Main Neurospaces logo neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo

Index of group ./specifications/switches

Index
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command line switches

1. Help message
2. Reporting of imported files
3. Setting of the model library directory
4. Reporting of symbols
5. Reporting of symbol table
6. Parsing states and tokens for debugging
7. Algorithm reporting
8. File importing
9. Activation of algorithms during parsing
10. Symbols during parsing
11. Symbol publication during parsing
12. Symbols creation during parsing
13. All reports during parsing
14. Turning off algorithm processing (1)
15. Turning off algorithm processing (2)
16. Processing of a single query machine command using a command line option
17. Processing of multiple query machine commands using a command line option (2)
18. Processing of multiple query machine commands using a command line option (3)
19. Timings when loading the test network

1. Help message

Startup command : ./neurospacesparse -h

(No model has been loaded for the following set of commands.)

1.1. Is a help message been given ?

1. Part of expected output 
Usage: .*?neurospacesparse <options> <filenames>
	options :
		-d <filename> : debug output to given file
		-h : give help and exit
		-i : print imported files to stderr at end of parsing
		-m <directory> : set model library location
		-p : only parse the files to check its syntax
		-q : enter query machine after parsing
		-t : report symbol table after parsing
		-v <level> : set verbosity level
		-A : turn off algorithm processing
		-D : turn on parser debug flag
		-M : report algorithm info after parsing
		-Q : followed by a query machine command
		-R : disable readline
		-T <level> : set timing report level
		-V <level> : set exclusive verbosity level


	verbosity levels :

	\(5\) = LEVEL_GLOBALMSG_IMPORTANT \(level for important messages\)
	\(-10\) = LEVEL_GLOBALMSG_FILEIMPORT \(report import of files\)
	\(-20\) = LEVEL_GLOBALMSG_ALGORITHMIMPORT \(report import of algorithms\)
	\(-30\) = LEVEL_GLOBALMSG_SYMBOLREPORT \(report actions taken on 'END \{PRIVATE,PUBLIC\}_MODELS' etc.\)
	\(-40\) = LEVEL_GLOBALMSG_SYMBOLADD \(report add of symbols\)
	\(-50\) = LEVEL_GLOBALMSG_SYMBOLCREATE \(report creation of symbols\)


	timing levels :

	2 : report timing for all logged messages.

2. Reporting of imported files

Startup command : ./neurospacesparse -i channels/golgi_gabaa.ndf

2.1. Have imported files been reported ?

1. Part of expected output 
    ------------------------------------------------------------------------------
    Imported file : \(.+?/mappers/spikereceiver.ndf\)
    Imported file : \(                                           spikereceiver.ndf\)
    ------------------------------------------------------------------------------
    Flags : \(00000000\)
    Parse Method : \(no info\)

    
    
    ------------------------------------------------------------------------------
    Imported file : \(.+?/channels/golgi_gabaa.ndf\)
    Imported file : \(                                             golgi_gabaa.ndf\)
    ------------------------------------------------------------------------------
    Flags : \(00000001\)
	Root imported file
    Parse Method : \(no info\)

3. Setting of the model library directory

Startup command : ./neurospacesparse -m /asfdsadfasdfasdf channels/golgi_gabaa.ndf

Comments, Preparation, Reparation

1. Preparation needed before the commands below : 
Removing the environment entry to point to a model library
2. And repared afterwards using : 
Restoring the environment entry to point to a model library

3.1. Can we set the model library directory ?

1. Part of expected output 
Could not find file (number 0, 0), path name (channels/golgi_gabaa.ndf)
Set one of the environment variables NEUROSPACES_NMC_USER_MODELS,
NEUROSPACES_NMC_PROJECT_MODELS, NEUROSPACES_NMC_SYSTEM_MODELS or NEUROSPACES_NMC_MODELS
to point to a library where the required model is located,
or use the -m switch to configure where neurospaces looks for models.

4. Reporting of symbols

This command definition is currently disabled (disabled is 'this was obsoleted a long time ago')

Startup command : ./neurospacesparse -s channels/golgi_gabab.ndf

4.1. Symbol reporting is broken for the moment.

1. Part of expected output 
Type \(T_sym_root\) : no specifics report implemented
2. This test is currently not executed
(disabled is 'this was obsoleted a long time ago')

5. Reporting of symbol table

Startup command : ./neurospacesparse -t channels/golgi_gabaa.ndf

5.1. Has the symbol table been reported ?

1. Part of expected output 
------------------------------------------------------------------------------
Imported file : \(.+?/mappers/spikereceiver.ndf\)
Imported file : \(                                           spikereceiver.ndf\)
------------------------------------------------------------------------------
Flags : \(00000000\)
Parse Method : \(no info\)



    PRIVATE_MODELS


    END PRIVATE_MODELS


    PUBLIC_MODELS

            Name, index \(Synapse,-1\)
            Type \(T_sym_attachment\)
            attachName, index \(Synapse,-1\)
                PARA  Name \(weight\)
                PARA  Type \(TYPE_PARA_ATTRIBUTE\), 
                PARA  Name \(delay\)
                PARA  Type \(TYPE_PARA_ATTRIBUTE\), 
            attach\{-- begin HIER sections ---
            attach\}--  end  HIER sections ---

    END PUBLIC_MODELS



------------------------------------------------------------------------------
Imported file : \(.+?/channels/golgi_gabaa.ndf\)
Imported file : \(                                             golgi_gabaa.ndf\)
------------------------------------------------------------------------------
Flags : \(00000001\)
	Root imported file
Parse Method : \(no info\)



    PRIVATE_MODELS

            Name, index \(Synapse,-1\)
            Type \(T_sym_attachment\)
            attachName, index \(Synapse,-1\)
            attach\{-- begin HIER sections ---
            attach\}--  end  HIER sections ---
                attachName, index \(Synapse,-1\)
                    PARA  Name \(weight\)
                    PARA  Type \(TYPE_PARA_ATTRIBUTE\), 
                    PARA  Name \(delay\)
                    PARA  Type \(TYPE_PARA_ATTRIBUTE\), 
                attach\{-- begin HIER sections ---
                attach\}--  end  HIER sections ---

    END PRIVATE_MODELS


    PUBLIC_MODELS

            Name, index \(GABAA,-1\)
            Type \(T_sym_channel\)
            channeName, index \(GABAA,-1\)
                PARA  Name \(G_MAX\)
                PARA  Type \(TYPE_PARA_NUMBER\), Value\(1.000000e\+00\)
                PARA  Name \(Erev\)
                PARA  Type \(TYPE_PARA_NUMBER\), Value\(-7.000000e-02\)
            channe\{-- begin HIER sections ---
                Name, index \(synapse,-1\)
                Type \(T_sym_attachment\)
                attachName, index \(synapse,-1\)
                attach\{-- begin HIER sections ---
                attach\}--  end  HIER sections ---
                    attachName, index \(Synapse,-1\)
                    attach\{-- begin HIER sections ---
                    attach\}--  end  HIER sections ---
                        attachName, index \(Synapse,-1\)
                            PARA  Name \(weight\)
                            PARA  Type \(TYPE_PARA_ATTRIBUTE\), 
                            PARA  Name \(delay\)
                            PARA  Type \(TYPE_PARA_ATTRIBUTE\), 
                        attach\{-- begin HIER sections ---
                        attach\}--  end  HIER sections ---
                Name, index \(exp2,-1\)
                Type \(T_sym_equation_exponential\)
                equatiName, index \(exp2,-1\)
                    PARA  Name \(TAU1\)
                    PARA  Type \(TYPE_PARA_NUMBER\), Value\(9.300000e-04\)
                    PARA  Name \(TAU2\)
                    PARA  Type \(TYPE_PARA_NUMBER\), Value\(2.650000e-02\)
                equati\{-- begin HIER sections ---
                equati\}--  end  HIER sections ---
            channe\}--  end  HIER sections ---

    END PUBLIC_MODELS

6. Parsing states and tokens for debugging

Startup command : ./neurospacesparse -D mappers/spikegenerator.ndf

6.1. Have parsing states been reported ?

1. Part of expected output 
Reducing stack by rule(.|\n)*ParseStateDone(.|\n)*Reading a token: Now at end of input.

7. Algorithm reporting

Startup command : ./neurospacesparse -M legacy/cells/purk2m9s.ndf

7.1. Have algorithms given feedback to stdout ?

1. Part of expected output 
---
number_of_algorithm_classes: 8
---
name: ConnectionCheckerClass
report:
    number_of_created_instances: 0
---
name: RandomizeClass
report:
    number_of_created_instances: 0
---
name: SpinesClass
report:
    number_of_created_instances: 1
---
name: ProjectionRandomizedClass
report:
    number_of_created_instances: 0
---
name: ProjectionVolumeClass
report:
    number_of_created_instances: 0
---
name: InserterClass
report:
    number_of_created_instances: 0
---
name: Grid3DClass
report:
    number_of_created_instances: 0
---
name: DendrogramClass
report:
    number_of_created_instances: 0
---
number_of_algorithm_instances: 1
---
name: SpinesInstance SpinesNormal_13_1
report:
    number_of_added_spines: 1474
    number_of_virtual_spines: 142982.466417
    number_of_spiny_segments: 1474
    number_of_failures_adding_spines: 0
    SpinesInstance_prototype: Purkinje_spine
    SpinesInstance_surface: 1.33079e-12

8. File importing

Startup command : ./neurospacesparse -v 1 -V -10 legacy/cells/golgi.ndf

8.1. Have imported files been reported to stdout ?

1. Part of expected output 
0,golgi.ndf   ,15	\|\|->Dependency file\(.*?/mappers/spikegenerator.ndf\)
0,golgi.ndf   ,15	\|\|->End\(.*?/mappers/spikegenerator.ndf\)
0,golgi.ndf   ,17	\|\|->Dependency file\(.*?/channels/golgi_inna.ndf\)
0,golgi.ndf   ,17	\|\|->End\(.*?/channels/golgi_inna.ndf\)
0,golgi.ndf   ,19	\|\|->Dependency file\(.*?/channels/golgi_kdr.ndf\)
0,golgi.ndf   ,19	\|\|->End\(.*?/channels/golgi_kdr.ndf\)
0,golgi.ndf   ,21	\|\|->Dependency file\(.*?/channels/golgi_ka.ndf\)
0,golgi.ndf   ,21	\|\|->End\(.*?/channels/golgi_ka.ndf\)
0,golgi.ndf   ,23	\|\|->Dependency file\(.*?/channels/golgi_cahva.ndf\)
0,golgi.ndf   ,23	\|\|->End\(.*?/channels/golgi_cahva.ndf\)
0,golgi.ndf   ,25	\|\|->Dependency file\(.*?/channels/golgi_h.ndf\)
0,golgi.ndf   ,25	\|\|->End\(.*?/channels/golgi_h.ndf\)
0,golgi.ndf   ,27	\|\|->Dependency file\(.*?/channels/golgi_kc.ndf\)
0,golgi.ndf   ,27	\|\|->End\(.*?/channels/golgi_kc.ndf\)
0,golgi.ndf   ,29	\|\|->Dependency file\(.*?/channels/golgi_nmda.ndf\)
1,golgi_nmda.n,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_nmda.n,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
0,golgi.ndf   ,29	\|\|->End\(.*?/channels/golgi_nmda.ndf\)
0,golgi.ndf   ,31	\|\|->Dependency file\(.*?/channels/golgi_ampa.ndf\)
1,golgi_ampa.n,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_ampa.n,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
0,golgi.ndf   ,31	\|\|->End\(.*?/channels/golgi_ampa.ndf\)
0,golgi.ndf   ,33	\|\|->Dependency file\(.*?/channels/golgi_gabaa.ndf\)
1,golgi_gabaa.,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_gabaa.,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
0,golgi.ndf   ,33	\|\|->End\(.*?/channels/golgi_gabaa.ndf\)
0,golgi.ndf   ,35	\|\|->Dependency file\(.*?/channels/golgi_gabab.ndf\)
1,golgi_gabab.,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_gabab.,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
0,golgi.ndf   ,35	\|\|->End\(.*?/channels/golgi_gabab.ndf\)
0,golgi.ndf   ,37	\|\|->Dependency file\(.*?/pools/golgi_ca.ndf\)
0,golgi.ndf   ,37	\|\|->End\(.*?/pools/golgi_ca.ndf\)
.*?neurospacesparse: No errors for .*?/cells/golgi.ndf.

9. Activation of algorithms during parsing

Startup command : ./neurospacesparse -v 1 -V -20 legacy/networks/networksmall.ndf

9.1. Have algorithms been activated during parsing ?

1. Part of expected output 
1,mossyfibersm,90	\|\|  Import Algorithm\(Grid3D -> MossyGrid\(.*?\)\)
1,mossyfibersm,124	\|\|  AlgorithmInstance\(MossyGrid\) handles \(no context\)
1,mossyfibersm,124	\|\|  AlgorithmInstance\(MossyGrid\) handled \(no context\)
1,mossyfibersm,124	\|\|  Disable Algorithm\(MossyGrid\)
1,golgismall.n,46	\|\|  Import Algorithm\(Grid3D -> GolgiGrid\(.*?\)\)
1,golgismall.n,64	\|\|  AlgorithmInstance\(GolgiGrid\) handles \(no context\)
1,golgismall.n,64	\|\|  AlgorithmInstance\(GolgiGrid\) handled \(no context\)
1,golgismall.n,64	\|\|  Disable Algorithm\(GolgiGrid\)
1,granulesmall,46	\|\|  Import Algorithm\(Grid3D -> GranuleGrid\(.*?\)\)
1,granulesmall,64	\|\|  AlgorithmInstance\(GranuleGrid\) handles \(no context\)
1,granulesmall,64	\|\|  AlgorithmInstance\(GranuleGrid\) handled \(no context\)
1,granulesmall,64	\|\|  Disable Algorithm\(GranuleGrid\)
2,purk2m9s.ndf,82	\|\|    Import Algorithm\(Spines -> SpinesNormal_13_1\(.*?\)\)
2,purk2m9s.ndf,14539	\|\|    AlgorithmInstance\(SpinesNormal_13_1\) handles \(no context\)
2,purk2m9s.ndf,14539	\|\|    AlgorithmInstance\(SpinesNormal_13_1\) handled \(no context\)
2,purk2m9s.ndf,14539	\|\|    Disable Algorithm\(SpinesNormal_13_1\)
1,purkinjesmal,46	\|\|  Import Algorithm\(Grid3D -> PurkinjeGrid\(.*?\)\)
1,purkinjesmal,64	\|\|  AlgorithmInstance\(PurkinjeGrid\) handles \(no context\)
1,purkinjesmal,64	\|\|  AlgorithmInstance\(PurkinjeGrid\) handled \(no context\)
1,purkinjesmal,64	\|\|  Disable Algorithm\(PurkinjeGrid\)
0,networksmall,82	\|\|Import Algorithm\(ProjectionVolume -> Mossies2Granules_NMDA\(.*?\)\)
0,networksmall,116	\|\|Import Algorithm\(ProjectionVolume -> Mossies2Granules_AMPA\(.*?\)\)
0,networksmall,151	\|\|Import Algorithm\(ProjectionVolume -> Granules2Golgis\(.*?\)\)
0,networksmall,185	\|\|Import Algorithm\(ProjectionVolume -> Golgis2Granules_GABAA\(.*?\)\)
0,networksmall,283	\|\|AlgorithmInstance\(Golgis2Granules_GABAA\) handles \(no context\)
0,networksmall,283	\|\|AlgorithmInstance\(Golgis2Granules_GABAA\) handled \(no context\)
0,networksmall,283	\|\|Disable Algorithm\(Golgis2Granules_GABAA\)
0,networksmall,283	\|\|AlgorithmInstance\(Granules2Golgis\) handles \(no context\)
0,networksmall,283	\|\|AlgorithmInstance\(Granules2Golgis\) handled \(no context\)
0,networksmall,283	\|\|Disable Algorithm\(Granules2Golgis\)
0,networksmall,283	\|\|AlgorithmInstance\(Mossies2Granules_AMPA\) handles \(no context\)
0,networksmall,283	\|\|AlgorithmInstance\(Mossies2Granules_AMPA\) handled \(no context\)
0,networksmall,283	\|\|Disable Algorithm\(Mossies2Granules_AMPA\)
0,networksmall,283	\|\|AlgorithmInstance\(Mossies2Granules_NMDA\) handles \(no context\)
0,networksmall,283	\|\|AlgorithmInstance\(Mossies2Granules_NMDA\) handled \(no context\)
0,networksmall,283	\|\|Disable Algorithm\(Mossies2Granules_NMDA\)
.*?neurospacesparse: No errors for .*?/networks/networksmall.ndf.

10. Symbols during parsing

Startup command : ./neurospacesparse -v 1 -V -30 legacy/cells/golgi.ndf

10.1. Have symbols been reported to stdout ?

1. Part of expected output 
1,golgi_nmda.n,17	\|\|  Activating golgi_nmda.ndf's dependencies\(dependency list not yet\)
1,golgi_nmda.n,23	\|\|  Activating golgi_nmda.ndf's private models\(private models list not yet\)
1,golgi_nmda.n,23	\|\|  Activating golgi_nmda.ndf's private models\(private models list not yet\)
1,golgi_ampa.n,15	\|\|  .*?/mappers/spikereceiver.ndf is cached\(public model list not yet\)
1,golgi_ampa.n,17	\|\|  Activating golgi_ampa.ndf's dependencies\(dependency list not yet\)
1,golgi_ampa.n,23	\|\|  Activating golgi_ampa.ndf's private models\(private models list not yet\)
1,golgi_ampa.n,23	\|\|  Activating golgi_ampa.ndf's private models\(private models list not yet\)
1,golgi_gabaa.,15	\|\|  .*?/mappers/spikereceiver.ndf is cached\(public model list not yet\)
1,golgi_gabaa.,17	\|\|  Activating golgi_gabaa.ndf's dependencies\(dependency list not yet\)
1,golgi_gabaa.,23	\|\|  Activating golgi_gabaa.ndf's private models\(private models list not yet\)
1,golgi_gabaa.,23	\|\|  Activating golgi_gabaa.ndf's private models\(private models list not yet\)
1,golgi_gabab.,15	\|\|  .*?/mappers/spikereceiver.ndf is cached\(public model list not yet\)
1,golgi_gabab.,17	\|\|  Activating golgi_gabab.ndf's dependencies\(dependency list not yet\)
1,golgi_gabab.,23	\|\|  Activating golgi_gabab.ndf's private models\(private models list not yet\)
1,golgi_gabab.,23	\|\|  Activating golgi_gabab.ndf's private models\(private models list not yet\)
1,golgi_ca.ndf,31	\|\|  Activating golgi_ca.ndf's private models\(private models list not yet\)
1,golgi_ca.ndf,31	\|\|  Activating golgi_ca.ndf's private models\(private models list not yet\)
0,golgi.ndf   ,39	\|\|Activating golgi.ndf's dependencies\(dependency list not yet\)
0,golgi.ndf   ,112	\|\|Activating golgi.ndf's private models\(private models list not yet\)
0,golgi.ndf   ,112	\|\|Activating golgi.ndf's private models\(private models list not yet\)
.*?neurospacesparse: No errors for .*?/cells/golgi.ndf.

11. Symbol publication during parsing

Startup command : ./neurospacesparse -v 1 -V -40 legacy/cells/granule.ndf

11.1. Have symbols been reported to be published to stdout ?

1. Part of expected output 
1,spikegenerat,20	\|\|  Add Public Model\(T_sym_attachment,SpikeGen\)
1,granule_inna,30	\|\|  Add Public Model\(T_sym_channel,InNa\)
1,granule_kdr.,30	\|\|  Add Public Model\(T_sym_channel,KDr\)
1,granule_ka.n,30	\|\|  Add Public Model\(T_sym_channel,KA\)
1,granule_cahv,30	\|\|  Add Public Model\(T_sym_channel,CaHVA\)
1,granule_h.nd,30	\|\|  Add Public Model\(T_sym_channel,H\)
1,granule_kc.n,36	\|\|  Add Public Model\(T_sym_channel,Moczyd_KC\)
2,spikereceive,22	\|\|    Add Public Model\(T_sym_attachment,Synapse\)
1,granule_nmda,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,granule_nmda,70	\|\|  Add Public Model\(T_sym_channel,NMDA\)
1,granule_ampa,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,granule_ampa,61	\|\|  Add Public Model\(T_sym_channel,AMPA\)
1,granule_gaba,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,granule_gaba,61	\|\|  Add Public Model\(T_sym_channel,GABAA\)
1,granule_gaba,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,granule_gaba,61	\|\|  Add Public Model\(T_sym_channel,GABAB\)
1,granule_ca.n,29	\|\|  Add Private Model\(T_sym_pool,Ca_concen\)
1,granule_ca.n,36	\|\|  Add Public Model\(T_sym_pool,Ca_concen\)
1,granule_ca.n,44	\|\|  Add Public Model\(T_sym_pool,Ca_concen_standalone\)
0,granule.ndf ,46	\|\|Add Private Model\(T_sym_attachment,SpikeGen\)
0,granule.ndf ,48	\|\|Add Private Model\(T_sym_channel,InNa\)
0,granule.ndf ,50	\|\|Add Private Model\(T_sym_channel,KDr\)
0,granule.ndf ,52	\|\|Add Private Model\(T_sym_channel,KA\)
0,granule.ndf ,54	\|\|Add Private Model\(T_sym_channel,CaHVA\)
0,granule.ndf ,56	\|\|Add Private Model\(T_sym_channel,H\)
0,granule.ndf ,58	\|\|Add Private Model\(T_sym_channel,Moczyd_KC\)
0,granule.ndf ,60	\|\|Add Private Model\(T_sym_channel,NMDA\)
0,granule.ndf ,62	\|\|Add Private Model\(T_sym_channel,AMPA\)
0,granule.ndf ,64	\|\|Add Private Model\(T_sym_channel,GABAA\)
0,granule.ndf ,66	\|\|Add Private Model\(T_sym_channel,GABAB\)
0,granule.ndf ,68	\|\|Add Private Model\(T_sym_pool,Ca_concen\)
0,granule.ndf ,318	\|\|Add Public Model\(T_sym_cell,Granule\)
.*?neurospacesparse: No errors for .*?/cells/granule.ndf.

12. Symbols creation during parsing

Startup command : ./neurospacesparse -V -50 legacy/cells/golgi.ndf

12.1. Have symbols been reported to be created to stdout ?

1. Part of expected output 







13. All reports during parsing
Startup command : ./neurospacesparse -v 1 -v -50 legacy/cells/golgi.ndf
13.1. Have all levels been reported to stdout ?





1. Part of expected output 
0,golgi.ndf   ,15	\|\|->Dependency file\(.*?/mappers/spikegenerator.ndf\)
1,spikegenerat,20	\|\|  Add Public Model\(T_sym_attachment,SpikeGen\)
0,golgi.ndf   ,15	\|\|->End\(.*?/mappers/spikegenerator.ndf\)
0,golgi.ndf   ,17	\|\|->Dependency file\(.*?/channels/golgi_inna.ndf\)
1,golgi_inna.n,30	\|\|  Add Public Model\(T_sym_channel,InNa\)
0,golgi.ndf   ,17	\|\|->End\(.*?/channels/golgi_inna.ndf\)
0,golgi.ndf   ,19	\|\|->Dependency file\(.*?/channels/golgi_kdr.ndf\)
1,golgi_kdr.nd,30	\|\|  Add Public Model\(T_sym_channel,KDr\)
0,golgi.ndf   ,19	\|\|->End\(.*?/channels/golgi_kdr.ndf\)
0,golgi.ndf   ,21	\|\|->Dependency file\(.*?/channels/golgi_ka.ndf\)
1,golgi_ka.ndf,30	\|\|  Add Public Model\(T_sym_channel,KA\)
0,golgi.ndf   ,21	\|\|->End\(.*?/channels/golgi_ka.ndf\)
0,golgi.ndf   ,23	\|\|->Dependency file\(.*?/channels/golgi_cahva.ndf\)
1,golgi_cahva.,30	\|\|  Add Public Model\(T_sym_channel,CaHVA\)
0,golgi.ndf   ,23	\|\|->End\(.*?/channels/golgi_cahva.ndf\)
0,golgi.ndf   ,25	\|\|->Dependency file\(.*?/channels/golgi_h.ndf\)
1,golgi_h.ndf ,30	\|\|  Add Public Model\(T_sym_channel,H\)
0,golgi.ndf   ,25	\|\|->End\(.*?/channels/golgi_h.ndf\)
0,golgi.ndf   ,27	\|\|->Dependency file\(.*?/channels/golgi_kc.ndf\)
1,golgi_kc.ndf,36	\|\|  Add Public Model\(T_sym_channel,Moczyd_KC\)
0,golgi.ndf   ,27	\|\|->End\(.*?/channels/golgi_kc.ndf\)
0,golgi.ndf   ,29	\|\|->Dependency file\(.*?/channels/golgi_nmda.ndf\)
1,golgi_nmda.n,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
2,spikereceive,22	\|\|    Add Public Model\(T_sym_attachment,Synapse\)
1,golgi_nmda.n,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
1,golgi_nmda.n,17	\|\|  Activating golgi_nmda.ndf's dependencies\(dependency list not yet\)
1,golgi_nmda.n,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,golgi_nmda.n,23	\|\|  Activating golgi_nmda.ndf's private models\(private models list not yet\)
1,golgi_nmda.n,23	\|\|  Activating golgi_nmda.ndf's private models\(private models list not yet\)
1,golgi_nmda.n,70	\|\|  Add Public Model\(T_sym_channel,NMDA\)
0,golgi.ndf   ,29	\|\|->End\(.*?/channels/golgi_nmda.ndf\)
0,golgi.ndf   ,31	\|\|->Dependency file\(.*?/channels/golgi_ampa.ndf\)
1,golgi_ampa.n,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_ampa.n,15	\|\|  .*?/mappers/spikereceiver.ndf is cached\(public model list not yet\)
1,golgi_ampa.n,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
1,golgi_ampa.n,17	\|\|  Activating golgi_ampa.ndf's dependencies\(dependency list not yet\)
1,golgi_ampa.n,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,golgi_ampa.n,23	\|\|  Activating golgi_ampa.ndf's private models\(private models list not yet\)
1,golgi_ampa.n,23	\|\|  Activating golgi_ampa.ndf's private models\(private models list not yet\)
1,golgi_ampa.n,61	\|\|  Add Public Model\(T_sym_channel,AMPA\)
0,golgi.ndf   ,31	\|\|->End\(.*?/channels/golgi_ampa.ndf\)
0,golgi.ndf   ,33	\|\|->Dependency file\(.*?/channels/golgi_gabaa.ndf\)
1,golgi_gabaa.,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_gabaa.,15	\|\|  .*?/mappers/spikereceiver.ndf is cached\(public model list not yet\)
1,golgi_gabaa.,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
1,golgi_gabaa.,17	\|\|  Activating golgi_gabaa.ndf's dependencies\(dependency list not yet\)
1,golgi_gabaa.,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,golgi_gabaa.,23	\|\|  Activating golgi_gabaa.ndf's private models\(private models list not yet\)
1,golgi_gabaa.,23	\|\|  Activating golgi_gabaa.ndf's private models\(private models list not yet\)
1,golgi_gabaa.,61	\|\|  Add Public Model\(T_sym_channel,GABAA\)
0,golgi.ndf   ,33	\|\|->End\(.*?/channels/golgi_gabaa.ndf\)
0,golgi.ndf   ,35	\|\|->Dependency file\(.*?/channels/golgi_gabab.ndf\)
1,golgi_gabab.,15	\|\|  ->Dependency file\(.*?/mappers/spikereceiver.ndf\)
1,golgi_gabab.,15	\|\|  .*?/mappers/spikereceiver.ndf is cached\(public model list not yet\)
1,golgi_gabab.,15	\|\|  ->End\(.*?/mappers/spikereceiver.ndf\)
1,golgi_gabab.,17	\|\|  Activating golgi_gabab.ndf's dependencies\(dependency list not yet\)
1,golgi_gabab.,21	\|\|  Add Private Model\(T_sym_attachment,Synapse\)
1,golgi_gabab.,23	\|\|  Activating golgi_gabab.ndf's private models\(private models list not yet\)
1,golgi_gabab.,23	\|\|  Activating golgi_gabab.ndf's private models\(private models list not yet\)
1,golgi_gabab.,61	\|\|  Add Public Model\(T_sym_channel,GABAB\)
0,golgi.ndf   ,35	\|\|->End\(.*?/channels/golgi_gabab.ndf\)
0,golgi.ndf   ,37	\|\|->Dependency file\(.*?/pools/golgi_ca.ndf\)
1,golgi_ca.ndf,29	\|\|  Add Private Model\(T_sym_pool,Ca_concen\)
1,golgi_ca.ndf,31	\|\|  Activating golgi_ca.ndf's private models\(private models list not yet\)
1,golgi_ca.ndf,31	\|\|  Activating golgi_ca.ndf's private models\(private models list not yet\)
1,golgi_ca.ndf,36	\|\|  Add Public Model\(T_sym_pool,Ca_concen\)
1,golgi_ca.ndf,44	\|\|  Add Public Model\(T_sym_pool,Ca_concen_standalone\)
0,golgi.ndf   ,37	\|\|->End\(.*?/pools/golgi_ca.ndf\)
0,golgi.ndf   ,39	\|\|Activating golgi.ndf's dependencies\(dependency list not yet\)
0,golgi.ndf   ,46	\|\|Add Private Model\(T_sym_attachment,SpikeGen\)
0,golgi.ndf   ,48	\|\|Add Private Model\(T_sym_channel,InNa\)
0,golgi.ndf   ,50	\|\|Add Private Model\(T_sym_channel,KDr\)
0,golgi.ndf   ,52	\|\|Add Private Model\(T_sym_channel,KA\)
0,golgi.ndf   ,54	\|\|Add Private Model\(T_sym_channel,CaHVA\)
0,golgi.ndf   ,56	\|\|Add Private Model\(T_sym_channel,H\)
0,golgi.ndf   ,58	\|\|Add Private Model\(T_sym_channel,Moczyd_KC\)
0,golgi.ndf   ,60	\|\|Add Private Model\(T_sym_channel,NMDA\)
0,golgi.ndf   ,62	\|\|Add Private Model\(T_sym_channel,AMPA\)
0,golgi.ndf   ,64	\|\|Add Private Model\(T_sym_channel,GABAA\)
0,golgi.ndf   ,66	\|\|Add Private Model\(T_sym_channel,GABAB\)
0,golgi.ndf   ,68	\|\|Add Private Model\(T_sym_pool,Ca_concen\)
0,golgi.ndf   ,109	\|\|Add Private Model\(T_sym_group,CalciumComplex\)
0,golgi.ndf   ,112	\|\|Activating golgi.ndf's private models\(private models list not yet\)
0,golgi.ndf   ,112	\|\|Activating golgi.ndf's private models\(private models list not yet\)
0,golgi.ndf   ,353	\|\|Add Public Model\(T_sym_cell,Golgi\)
.*?neurospacesparse: No errors for .*?/cells/golgi.ndf.








14. Turning off algorithm processing (1)
Startup command : ./neurospacesparse -q -R -A cells/purkinje/edsjb1994.ndf
14.1. Has algorithm processing been disabled ?





1. Executed command
algorithmset




2. Part of expected output 
number_of_algorithm_classes: 8
---
name: ConnectionCheckerClass
report:
    number_of_created_instances: 0
---
name: RandomizeClass
report:
    number_of_created_instances: 0
---
name: SpinesClass
report:
    number_of_created_instances: 0
---
name: ProjectionRandomizedClass
report:
    number_of_created_instances: 0
---
name: ProjectionVolumeClass
report:
    number_of_created_instances: 0
---
name: InserterClass
report:
    number_of_created_instances: 0
---
name: Grid3DClass
report:
    number_of_created_instances: 0
---
name: DendrogramClass
report:
    number_of_created_instances: 0
---
number_of_algorithm_instances: 0








15. Turning off algorithm processing (2)
Startup command : ./neurospacesparse -q -R -A legacy/networks/network-test.ndf
15.1. Has algorithm processing been disabled ?





1. Executed command
algorithmset




2. Part of expected output 
number_of_algorithm_classes: 8
---
name: ConnectionCheckerClass
report:
    number_of_created_instances: 0
---
name: RandomizeClass
report:
    number_of_created_instances: 0
---
name: SpinesClass
report:
    number_of_created_instances: 0
---
name: ProjectionRandomizedClass
report:
    number_of_created_instances: 0
---
name: ProjectionVolumeClass
report:
    number_of_created_instances: 0
---
name: InserterClass
report:
    number_of_created_instances: 0
---
name: Grid3DClass
report:
    number_of_created_instances: 0
---
name: DendrogramClass
report:
    number_of_created_instances: 0
---
number_of_algorithm_instances: 0








16. Processing of a single query machine command using a command line option
Startup command : ./neurospacesparse -Q expand /* -R legacy/cells/golgi.ndf
16.1. Are single query commands using a command line option processed properly ?





1. Part of expected output 
query: 'expand /*'
---
- /Golgi








17. Processing of multiple query machine commands using a command line option (2)
Startup command : ./neurospacesparse -Q expand /* -Q expand /* -R legacy/cells/golgi.ndf
17.1. Are multiple query commands using a command line option processed properly (2) ?





1. Part of expected output 
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi








18. Processing of multiple query machine commands using a command line option (3)
Startup command : ./neurospacesparse -Q expand /* -Q expand /* -Q expand /* -Q expand /* -Q expand /* -Q expand /* -Q expand /* -Q expand /* -Q expand /* -Q expand /* -R legacy/cells/golgi.ndf
18.1. Are multiple query commands using a command line option processed properly (3) ?





1. Part of expected output 
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi
query: 'expand /*'
---
- /Golgi








19. Timings when loading the test network
This command definition is currently disabled (disabled is 'my laziness')
Startup command : ./neurospacesparse -R legacy/networks/network-test.ndf