examples

src/programs/crawl.py

+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+
+from caosadvancedtools.crawler import Crawler
+from example_cfood import ExampleCFood
+import argparse
+import caosdb as db
+from argparse import RawTextHelpFormatter
+
+def get_parser():
+    parser = argparse.ArgumentParser(description=__doc__,
+                                     formatter_class=RawTextHelpFormatter)
+
+    return parser
+
+
+if __name__ == "__main__":
+    parser = get_parser()
+    args = parser.parse_args()
+
+    fi = db.File(file=__file__, path="filepath")
+    f = ExampleCFood(pattern="(.*)craw(.*)")
+    c = Crawler(food=[f])
+    c.crawl([fi])

src/programs/example_cfood.py

+#!/usr/bin/env python
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+# ** end header
+#
+
+from caosadvancedtools.cfood import AbstractCFood
+
+class ExampleCFood(AbstractCFood):
+    def create_identifiables(self, crawled_file, match):
+        entities = {}
+        entities["exp"] = db.Record()
+        #import IPython
+        # IPython.embed()
+        entities["exp"].add_parent(name="Experiment")
+        entities["exp"].add_property(name="species", value=match.group)
+
+        return entities
+
+    def update_identifiables(self, entities, crawled_file, match):
+        entities["exp"].add_property(name="date",
+                                     value=datetime.today().isoformat())
+        db.Container().extend(entities.values).update()