Merge branch 'feature/extended-logging' into develop

FourmiCrawler/sources/ChemSpider.py

@@ -26,9 +26,8 @@ class ChemSpider(Source):
     structure = 'Chemical-Structure.%s.html'
     extendedinfo = 'MassSpecAPI.asmx/GetExtendedCompoundInfo?csid=%s&token='
 
-    def __init__(self, config={}):
+    def __init__(self, config=None):
         Source.__init__(self, config)
-        self.cfg = config
         self.ignore_list = []
         if 'token' not in self.cfg or self.cfg['token'] == '':
             log.msg('ChemSpider token not set or empty, search/MassSpec API '
@@ -37,7 +36,6 @@ class ChemSpider(Source):
         self.search += self.cfg['token']
         self.extendedinfo += self.cfg['token']
 
-
     def parse(self, response):
         sel = Selector(response)
         requests = []
@@ -199,7 +197,8 @@ class ChemSpider(Source):
         return properties
 
     def newresult(self, attribute, value, conditions='', source='ChemSpider'):
-        return Result({
+        return Result(
+            {
                 'attribute': attribute,
                 'value': value,
                 'source': source,

FourmiCrawler/sources/NIST.py

@@ -22,12 +22,9 @@ class NIST(Source):
 
     search = 'cgi/cbook.cgi?Name=%s&Units=SI&cTP=on'
 
-    cfg = {}
+    def __init__(self, config=None):
-
-    def __init__(self, config={}):
         Source.__init__(self, config)
         self.ignore_list = set()
-        self.cfg = config
 
     def parse(self, response):
         sel = Selector(response)
@@ -88,7 +85,6 @@ class NIST(Source):
         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'):
@@ -255,7 +251,8 @@ class NIST(Source):
         return results
 
     def newresult(self, attribute, value, conditions=''):
-        return Result({
+        return Result(
+            {
                 'attribute': attribute,
                 'value': value,
                 'source': 'NIST',

FourmiCrawler/sources/WikipediaParser.py

@@ -1,9 +1,11 @@
+import re
+
 from scrapy.http import Request
 from scrapy import log
-from source import Source
 from scrapy.selector import Selector
+
+from source import Source
 from FourmiCrawler.items import Result
-import re
 
 
 class WikipediaParser(Source):
@@ -17,11 +19,8 @@ class WikipediaParser(Source):
     __spider = None
     searched_compounds = []
 
-    cfg = {}
+    def __init__(self, config=None):
-
-    def __init__(self, config={}):
         Source.__init__(self, config)
-        self.cfg = config
 
     def parse(self, response):
         """
@@ -53,7 +52,7 @@ class WikipediaParser(Source):
         # scrape the chembox (wikipedia template)
         items = self.parse_chembox(sel, items)
 
-        #scrape the drugbox (wikipedia template)
+        # scrape the drugbox (wikipedia template)
         items = self.parse_drugbox(sel, items)
 
         items = filter(lambda a: a['value'] != '', items)  # remove items with an empty value
@@ -123,7 +122,6 @@ class WikipediaParser(Source):
                     level=log.DEBUG)
         return items
 
-
     def new_compound_request(self, compound):
         return Request(url=self.website[:-1] + compound, callback=self.parse)
 
@@ -161,7 +159,8 @@ class WikipediaParser(Source):
         return links
 
     def newresult(self, attribute, value):
-        return Result({
+        return Result(
+            {
                 'attribute': attribute,
                 'value': value,
                 'source': 'Wikipedia',

FourmiCrawler/sources/source.py

@@ -6,10 +6,13 @@ class Source:
     website = "http://something/*"  # Regex of URI's the source is able to parse
     _spider = None
 
-    def __init__(self, config={}):
+    def __init__(self, config=None):
         """
         Initiation of a new Source
         """
+        self.cfg = {}
+        if config is not None:
+            self.cfg = config
         pass
 
     def parse(self, response):

FourmiCrawler/spider.py

@@ -10,7 +10,7 @@ class FourmiSpider(Spider):
     """
     name = "FourmiSpider"
 
-    def __init__(self, compound=None, selected_attributes=[".*"], *args, **kwargs):
+    def __init__(self, compound=None, selected_attributes=None, *args, **kwargs):
         """
         Initiation of the Spider
         :param compound: compound that will be searched.
@@ -20,6 +20,9 @@ class FourmiSpider(Spider):
         self.synonyms = set()
         super(FourmiSpider, self).__init__(*args, **kwargs)
         self.synonyms.add(compound)
+        if selected_attributes is None:
+            self.selected_attributes = [".*"]
+        else:
             self.selected_attributes = selected_attributes
 
     def parse(self, response):

fourmi.py

@@ -5,6 +5,7 @@ Fourmi, a web scraper build to search specific information for a given compound
 Usage:
     fourmi search <compound>
     fourmi [options] search <compound>
+    fourmi [-v | -vv | -vvv] [options] search <compound>
     fourmi [options] [--include=<sourcename> | --exclude=<sourcename>] search <compound>
     fourmi list
     fourmi [--include=<sourcename> | --exclude=<sourcename>] list
@@ -15,7 +16,7 @@ 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.
+    -v                              Verbose logging output. (Multiple occurrences increase logging level)
     --log=<file>                    Save log to an file.
     -o <file> --output=<file>       Output file [default: results.*format*]
     -f <format> --format=<format>   Output formats (supported: csv, json, jsonlines, xml) [default: csv]
@@ -25,8 +26,7 @@ Options:
 
 from twisted.internet import reactor
 from scrapy.crawler import Crawler
-from scrapy import log, signals
+from scrapy import signals, log
-from scrapy.utils.project import get_project_settings
 import docopt
 
 from FourmiCrawler.spider import FourmiSpider
@@ -58,9 +58,12 @@ def search(docopt_arguments, source_loader):
     :param source_loader: An initiated SourceLoader object pointed at the directory with the sources.
     """
     conf = Configurator()
-    conf.start_log(docopt_arguments["--log"], docopt_arguments["--verbose"])
+    conf.set_logging(docopt_arguments["--log"], docopt_arguments["-v"])
     conf.set_output(docopt_arguments["--output"], docopt_arguments["--format"])
-    setup_crawler(docopt_arguments["<compound>"], conf.scrapy_settings, source_loader, docopt_arguments["--attributes"].split(','))
+    setup_crawler(docopt_arguments["<compound>"], conf.scrapy_settings,
+                  source_loader, docopt_arguments["--attributes"].split(','))
+    log.start(conf.scrapy_settings.get("LOG_FILE"),
+              conf.scrapy_settings.get("LOG_LEVEL"), conf.scrapy_settings.get("LOG_STDOUT"))
     reactor.run()
 
 

tests/test_configurator.py

@@ -1,7 +1,8 @@
 import unittest
+import ConfigParser
+
 from utils.configurator import Configurator
 
-import ConfigParser
 
 class TestConfigurator(unittest.TestCase):
 
@@ -21,11 +22,28 @@ class TestConfigurator(unittest.TestCase):
         self.assertEqual(self.conf.scrapy_settings["FEED_URI"], "results.csv")
         self.assertEqual(self.conf.scrapy_settings["FEED_FORMAT"], "csv")
 
-    # def test_start_log(self):
+    def test_start_log(self):
-    #     self.conf.start_log("test.log", True)
+        for i in range(0, 3):
-    #     self.conf.start_log("test.log", False)
+            self.conf.set_logging("TEST", i)
-    #     self.conf.start_log(None, True)
+            self.assertEqual(self.conf.scrapy_settings.get("LOG_FILE"), "TEST")
-    #     self.conf.start_log(None, False)
+            if i > 0:
+                self.assertEqual(self.conf.scrapy_settings.get("LOG_ENABLED"), True)
+                if i > 1:
+                    self.assertEqual(self.conf.scrapy_settings.get("LOG_STDOUT"), False)
+                else:
+                    self.assertEqual(self.conf.scrapy_settings.get("LOG_STDOUT"), True)
+            else:
+                self.assertEqual(self.conf.scrapy_settings.get("LOG_ENABLED"), False)
+                self.assertEqual(self.conf.scrapy_settings.get("LOG_STDOUT"), True)
+            if i == 1:
+                self.assertEqual(self.conf.scrapy_settings.get("LOG_LEVEL"), "WARNING")
+            elif i == 2:
+                self.assertEqual(self.conf.scrapy_settings.get("LOG_LEVEL"), "INFO")
+            elif i == 3:
+                self.assertEqual(self.conf.scrapy_settings.get("LOG_LEVEL"), "DEBUG")
+
+            self.conf.set_logging(verbose=i)
+            self.assertEqual(self.conf.scrapy_settings.get("LOG_FILE"), None)
 
     def test_read_sourceconfiguration(self):
         config = self.conf.read_sourceconfiguration()

tests/test_pipeline.py

@@ -13,6 +13,7 @@ class TestPipelines(unittest.TestCase):
     def test_none_pipeline(self):
         # Testing the pipeline that replaces the None values in items.
         self.testItem["value"] = "abc"
+        self.testItem["source"] = None
         pipe = pipelines.RemoveNonePipeline()
         processed = pipe.process_item(self.testItem, spider.FourmiSpider())
 

tests/test_spider.py

@@ -47,7 +47,6 @@ class TestFoumiSpider(unittest.TestCase):
         self.assertGreater(len(requests), 0)
         self.assertIsInstance(requests[0], Request)
 
-
     def test_synonym_requests(self):
         # A test for the synonym request function
         self.spi._sources = []

utils/configurator.py

@@ -1,7 +1,8 @@
-from scrapy import log
-from scrapy.utils.project import get_project_settings
 import ConfigParser
 
+from scrapy.utils.project import get_project_settings
+
+
 class Configurator:
     """
     A helper class in the fourmi class. This class is used to process the settings as set
@@ -11,7 +12,6 @@ class Configurator:
     def __init__(self):
         self.scrapy_settings = get_project_settings()
 
-
     def set_output(self, filename, fileformat):
         """
         This function manipulates the Scrapy output file settings that normally would be set in the settings file.
@@ -30,23 +30,34 @@ class Configurator:
         if fileformat is not None:
             self.scrapy_settings.overrides["FEED_FORMAT"] = fileformat
 
-
+    def set_logging(self, logfile=None, verbose=0):
-    def start_log(self, logfile, verbose):
         """
-        This function starts the logging functionality of Scrapy using the settings given by the CLI.
+        This function changes the default settings of Scapy's logging functionality
+        using the settings given by the CLI.
         :param logfile: The location where the logfile will be saved.
-        :param verbose: A boolean value to switch between loglevels.
+        :param verbose: A integer value to switch between loglevels.
         """
+        if verbose != 0:
+            self.scrapy_settings.overrides["LOG_ENABLED"] = True
+        else:
+            self.scrapy_settings.overrides["LOG_ENABLED"] = False
+
+        if verbose == 1:
+            self.scrapy_settings.overrides["LOG_LEVEL"] = "WARNING"
+        elif verbose == 2:
+            self.scrapy_settings.overrides["LOG_LEVEL"] = "INFO"
+        else:
+            self.scrapy_settings.overrides["LOG_LEVEL"] = "DEBUG"
+
+        if verbose > 1:
+            self.scrapy_settings.overrides["LOG_STDOUT"] = False
+        else:
+            self.scrapy_settings.overrides["LOG_STDOUT"] = True
+
         if logfile is not None:
-            if verbose:
+            self.scrapy_settings.overrides["LOG_FILE"] = logfile
-                log.start(logfile=logfile, logstdout=False, loglevel=log.DEBUG)
         else:
-                log.start(logfile=logfile, logstdout=True, loglevel=log.WARNING)
+            self.scrapy_settings.overrides["LOG_FILE"] = None
-        else:
-            if verbose:
-                log.start(logstdout=False, loglevel=log.DEBUG)
-            else:
-                log.start(logstdout=True, loglevel=log.WARNING)
 
     @staticmethod
     def read_sourceconfiguration():
@@ -75,7 +86,6 @@ class Configurator:
         elif config.defaults():
             section = config.defaults()
         if 'reliability' not in section:
-            log.msg('Reliability not set for %s' % sourcename,
+            print 'WARNING: Reliability not set for %s' % sourcename
-                    level=log.WARNING)
             section['reliability'] = ''
         return section

utils/sourceloader.py

@@ -5,6 +5,7 @@ import re
 from FourmiCrawler.sources.source import Source
 from utils.configurator import Configurator
 
+
 class SourceLoader:
     sources = []