Coverage for python/lsst/ctrl/mpexec/cli/script/qgraph.py: 38%

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1# This file is part of ctrl_mpexec. 

2# 

3# Developed for the LSST Data Management System. 

4# This product includes software developed by the LSST Project 

5# (http://www.lsst.org). 

6# See the COPYRIGHT file at the top-level directory of this distribution 

7# for details of code ownership. 

8# 

9# This program is free software: you can redistribute it and/or modify 

10# it under the terms of the GNU General Public License as published by 

11# the Free Software Foundation, either version 3 of the License, or 

12# (at your option) any later version. 

13# 

14# This program is distributed in the hope that it will be useful, 

15# but WITHOUT ANY WARRANTY; without even the implied warranty of 

16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

17# GNU General Public License for more details. 

18# 

19# You should have received a copy of the GNU General Public License 

20# along with this program. If not, see <http://www.gnu.org/licenses/>. 

21 

22import logging 

23from types import SimpleNamespace 

24 

25from lsst.pipe.base.graphBuilder import DatasetQueryConstraintVariant 

26 

27from ... import CmdLineFwk 

28 

29_log = logging.getLogger(__name__) 

30 

31 

32def qgraph( # type: ignore 

33 pipelineObj, 

34 qgraph, 

35 qgraph_id, 

36 qgraph_node_id, 

37 qgraph_datastore_records, 

38 skip_existing_in, 

39 skip_existing, 

40 save_qgraph, 

41 save_single_quanta, 

42 qgraph_dot, 

43 butler_config, 

44 input, 

45 output, 

46 output_run, 

47 extend_run, 

48 replace_run, 

49 prune_replaced, 

50 data_query, 

51 show, 

52 save_execution_butler, 

53 clobber_execution_butler, 

54 target_datastore_root, 

55 transfer, 

56 clobber_outputs, 

57 dataset_query_constraint, 

58 show_qgraph_header=False, 

59 mock=False, 

60 unmocked_dataset_types=(), 

61 mock_failure=(), 

62 **kwargs, 

63): 

64 """Implement the command line interface `pipetask qgraph` subcommand. 

65 

66 Should only be called by command line tools and unit test code that test 

67 this function. 

68 

69 Parameters 

70 ---------- 

71 pipelineObj : `lsst.pipe.base.Pipeline` or None. 

72 The pipeline object used to generate a qgraph. If this is not `None` 

73 then `qgraph` should be `None`. 

74 qgraph : `str` or `None` 

75 URI location for a serialized quantum graph definition as a pickle 

76 file. If this option is not None then `pipeline` should be `None`. 

77 qgraph_id : `str` or `None` 

78 Quantum graph identifier, if specified must match the identifier of the 

79 graph loaded from a file. Ignored if graph is not loaded from a file. 

80 qgraph_node_id : `list` of `int`, optional 

81 Only load a specified set of nodes if graph is loaded from a file, 

82 nodes are identified by integer IDs. 

83 qgraph_datastore_records : `bool` 

84 If True then include datastore records into generated quanta. 

85 skip_existing_in : `list` [ `str` ] 

86 Accepts list of collections, if all Quantum outputs already exist in 

87 the specified list of collections then that Quantum will be excluded 

88 from the QuantumGraph. 

89 skip_existing : `bool` 

90 Appends output RUN collection to the ``skip_existing_in`` list. 

91 save_qgraph : `str` or `None` 

92 URI location for storing a serialized quantum graph definition as a 

93 pickle file. 

94 save_single_quanta : `str` or `None` 

95 Format string of URI locations for storing individual quantum graph 

96 definition (pickle files). The curly brace {} in the input string will 

97 be replaced by a quantum number. 

98 qgraph_dot : `str` or `None` 

99 Path location for storing GraphViz DOT representation of a quantum 

100 graph. 

101 butler_config : `str`, `dict`, or `lsst.daf.butler.Config` 

102 If `str`, `butler_config` is the path location of the gen3 

103 butler/registry config file. If `dict`, `butler_config` is key value 

104 pairs used to init or update the `lsst.daf.butler.Config` instance. If 

105 `Config`, it is the object used to configure a Butler. 

106 input : `list` [ `str` ] 

107 List of names of the input collection(s). 

108 output : `str` 

109 Name of the output CHAINED collection. This may either be an existing 

110 CHAINED collection to use as both input and output (if `input` is 

111 `None`), or a new CHAINED collection created to include all inputs 

112 (if `input` is not `None`). In both cases, the collection's children 

113 will start with an output RUN collection that directly holds all new 

114 datasets (see `output_run`). 

115 output_run : `str` 

116 Name of the new output RUN collection. If not provided then `output` 

117 must be provided and a new RUN collection will be created by appending 

118 a timestamp to the value passed with `output`. If this collection 

119 already exists then `extend_run` must be passed. 

120 extend_run : `bool` 

121 Instead of creating a new RUN collection, insert datasets into either 

122 the one given by `output_run` (if provided) or the first child 

123 collection of `output` (which must be of type RUN). 

124 replace_run : `bool` 

125 Before creating a new RUN collection in an existing CHAINED collection, 

126 remove the first child collection (which must be of type RUN). This can 

127 be used to repeatedly write to the same (parent) collection during 

128 development, but it does not delete the datasets associated with the 

129 replaced run unless `prune-replaced` is also True. Requires `output`, 

130 and `extend_run` must be `None`. 

131 prune_replaced : `str` or `None` 

132 If not `None`, delete the datasets in the collection replaced by 

133 `replace_run`, either just from the datastore ("unstore") or by 

134 removing them and the RUN completely ("purge"). Requires 

135 ``replace_run`` to be `True`. 

136 data_query : `str` 

137 User query selection expression. 

138 show : `lsst.ctrl.mpexec.showInfo.ShowInfo` 

139 Descriptions of what to dump to stdout. 

140 save_execution_butler : `str` or `None` 

141 URI location for storing an execution Butler build from the 

142 QuantumGraph. 

143 clobber_execution_butler : `bool` 

144 It True overwrite existing execution butler files if present. 

145 target_datastore_root : `str` or `None` 

146 URI location for the execution butler's datastore. 

147 transfer : `str` or `None` 

148 Transfer mode for execution butler creation. This should be a 

149 ``transfer`` string recognized by 

150 :func:`lsst.resources.ResourcePath.transfer_from`. 

151 clobber_outputs : `bool` 

152 Remove outputs from previous execution of the same quantum before new 

153 execution. If ``skip_existing`` is also passed, then only failed 

154 quanta will be clobbered. 

155 dataset_query_constraint : `str` 

156 Control constraining graph building using pre-existing dataset types. 

157 Valid values are off, all, or a comma separated list of dataset type 

158 names. 

159 show_qgraph_header : bool, optional 

160 Controls if the headerData of a QuantumGraph should be printed to the 

161 terminal. Defaults to False. 

162 mock : `bool`, optional 

163 If True, use a mocked version of the pipeline. 

164 unmocked_dataset_types : `collections.abc.Sequence` [ `str` ], optional 

165 List of overall-input dataset types that should not be mocked. 

166 mock_failure : `~collections.abc.Sequence`, optional 

167 List of quanta that should raise exceptions. 

168 kwargs : `dict` [`str`, `str`] 

169 Ignored; click commands may accept options for more than one script 

170 function and pass all the option kwargs to each of the script functions 

171 which ignore these unused kwargs. 

172 

173 Returns 

174 ------- 

175 qgraph : `lsst.pipe.base.QuantumGraph` 

176 The qgraph object that was created. 

177 """ 

178 dataset_query_constraint = DatasetQueryConstraintVariant.fromExpression(dataset_query_constraint) 

179 args = SimpleNamespace( 

180 qgraph=qgraph, 

181 qgraph_id=qgraph_id, 

182 qgraph_node_id=qgraph_node_id, 

183 qgraph_datastore_records=qgraph_datastore_records, 

184 save_qgraph=save_qgraph, 

185 save_single_quanta=save_single_quanta, 

186 qgraph_dot=qgraph_dot, 

187 butler_config=butler_config, 

188 input=input, 

189 output=output, 

190 output_run=output_run, 

191 extend_run=extend_run, 

192 replace_run=replace_run, 

193 prune_replaced=prune_replaced, 

194 data_query=data_query, 

195 skip_existing_in=skip_existing_in, 

196 skip_existing=skip_existing, 

197 execution_butler_location=save_execution_butler, 

198 clobber_execution_butler=clobber_execution_butler, 

199 target_datastore_root=target_datastore_root, 

200 transfer=transfer, 

201 clobber_outputs=clobber_outputs, 

202 dataset_query_constraint=dataset_query_constraint, 

203 show_qgraph_header=show_qgraph_header, 

204 mock=mock, 

205 unmocked_dataset_types=list(unmocked_dataset_types), 

206 mock_failure=mock_failure, 

207 ) 

208 

209 f = CmdLineFwk() 

210 qgraph = f.makeGraph(pipelineObj, args) 

211 

212 if qgraph is None: 

213 return None 

214 

215 # optionally dump some info. 

216 show.show_graph_info(qgraph, args) 

217 

218 return qgraph