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Eliminate the _monkeypatch_session_method from assignmapper by cleaning up remaining object flushes. The _monkeypatch_query_method remains due to a single object query in ~/datatypes/metadata.py in the FileParameter.wrap() method. The sqlalchemy session is now also passed into the __init__ methods for both HistoryDatasetAssociation and LibraryDatasetDatasetAssociation when the create_dataset param is True to enable methods in the DatasetInstance class to correctly add the created dataset to the sqlalchemy session and flush it.

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Greg Von Kuster
2009-11-12 15:25:48 -05:00
parent 468a631370
commit dc8e7c1039
13 changed files with 94 additions and 62 deletions
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tools/data_source/microbial_import_code.py
+1 -1
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@@ -131,7 +131,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
dbkey = fields[3]
filepath = fields[4]
file_type = fields[5]
newdata = app.model.HistoryDatasetAssociation( create_dataset = True ) #This import should become a library
newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library
newdata.set_size()
newdata.extension = file_type
newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"