request objects
+        """
         requests = []
-        for parser in self.__parsers:
+        for parser in self.__sources:
             parser_requests = parser.new_compound_request(compound)
             if parser_requests is not None:
                 requests.append(parser_requests)
         return requests
 
     def start_requests(self):
+        """
+        The function called by Scrapy for it's first Requests
+        :return: A list of Scrapy Request generated from the known synonyms using the available sources.
+        """
         requests = []
         for synonym in self.synonyms:
             requests.extend(self.get_synonym_requests(synonym))
         return requests
 
-    def add_parsers(self, parsers):
+    def add_sources(self, sources):
-        for parser in parsers:
+        """
-            self.add_parser(parser)
+        A function to add a new Parser objects to the list of available sources.
+        :param sources: A list of Source Objects.
+        """
+        for parser in sources:
+            self.add_source(parser)
 
-    def add_parser(self, parser):
+    def add_source(self, source):
-        self.__parsers.append(parser)
+        """
-        parser.set_spider(self)
+        A function add a new Parser object to the list of available parsers.
+        :param source: A Source Object
+        """
+        self.__sources.append(source)
+        source.set_spider(self)

fourmi.py

@@ -33,9 +33,16 @@ from FourmiCrawler.spider import FourmiSpider
 from sourceloader import SourceLoader
 
 
-def setup_crawler(searchable, settings, source_loader, attributes):
+def setup_crawler(compound, settings, source_loader, attributes):
-    spider = FourmiSpider(compound=searchable, selected_attributes=attributes)
+    """
-    spider.add_parsers(source_loader.sources)
+    This function prepares and start the crawler which starts the actual search on the internet
+    :param compound: The compound which should be searched
+    :param settings: A scrapy settings object
+    :param source_loader: A fully functional SourceLoader object which contains only the sources that should be used.
+    :param attributes: A list of regular expressions which the attribute names should match.
+    """
+    spider = FourmiSpider(compound=compound, selected_attributes=attributes)
+    spider.add_sources(source_loader.sources)
     crawler = Crawler(settings)
     crawler.signals.connect(reactor.stop, signal=signals.spider_closed)
     crawler.configure()
@@ -44,8 +51,13 @@ def setup_crawler(searchable, settings, source_loader, attributes):
 
 
 def scrapy_settings_manipulation(docopt_arguments):
+    """
+    This function manipulates the Scrapy settings that normally would be set in the settings file. In the Fourmi
+    project these are command line arguments.
+    :param docopt_arguments: A dictionary generated by docopt containing all CLI arguments.
+    """
     settings = get_project_settings()
-    # [todo] - add at least a warning for files that already exist
+
     if docopt_arguments["--output"] != 'result.*format*':
         settings.overrides["FEED_URI"] = docopt_arguments["--output"]
     elif docopt_arguments["--format"] == "jsonlines":
@@ -60,6 +72,10 @@ def scrapy_settings_manipulation(docopt_arguments):
 
 
 def start_log(docopt_arguments):
+    """
+    This function starts the logging functionality of Scrapy using the settings given by the CLI.
+    :param docopt_arguments:  A dictionary generated by docopt containing all CLI arguments.
+    """
     if docopt_arguments["--log"] is not None:
         if docopt_arguments["--verbose"]:
             log.start(logfile=docopt_arguments["--log"], logstdout=False, loglevel=log.DEBUG)
@@ -73,14 +89,20 @@ def start_log(docopt_arguments):
 
 
 def search(docopt_arguments, source_loader):
+    """
+    The function that facilitates the search for a specific compound.
+    :param docopt_arguments: A dictionary generated by docopt containing all CLI arguments.
+    :param source_loader: An initiated SourceLoader object pointed at the directory with the sources.
+    """
     start_log(docopt_arguments)
     settings = scrapy_settings_manipulation(docopt_arguments)
     setup_crawler(docopt_arguments["<compound>"], settings, source_loader, docopt_arguments["--attributes"].split(','))
     reactor.run()
 
 
+# The start for the Fourmi Command Line interface.
 if __name__ == '__main__':
-    arguments = docopt.docopt(__doc__, version='Fourmi - V0.3.0')
+    arguments = docopt.docopt(__doc__, version='Fourmi - V0.4.0')
     loader = SourceLoader()
 
     if arguments["--include"]:

sourceloader.py

@@ -2,24 +2,25 @@ import inspect
 import sys
 import os
 import re
+
 from FourmiCrawler.sources.source import Source
 
 
 class SourceLoader:
     sources = []
 
-    def __init__(self, rel_dir="FourmiCrawler\\sources"):
+    def __init__(self, rel_dir="FourmiCrawler/sources"):
 
         if hasattr(sys,'frozen'):
             path = os.path.dirname(sys.executable)
         else:
             path = os.path.dirname(os.path.abspath(__file__))
 
-        path += "\\" + rel_dir
+        path += "/" + rel_dir
         known_parser = set()
 
         for py in [f[:-3] for f in os.listdir(path) if f.endswith('.py') and f != '__init__.py']:
-            mod = __import__('.'.join([rel_dir.replace('\\', "."), py]), fromlist=[py])
+            mod = __import__('.'.join([rel_dir.replace('/', "."), py]), fromlist=[py])
             classes = [getattr(mod, x) for x in dir(mod) if inspect.isclass(getattr(mod, x))]
             for cls in classes:
                 if issubclass(cls, Source) and cls not in known_parser:
@@ -27,18 +28,30 @@ class SourceLoader:
                    # known_parser.add(cls)
 
     def include(self, source_names):
+        """
+        This function excludes all sources that don't match the given regular expressions.
+        :param source_names: A list of regular expression (strings)
+        """
         new = set()
         for name in source_names:
             new.update([src for src in self.sources if re.match(name, src.__class__.__name__)])
         self.sources = list(new)
 
     def exclude(self, source_names):
+        """
+        This function excludes all sources that match the given regular expressions.
+        :param source_names: A list of regular expression (strings)
+        """
         exclude = []
         for name in source_names:
             exclude.extend([src for src in self.sources if re.match(name, src.__class__.__name__)])
         self.sources = [src for src in self.sources if src not in exclude]
 
     def __str__(self):
+        """
+        This function returns a string with all sources currently available in the SourceLoader.
+        :return: a string with all available sources.
+        """
         string = ""
         for src in self.sources:
             string += "Source: " + src.__class__.__name__