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Merge pull request #114 from VH-Lab/id_changes
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change "reference"/"identifier" to "id"; add "depends_on"
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@stevevanhooser
stevevanhooser authored Dec 11, 2019
2 parents ecd318f + 288995e commit ccbf6e8
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Showing 19 changed files with 155 additions and 55 deletions.
8 changes: 6 additions & 2 deletions ndi_common/database_documents/apps/spikeextractor/spiketimes.json
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Expand Up @@ -11,9 +11,13 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_app.json" }
]
},
"depends_on": [
{ "name": "extraction_parameters_id",
"value": ""
}
],
"spiketimes": {
"extraction_name": "",
"extraction_parameters_file_id": ""
"extraction_name": ""
}
}

8 changes: 6 additions & 2 deletions ndi_common/database_documents/apps/spikeextractor/spikewaves.json
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Expand Up @@ -11,8 +11,12 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_app.json" }
]
},
"depends_on": [
{ "name": "extraction_parameters_id",
"value": ""
}
],
"spikewaves": {
"extraction_name": "",
"extraction_parameters_file_id": ""
"extraction_name": ""
}
}
8 changes: 6 additions & 2 deletions ndi_common/database_documents/apps/spikesorter/spike_clusters.json
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Expand Up @@ -10,8 +10,12 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_app.json" }
]
},
"depends_on":[
{ "name": "sorting_parameters_id",
"value": ""
}
],
"spike_clusters": {
"sort_name": "",
"sorting_parameters_file_id": ""
"sort_name": ""
}
}
6 changes: 5 additions & 1 deletion ndi_common/database_documents/apps/vhlab_voltage2firingrate/binnedspikeratevm.json
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Expand Up @@ -11,9 +11,13 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_app.json" }
]
},
"depends_on": [
{ "name": "vmspikefilteringparameters_id",
"value": 0
}
],
"binnedspikeratevm": {
"parameters": {
"vmspikefilteringparameters_id": 0,
"binsize": "0.030",
"vm_baseline_correction": "0",
"vm_baseline_correct_time": "0",
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6 changes: 5 additions & 1 deletion ndi_common/database_documents/apps/vhlab_voltage2firingrate/vmspikefit.json
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Expand Up @@ -11,8 +11,12 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_app.json" }
]
},
"depends_on":[
{ "name": "fit_input_id",
"value": 0
}
],
"vmspikefit": {
"fit_input_document_id": 0,
"fit_name": 0,
"fit_equation": 0,
"fit_parameters": 0,
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2 changes: 1 addition & 1 deletion ndi_common/database_documents/data/fitcurve.json
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Expand Up @@ -22,7 +22,7 @@
}
],
"fit_data": {
"exampledata_document_id": 0,
"exampledata_id": 0,
"input_data_field": "mydocumenttype.x",
"output_data_field": "mydocumenttype.y",
"output_number_examples": 20
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4 changes: 2 additions & 2 deletions ndi_common/database_documents/ndi_document.json
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Expand Up @@ -7,8 +7,8 @@
"superclasses": [ ]
},
"ndi_document": {
"experiment_unique_reference": "",
"document_unique_reference": "",
"experiment_id": "",
"document_id": "",
"name": "",
"type": "",
"datestamp": "2018-12-05T18:36:47.241Z",
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2 changes: 1 addition & 1 deletion ndi_common/database_documents/ndi_document_subject.json
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Expand Up @@ -9,7 +9,7 @@
]
},
"subject": {
"identifier": "",
"reference": "",
"species": "",
"strain": "",
"variant": ""
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6 changes: 5 additions & 1 deletion ndi_common/database_documents/ndi_document_thing_epoch.json
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Expand Up @@ -10,8 +10,12 @@
{ "definition": "$NDIDOCUMENTPATH\/data\/ndi_document_binaryseries.json" }
]
},
"depends_on": [
{ "name": "thing_id",
"value": ""
}
],
"thing_epoch": {
"thing_unique_reference": "",
"epoch_clock": "",
"t0_t1": ""
}
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4 changes: 2 additions & 2 deletions ...ocuments/ndi_document_thingreference.json → ...base_documents/ndi_document_thing_id.json
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Expand Up @@ -8,8 +8,8 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json" }
]
},
"thingreference": {
"thing_unique_id": []
"thing_id": {
"thing_id": []
}
}

18 changes: 0 additions & 18 deletions ndi_common/database_documents/stimulus/ndi_document_control_stimulus_ids.json
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This file was deleted.

22 changes: 22 additions & 0 deletions ndi_common/database_documents/stimulus/ndi_document_control_stimulusids.json
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@@ -0,0 +1,22 @@
{
"document_class": {
"definition": "$NDIDOCUMENTPATH\/stimulus\/.json",
"validation": "$NDISCHEMAPATH\/stimulus\/.json",
"class_name": "ndi_document_control_stim_ids",
"class_version": 1,
"superclasses": [
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"}
]
},
"depends_on": [
{ "name": "stimulus_presentation_id",
"value": []
}
],
"control_stimids": {
"control_stimids": []
},
"control_stimid_method": {
}
}

28 changes: 19 additions & 9 deletions ndi_common/database_documents/stimulus/ndi_document_stimulus_response.json
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@@ -1,20 +1,30 @@
{
"document_class": {
"definition": "$NDIDOCUMENTPATH\/stimulus\/ndi_document_stimulus_response.json",
"validation": "$NDISCHEMAPATH\/stimulus\/ndi_document_stimulus_response_schema.json",
"class_name": "stimulus-ndi_document_stimulus_response",
"definition": "$NDIDOCUMENTPATH\/stimulus\/.json",
"validation": "$NDISCHEMAPATH\/stimulus\/_schema.json",
"class_name": "stimulus-",
"class_version": 1,
"superclasses": [
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"},
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_thingreference.json"}
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"}
]
},
"depends_on": [
{ "name": "thing_id",
"value": []
},
{ "name": "stimulator_id",
"value": []
},
{ "name": "stimulus_presentation_document_id",
"value": []
},
{ "name": "stimulus_control_document_id",
"value": []
}
],
"stimulus_response": {
"stimulator_unique_reference": [],
"stimulator_epochid": [],
"thing_epochid": [],
"stimulus_presentation_document_identifier": [],
"stimulus_control_document_identifier": []
"thing_epochid": []
}
}

12 changes: 8 additions & 4 deletions ndi_common/database_documents/stimulus/ndi_document_stimulus_response_scalar.json
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Expand Up @@ -4,13 +4,17 @@
"validation": "$NDISCHEMAPATH\/stimulus\/ndi_document_stimulus_response_scalar_schema.json",
"class_name": "stimulus-ndi_document_stimulus_response_scalar",
"class_version": 1,
"superclasses": [
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"},
{ "definition": "$NDIDOCUMENTPATH\/stimulus\/ndi_document_stimulus_response.json"}
"superclasses": [
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json" },
{ "definition": "$NDIDOCUMENTPATH\/stimulus\/ndi_document_stimulus_response.json"}
]
},
"depends_on": [
{ "name": "stimulus_response_scalar_parameters_id",
"value": ""
}
],
"stimulus_response_scalar": {
"stimulus_response_scalar_parameters_identifier": [],
"response_type": [],
"responses": {
"stimid": [],
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2 changes: 1 addition & 1 deletion ...t_stimulus_response_scalar_reference.json → ...document_stimulus_response_scalar_id.json
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Expand Up @@ -8,6 +8,6 @@
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"}
]
},
"stimulus_response_scalar_reference": []
"stimulus_response_scalar_id": []
}

12 changes: 9 additions & 3 deletions ndi_common/database_documents/stimulus/ndi_document_stimulus_tuningcurve.json
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Expand Up @@ -5,11 +5,17 @@
"class_name": "stimulus-ndi_document_stimulus_tuningcurve",
"class_version": 1,
"superclasses": [
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json" },
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_thingreference.json" },
{ "definition": "$NDIDOCUMENTPATH\/stimulus\/ndi_document_stimulus_response_scalar_reference.json" }
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json" }
]
},
"depends_on": [
{ "name": "thing_id",
"value": ""
},
{ "name": "stimulus_response_scalar_id",
"value": ""
}
],
"tuning_curve": {
"independent_variable_label": [[]],
"independent_variable_value": [],
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12 changes: 7 additions & 5 deletions .../database_documents/stimulus/vision/oridir/ndi_document_orientation_direction_tuning.json
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Expand Up @@ -5,11 +5,13 @@
"class_name": "oridir-ndi_document_orientation_direction_tuning",
"class_version": 1,
"superclasses": [
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"},
{ "definition": "$NDIDOCUMENTPATH\/ndi_document_thingreference.json"},
{ "definition": "$NDIDOCUMENTPATH\/stimulus\/ndi_document_stimulus_tuningcurve_reference.json"}
{ "definition": "$NDIDOCUMENTPATH\/ndi_document.json"}
]
},
"depends_on": [
{ "name": "thing_id",
"value": "" }
],
"orientation_direction_tuning": {
"properties": {
"coordinates": "compass",
Expand Down Expand Up @@ -42,8 +44,8 @@
"dot_direction_significance": 1
},
"fit": {
"double_gaussian_parameters": 0,
"double_gaussian_fit_angles": 0,
"double_gaussian_parameters": [0],
"double_gaussian_fit_angles": [0],
"double_gaussian_fit_values": [0],
"orientation_preferred_orthogonal_ratio": [0],
"direction_preferred_null_ratio": [0],
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49 changes: 49 additions & 0 deletions test/database/test_ndi_document_jsons.m
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@@ -0,0 +1,49 @@
function [b, successes, failures] = test_ndi_document_jsons(generate_error)
% TEST_NDI_DOCUMNET_JSONS - test validity of all NDI_DOCUMENT json definitions
%
% [B, SUCCESSES, FAILURES] = TEST_NDI_DOCUMENT_JSONS(GENERATE_ERROR)
%
% Tries to make a blank NDI_DOCUMENT from all NDI_DOCUMENT JSON definitions.
% Returns a cell array of all JSON file names that were successfully created in
% SUCCESSES, and a cell array of JSON file names there unsuccessfully created in
% FAILURES. B is 1 if all ndi documents were created successfully.
%
% If GENERATE_ERROR is present and is 1, then an error is generated if B is 0.
%

if nargin<1,
generate_error = 0;
end;

b = 0;
successes = {};
failures = {};

ndi_globals;

json_docs = findfilegroups(ndidocumentpath,{'.*\.json\>'});

for i=1:numel(json_docs),
[parentdir,filename,ext] = fileparts(json_docs{i}{1});
ndidoc = [filename ext];

if filename(1)=='.', % ignore swap files and hidden files
continue;
end;
try,
mydoc = ndi_document(ndidoc);
successes{end+1} = ndidoc;
catch,
failures{end+1} = ndidoc;
end;
end;

b = isempty(failures);

if generate_error & ~b,
disp(['NDI_DOCUMENT definitions failed']);
failures'
error(['At least one ndi_document failed to be built from its definition.']);
end;


1 change: 1 addition & 0 deletions test/testsuite/ndi_testsuite_list.txt
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Expand Up @@ -9,6 +9,7 @@ build_intan_flat_exp 1 Tests saving experiment parameters, documents
test_sg_flat 1 Tests reading from SpikeGadgets ndi_daqsystem_mfdaq_sg
test_ndi_probe 1 Tests basic probe functions
test_ndi_thing 1 Test basic nsd_thing functions
test_ndi_document_jsons 1 Test ability to make an NDI_DOCUMENT out of all JSON definitions
test_ndi_device_image_tiffstack 0 Not in current testing stream
test_ndi_image_tiffstack_multipleepoch 0 Not in current testing stream
test_ndi_filenavigator_fileIDfunction 0 Note in current testing stream

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