Merge branch 'master' into im_und_export

integrationtests/full_test/crawl.py

@@ -50,18 +50,21 @@ def access(path):
 
 
 if __name__ == "__main__":
-    set_log_level(logging.DEBUG)
+    logger = logging.getLogger("caosadvancedtools")
+    conlogger = logging.getLogger("connection")
+    conlogger.setLevel(level=logging.ERROR)
+    logger.setLevel(level=logging.WARN)
 
     parser = get_parser()
     args = parser.parse_args()
 
-    print("Starting query...")
+    logger.info("Starting query...")
     files = Crawler.query_files(args.path)
-    print("Query done...")
+    logger.info("Query done...")
     config = db.configuration.get_config()
     c = Crawler(use_cache=True, access=access,
                 food=[ProjectCFood,
                       ExperimentCFood, AnalysisCFood,
                       PublicationCFood, SimulationCFood,
                       ])
-    c.crawl(files, interactive=False, security_level=UPDATE)
+    c.crawl(files, interactive=False, security_level=INSERT, hideKnown=True)

src/caosadvancedtools/cfood.py

@@ -38,6 +38,7 @@ import logging
 import re
 
 import caosdb as db
+from caosdb.exceptions import EntityDoesNotExistError
 
 from .guard import global_guard as guard
 
@@ -77,7 +78,7 @@ class AbstractCFood(object):
                  A function that takes a CaosDB path and returns a local path
         """
         self.access = access
-        self.crawled_file = None
+        self._crawled_file = None
         self.crawled_path = crawled_file
         self.match = type(self).match(crawled_file)
         self.to_be_updated = db.Container()
@@ -85,6 +86,25 @@ class AbstractCFood(object):
         self.attached_ones = []
         self.attached_filenames = []
 
+    @property
+    def crawled_file(self):
+        if self._crawled_file is None:
+            try:
+                q = "FIND FILE WHICH IS STORED AT '{}'".format(
+                    self.crawled_path)
+                self._crawled_file = db.execute_query(q, unique=True)
+            except EntityDoesNotExistError:
+                path = "**"
+
+                if not self.crawled_path.startswith("/"):
+                    path = path + "/"
+                q = "FIND FILE WHICH IS STORED AT '{}{}'".format(path,
+                                                                 self.crawled_path)
+                logger.debug(q)
+                self._crawled_file = db.execute_query(q, unique=True)
+
+        return self._crawled_file
+
     def collect_information(self):
         """ The CFood collects information for further processing.
 

src/caosadvancedtools/crawler.py

@@ -37,6 +37,7 @@ match. This occurs in basically three steps:
 
 
 import logging
+import os
 import traceback
 from datetime import datetime
 
@@ -55,11 +56,15 @@ def separated(text):
 
 
 class UnknownCache(object):
-    def __init__(self, interactive=False):
+    def __init__(self, interactive=False, load=False):
+
         if interactive and "y" == input(
                 "\nDo you want to load filenames that previously were not "
                 "matched by any CFood?\nIn that case, they will not show up "
                 "again. (y)"):
+            load = True
+
+        if load and os.path.exists("known_cache.db"):
             with open("known_cache.db") as fi:
                 self.filenames = [el.strip("\n") for el in fi.readlines()]
         else:
@@ -99,7 +104,7 @@ class Crawler(object):
         if self.use_cache:
             self.cache = Cache()
 
-    def match(self, files, interactive):
+    def match(self, files, interactive, hideKnown=False):
         errors_occured = False
         tbs = []
         cfoods = []
@@ -151,12 +156,12 @@ class Crawler(object):
 
         # possibly load previously encountered "Missing matches" and
         # "Multiple matches"
-        ucache = UnknownCache(interactive=interactive)
+        ucache = UnknownCache(interactive=interactive, load=hideKnown)
 
         for crawled_file in files:
             if len(matches[crawled_file]) == 0:
                 msg = ("ATTENTION: No matching cfood!\n"
-                       "Tried to match {}".format(crawled_file))
+                       "Tried to match {}\n".format(crawled_file))
 
                 if crawled_file in ucache.filenames:
                     logger.debug(msg)
@@ -165,28 +170,30 @@ class Crawler(object):
                 ucache.add(crawled_file)
 
             if len(matches[crawled_file]) > 1:
-                msg = ("Attention: More than one matching cfood!"
+                msg = ("Attention: More than one matching cfood!\n"
                        + "Tried to match {}\n".format(crawled_file)
                        + "\tRecordTypes:\t" + ", ".join(
-                            matches[crawled_file]))
+                            matches[crawled_file])+"\n")
 
                 if crawled_file in ucache.filenames:
                     logger.debug(msg)
                 else:
                     logger.warn(msg)
-                    ucache.add(crawled_file)
+                ucache.add(crawled_file)
 
         # Save the encountered prblem matches
         ucache.save()
 
         return cfoods, matches, tbs, errors_occured
 
-    def crawl(self, files, interactive=True, security_level=RETRIEVE):
+    def crawl(self, files, interactive=True, hideKnown=False,
+              security_level=RETRIEVE):
         guard.set_level(level=security_level)
 
         files = sorted([f.path for f in files])
 
-        cfoods, matches, tbs, errors_occured = self.match(files, interactive)
+        cfoods, matches, tbs, errors_occured = self.match(files, interactive,
+                                                          hideKnown=hideKnown)
 
         if interactive and "y" != input("Do you want to continue? (y)"):
             return