Merge branch 'release/v0.3.0'

FourmiCrawler/pipelines.py

@@ -2,10 +2,11 @@
 #
 # 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 FourmiPipeline(object):
+class DuplicatePipeline(object):
 
     def __init__(self):
         self.known_values = set()
@@ -17,9 +18,27 @@ class FourmiPipeline(object):
         :param spider: The spider which scraped the spider
         :return: :raise DropItem: Returns the item if unique or drops them if it's already known
         """
-        value = item['attribute'], item['value']
+        value = (item['attribute'], item['value'], item['conditions'])
         if value in self.known_values:
             raise DropItem("Duplicate item found: %s" % item) # #[todo] append sources of first item.
         else:
             self.known_values.add(value)
             return item
+
+class AttributeSelectionPipeline(object):
+
+    def __init__(self):
+        pass;
+
+    def process_item(self, item, spider):
+        """
+        The items are processed using the selected attribute list available in the spider,
+        items that don't match the selected items are dropped.
+        :param item: The incoming item
+        :param spider: The spider which scraped the item. Should have an attribute "selected_attributes".
+        :return: :raise DropItem: Returns item if it matches an selected attribute, else it is dropped.
+        """
+        if [x for x in spider.selected_attributes if re.match(x, item["attribute"])]:
+            return item
+        else:
+            raise DropItem("Attribute not selected by used: %s" % item)

FourmiCrawler/settings.py

@@ -11,7 +11,8 @@ BOT_NAME = 'FourmiCrawler'
 SPIDER_MODULES = ['FourmiCrawler']
 NEWSPIDER_MODULE = 'FourmiCrawler'
 ITEM_PIPELINES = {
-    'FourmiCrawler.pipelines.FourmiPipeline': 100
+    'FourmiCrawler.pipelines.AttributeSelectionPipeline': 100,
+    'FourmiCrawler.pipelines.DuplicatePipeline': 200,
 }
 FEED_URI = 'results.json'
 FEED_FORMAT = 'jsonlines'

FourmiCrawler/sources/ChemSpider.py

@@ -47,7 +47,6 @@ class ChemSpider(Source):
         properties = []
 
         # Predicted - ACD/Labs tab
-        # [TODO] - test if tab contains data, some chemicals do not have data here
         td_list = sel.xpath('.//table[@id="acdlabs-table"]//td').xpath(
             'normalize-space(string())')
         prop_names = td_list[::2]
@@ -58,6 +57,12 @@ class ChemSpider(Source):
             prop_value = prop_value.extract().encode('utf-8')
             prop_conditions = ''
 
+            # Test for properties without values, with one hardcoded exception
+            if (not re.match(r'^\d', prop_value) or
+                    (prop_name == 'Polarizability' and
+                    prop_value == '10-24cm3')):
+                continue
+
             # Match for condition in parentheses
             m = re.match(r'(.*) \((.*)\)', prop_name)
             if m:
@@ -192,7 +197,8 @@ class ChemSpider(Source):
                 'reliability': 'Unknown',
                 'conditions': ''
             })
-            properties.append(result)
+            if result['value']:
+                properties.append(result)
         return properties
 
     def parse_searchrequest(self, response):
@@ -200,8 +206,14 @@ class ChemSpider(Source):
         sel = Selector(response)
         log.msg('chemspider parse_searchrequest', level=log.DEBUG)
         sel.register_namespace('cs', 'http://www.chemspider.com/')
-        csid = sel.xpath('.//cs:int/text()').extract()[0]
-        # [TODO] - handle multiple csids in case of vague search term
+        csids = sel.xpath('.//cs:int/text()').extract()
+        if len(csids) == 0:
+            log.msg('ChemSpider found nothing', level=log.ERROR)
+            return
+        elif len(csids) > 1:
+            log.msg('ChemSpider found multiple substances, taking first '
+                    'element', level=log.DEBUG)
+        csid = csids[0]
         structure_url = self.website[:-1] + self.structure % csid
         extendedinfo_url = self.website[:-1] + self.extendedinfo % csid
         log.msg('chemspider URL: %s' % structure_url, level=log.DEBUG)
@@ -215,4 +227,4 @@ class ChemSpider(Source):
             return None
         searchurl = self.website[:-1] + self.search % compound
         log.msg('chemspider compound', level=log.DEBUG)
-        return Request(url=searchurl, callback=self.parse_searchrequest)
+        return Request(url=searchurl, callback=self.parse_searchrequest)

FourmiCrawler/sources/WikipediaParser.py

@@ -36,8 +36,8 @@ class WikipediaParser(Source):
         """ scrape data from infobox on wikipedia. """
         items = []
 
-        #be sure to get both chembox (wikipedia template) and drugbox (wikipedia template) to scrape
-        tr_list = sel.xpath('.//table[@class="infobox bordered" or @class="infobox"]//td[not(@colspan)]').\
+        #be sure to get chembox (wikipedia template)
+        tr_list = sel.xpath('.//table[@class="infobox bordered"]//td[not(@colspan)]'). \
             xpath('normalize-space(string())')
         prop_names = tr_list[::2]
         prop_values = tr_list[1::2]
@@ -46,11 +46,31 @@ class WikipediaParser(Source):
                 'attribute': prop_name.extract().encode('utf-8'),
                 'value': prop_values[i].extract().encode('utf-8'),
                 'source': "Wikipedia",
-                'reliability': "",
+                'reliability': "Unknown",
                 'conditions': ""
             })
             items.append(item)
             log.msg('Wiki prop: |%s| |%s| |%s|' % (item['attribute'], item['value'], item['source']), level=log.DEBUG)
+
+        #scrape the  drugbox (wikipedia template)
+        tr_list2 = sel.xpath('.//table[@class="infobox"]//tr')
+        log.msg('dit: %s' % tr_list2, level=log.DEBUG)
+        for tablerow in tr_list2:
+            log.msg('item: %s' % tablerow.xpath('./th').xpath('normalize-space(string())'), level=log.DEBUG)
+            if tablerow.xpath('./th').xpath('normalize-space(string())') and tablerow.xpath('./td').xpath(
+                    'normalize-space(string())'):
+                item = Result({
+                    'attribute': tablerow.xpath('./th').xpath('normalize-space(string())').extract()[0].encode('utf-8'),
+                    'value': tablerow.xpath('./td').xpath('normalize-space(string())').extract()[0].encode('utf-8'),
+                    'source': "Wikipedia",
+                    'reliability': "Unknown",
+                    'conditions': ""
+                })
+                items.append(item)
+                log.msg(
+                    'Wiki prop: |attribute: %s| |value: %s| |%s|' % (item['attribute'], item['value'], item['source']),
+                    level=log.DEBUG)
+
         items = filter(lambda a: a['value'] != '', items)  # remove items with an empty value
         item_list = self.clean_items(items)
 

FourmiCrawler/spider.py

@@ -8,9 +8,10 @@ class FourmiSpider(Spider):
     __parsers = []
     synonyms = []
 
-    def __init__(self, compound=None, *args, **kwargs):
+    def __init__(self, compound=None, selected_attributes=[".*"], *args, **kwargs):
         super(FourmiSpider, self).__init__(*args, **kwargs)
         self.synonyms.append(compound)
+        self.selected_attributes = selected_attributes;
 
     def parse(self, reponse):
         for parser in self.__parsers:

README.md

@@ -0,0 +1,81 @@
+# Fourmi
+
+Fourmi is an web scraper for chemical substances. The program is designed to be
+used as a search engine to search multiple chemical databases for a specific
+substance. The program will produce all available attributes of the substance
+and conditions associated with the attributes. Fourmi also attempts to estimate
+the reliability of each data point to assist the user in deciding which data
+should be used.
+
+The Fourmi project is open source project licensed under the MIT license. Feel
+free to contribute!
+
+Fourmi is based on the [Scrapy framework](http://scrapy.org/), an open source
+web scraping framework for python. Most of the functionality of this project can
+be traced to this framework. Should the documentation for this application fall
+short, we suggest you take a close look at the [Scrapy architecture]
+(http://doc.scrapy.org/en/latest/topics/architecture.html) and the [Scrapy
+documentation](http://doc.scrapy.org/en/latest/index.html).
+
+### Installing 
+
+If you're installing Fourmi, please take a look at our [installation guide](...)
+on our wiki. When you've installed the application, make sure to check our
+[usage guide](...).
+
+### Using the Source
+
+To use the Fourmi source code multiple dependencies are required. Take a look at
+the [wiki page](...) on using the application source code for a step by step
+installation guide.
+
+When developing for the Fourmi project keep in mind that code readability is a
+must. To maintain the readability, code should be conform with the
+[PEP-8](http://legacy.python.org/dev/peps/pep-0008/) style guide for Python
+code. More information about the different structures and principles of the
+Fourmi application can be found on our [wiki](...).
+
+### To Do
+
+The Fourmi project has the following goals for the nearby future:
+
+__Main goals:__
+
+- Improve our documentation and guides. (Assignee: Dekker)
+- Build an graphical user interface(GUI) as alternative for the command line
+interface(CLI). (Assignee: Harmen)
+- Compiling the source into an windows executable. (Assignee: Bas)
+- Create an configuration file to hold logins and API keys.
+- Determine reliability of our data point.
+- Create an module to gather data from NIST. (Assignee: Rob)
+- Create an module to gather data from PubChem. (Assignee: Rob)
+
+__Side goals:__
+
+- Clean and unify data.
+- Extensive reliability analysis using statistical tests.
+- Test data with Descartes 1.
+
+### Project Origin
+
+The Fourmi project was started in February of 2014 as part of a software
+engineering course at the Radboud University for students studying Computer
+Science, Information Science or Artificial Intelligence. Students participate in
+a real software development project as part of the
+[Giphouse](http://www.giphouse.nl/).
+
+This particular project was started on behalf of Ivo B. Rietveld. As a chemist
+he was in need of an application to automatically search information on chemical
+substances and create an phase diagram. The so called "Descrates" project was
+split into two teams each creating a different application that has part of the
+functionality. We are the team Descartes 2 and as we were responsible for
+creating a web crawler, we've named our application Fourmi (Englis: Ants).
+
+The following people were part of the original team:
+
+- [Jip J. Dekker](http://jip.dekker.li)
+- Rob ten Berge
+- Harmen Prins
+- Bas van Berkel
+- Nout van Deijck
+- Michail Kuznetcov

README.rst

@@ -1,16 +0,0 @@
-We are the team Descartes 2.
-----------------------------
-
-Our team members are:
-
-+ Rob ten Berge
-
-+ Bas van Berkel
-
-+ Nout van Deijck
-
-+ Jip J. Dekker
-
-+ Michail Kuznetcov
-
-+ Harmen Prins

fourmi.py

@@ -12,14 +12,15 @@ Usage:
     fourmi --version
 
 Options:
+    --attributes=<regex>            Include only that match these regular expressions split by a comma. [default: .*]
     -h --help                       Show this screen.
     --version                       Show version.
     --verbose                       Verbose logging output.
     --log=<file>                    Save log to an file.
     -o <file> --output=<file>       Output file [default: result.*format*]
     -f <format> --format=<format>   Output formats (supported: csv, json, jsonlines, xml) [default: jsonlines]
-    --include=<sourcenames>         Include only sources that match the regular these expressions split by a comma.
-    --exclude=<sourcenames>         Exclude the sources that match the regular these expressions split by a comma.
+    --include=<regex>               Include only sources that match these regular expressions split by a comma.
+    --exclude=<regex>               Exclude the sources that match these regular expressions split by a comma.
 """
 
 from twisted.internet import reactor
@@ -32,8 +33,8 @@ from FourmiCrawler.spider import FourmiSpider
 from sourceloader import SourceLoader
 
 
-def setup_crawler(searchable, settings, source_loader):
-    spider = FourmiSpider(compound=searchable)
+def setup_crawler(searchable, settings, source_loader, attributes):
+    spider = FourmiSpider(compound=searchable, selected_attributes=attributes)
     spider.add_parsers(source_loader.sources)
     crawler = Crawler(settings)
     crawler.signals.connect(reactor.stop, signal=signals.spider_closed)
@@ -74,12 +75,12 @@ def start_log(docopt_arguments):
 def search(docopt_arguments, source_loader):
     start_log(docopt_arguments)
     settings = scrapy_settings_manipulation(docopt_arguments)
-    setup_crawler(docopt_arguments["<compound>"], settings, source_loader)
+    setup_crawler(docopt_arguments["<compound>"], settings, source_loader, docopt_arguments["--attributes"].split(','))
     reactor.run()
 
 
 if __name__ == '__main__':
-    arguments = docopt.docopt(__doc__, version='Fourmi - V0.2.6')
+    arguments = docopt.docopt(__doc__, version='Fourmi - V0.3.0')
     loader = SourceLoader()
 
     if arguments["--include"]: