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Cython: fixed history dot graph for all views, and fixed history

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recording for build_ref_db and ecotag
This commit is contained in:
Celine Mercier
2018-12-10 17:09:00 +01:00
parent eb586b2f53
commit c437931a35
3 changed files with 14 additions and 3 deletions
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7
python/obitools3/commands/build_ref_db.pyx
View File

@ -75,7 +75,11 @@ def run(config):
# Save command config in View comments # Save command config in View comments
command_line = " ".join(sys.argv[1:]) command_line = " ".join(sys.argv[1:])
comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name]) input_dms_name=[i_dms_name]
input_view_name= [i_view_name]
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0: if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
raise Exception("Error building a reference database") raise Exception("Error building a reference database")
@ -96,3 +100,4 @@ def run(config):
o_dms.close() o_dms.close()
i_dms.close() i_dms.close()

8
python/obitools3/commands/ecotag.pyx
View File

@ -93,7 +93,13 @@ def run(config):
# Save command config in View comments # Save command config in View comments
command_line = " ".join(sys.argv[1:]) command_line = " ".join(sys.argv[1:])
comments = View.print_config(config, "ecotag", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name]) # TODO no. fix input_dms_name=[i_dms_name]
input_view_name= [i_view_name]
input_dms_name.append(ref_dms_name)
input_view_name.append(ref_view_name)
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
if obi_ecotag(tobytes(i_dms_name), tobytes(i_view_name), \ if obi_ecotag(tobytes(i_dms_name), tobytes(i_view_name), \
tobytes(ref_dms_name), tobytes(ref_view_name), \ tobytes(ref_dms_name), tobytes(ref_view_name), \

2
python/obitools3/dms/view/view.pyx
View File

@ -485,7 +485,7 @@ cdef class View(OBIWrapper) :
@property @property
def dot_history_graph(self): def dot_history_graph(self):
uniq_graph = [] uniq_graph = []
for elt in self.history_graph_list: for elt in self.dot_history_graph_list:
if elt not in uniq_graph: if elt not in uniq_graph:
uniq_graph.append(elt) uniq_graph.append(elt)
uniq_graph.insert(0, b"digraph \""+self.name+b"\" {\n") uniq_graph.insert(0, b"digraph \""+self.name+b"\" {\n")