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Updates from Retreat User Test 1 #419

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merged 6 commits into from
Oct 3, 2023
Merged

Updates from Retreat User Test 1 #419

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0641300
All updates from Retreat User Test 1
garrettmflynn Oct 3, 2023
81b6f26
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 3, 2023
b21629a
Update server.svg
garrettmflynn Oct 3, 2023
79c88b9
remove SpikeGLXLFP
Oct 3, 2023
2322e9b
Merge branch 'user-test-retreat-1' of https://github.com/NeurodataWit…
garrettmflynn Oct 3, 2023
2d87363
Merge branch 'user-test-retreat-1' of https://github.com/NeurodataWit…
garrettmflynn Oct 3, 2023
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9 changes: 5 additions & 4 deletions pyflask/manageNeuroconv/manage_neuroconv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,10 +132,11 @@ def get_all_interface_info() -> dict:
"""Format an information structure to be used for selecting interfaces based on modality and technique."""
from neuroconv.datainterfaces import interface_list

# Hard coded for now - eventual goal will be to import this from NeuroConv
interfaces_to_load = {
interface.__name__.replace("Interface", ""): interface for interface in interface_list
} # dict(SpikeGLX=SpikeGLXRecordingInterface, Phy=PhySortingInterface)
exclude_interfaces_from_selection = ["SpikeGLXLFP"] # Should have 'interface' stripped from name

interfaces_to_load = {interface.__name__.replace("Interface", ""): interface for interface in interface_list}
for excluded_interface in exclude_interfaces_from_selection:
interfaces_to_load.pop(excluded_interface)

return {
interface.__name__: {
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330 changes: 164 additions & 166 deletions schemas/json/base_metadata_schema.json
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@@ -1,173 +1,171 @@
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "base_metafile.schema.json",
"title": "Base schema for the metafile",
"description": "Base schema for the metafile",
"version": "0.1.0",
"type": "object",
"required": ["NWBFile"],
"properties": {
"NWBFile": {
"type": "object",
"additionalProperties": false,
"required": ["session_start_time"],
"properties": {
"keywords": {
"description": "Terms to search over",
"type": "array",
"items": {
"title": "keyword",
"type": "string"
}
},
"experiment_description": {
"type": "string",
"description": "general description of the experiment"
},
"session_id": {
"type": "string",
"description": "lab-specific ID for the session"
},
"experimenter": {
"description": "Name of person/people who performed experiment",
"type": "array",
"items": {
"type": "string",
"title": "experimenter"
}
},
"identifier": {
"type": "string",
"description": "A unique text identifier for the file. If one is not provided it will be randomly assigned"
},
"institution": {
"type": "string",
"description": "Institution(s) where experiment is performed"
},
"lab": {
"type": "string",
"description": "Lab where experiment was performed"
},
"session_description": {
"type": "string",
"description": "A description of the session where this data was generated"
},
"session_start_time": {
"type": "string",
"format": "date-time",
"description": "The start date and time of the recording session"
},
"surgery": {
"type": "string",
"description": "Narrative description about surgery/surgeries, including date(s) and who performed surgery."
},
"pharmacology": {
"type": "string",
"description": "Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc."
},
"protocol": {
"type": "string",
"description": "Experimental protocol, if applicable. E.g., include IACUC protocol"
},
"related_publications": {
"type": "array",
"items": {
"title": "related publication",
"type": "string"
}
},
"slices": {
"type": "string",
"description": "Description of slices, including information about preparation thickness, orientation, temperature and bath solution."
},
"source_script": {
"type": "string",
"description": "Script file used to create this NWB file."
},
"source_script_file_name": {
"type": "string",
"description": "Script file used to create this NWB file."
},
"notes": {
"type": "string",
"description": "Notes about the experiment."
},
"virus": {
"type": "string",
"description": "Narrative description about surgery/surgeries, including date(s) and who performed surgery."
},
"data_collection": {
"type": "string",
"description": "Notes about data collection and analysis."
},
"stimulus_notes": {
"type": "string",
"description": "Notes about data collection and analysis."
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "base_metafile.schema.json",
"title": "Base schema for the metafile",
"description": "Base schema for the metafile",
"version": "0.1.0",
"type": "object",
"required": ["NWBFile"],
"properties": {
"NWBFile": {
"type": "object",
"additionalProperties": false,
"required": ["session_start_time"],
"properties": {
"keywords": {
"description": "Terms to search over",
"type": "array",
"items": {
"title": "keyword",
"type": "string"
}
}
},
"Subject": {
"type": "object",
"required": [
"subject_id",
"sex",
"species"
],
"additionalProperties": false,
"properties": {
"age": {
"type": "string",
"description": "The age of the subject. The ISO 8601 Duration format is recommended, e.g., ‘P90D‘ for 90 days old, ‘P2W‘ for 2 weeks old, ‘P18Y‘ for 18 years old.",
"pattern": "^P((\\d+Y)?(\\d+M)?(\\d+D)?(T(\\d+H)?(\\d+M)?(\\d+S)?))|(\\d+W)?$"
},
"age__reference": {
"type": "string",
"enum": ["birth", "gestational"],
"description": "Age is with reference to this event. Can be ‘birth’ or ‘gestational’.",
"default": "birth"
},
"description": {
"type": "string",
"default": "no description",
"description": "Description of subject and where subject came from (e.g., breeder, if animal)."
},
"genotype": {
"type": "string",
"description": "Genetic strain. If absent, assume Wild Type (WT)"
},
"sex": {
"type": "string",
"enum": [
"M",
"F",
"U",
"O"
],
"default": "U"
},
"species": {
"type": "string",
"description": "Species of subject. Use latin name.",
"pattern": "^[A-Z][a-z]+ [a-z]+"
},
"subject_id": {
"type": "string",
"description": "ID of animal/person used/participating in experiment (lab convention)"
},
"weight": {
"type": "string",
"description": "Weight at time of experiment, at time of surgery and at other important times."
},
"date_of_birth": {
"type": "string",
"format": "date-time",
"description": "Date of birth of subject. Can be supplied instead of 'age'."
},
"strain": {
"type": "string",
"description": "The strain of the subject, e.g., ‘C57BL/6J‘"
},
"experiment_description": {
"type": "string",
"description": "general description of the experiment"
},
"session_id": {
"type": "string",
"description": "lab-specific ID for the session"
},
"experimenter": {
"description": "Name of person/people who performed experiment",
"type": "array",
"items": {
"type": "string",
"title": "experimenter"
}
},
"identifier": {
"type": "string",
"description": "A unique text identifier for the file. If one is not provided it will be randomly assigned"
},
"institution": {
"type": "string",
"description": "Institution(s) where experiment is performed"
},
"lab": {
"type": "string",
"description": "Lab where experiment was performed"
},
"session_description": {
"type": "string",
"description": "A description of the session where this data was generated"
},
"session_start_time": {
"type": "string",
"format": "date-time",
"description": "The start date and time of the recording session"
},
"surgery": {
"type": "string",
"description": "Narrative description about surgery/surgeries, including date(s) and who performed surgery."
},
"pharmacology": {
"type": "string",
"description": "Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc."
},
"protocol": {
"type": "string",
"description": "Experimental protocol, if applicable. E.g., include IACUC protocol"
},
"related_publications": {
"type": "array",
"items": {
"title": "related publication",
"type": "string"
}
},
"slices": {
"type": "string",
"description": "Description of slices, including information about preparation thickness, orientation, temperature and bath solution."
},
"source_script": {
"type": "string",
"description": "Script file used to create this NWB file."
},
"source_script_file_name": {
"type": "string",
"description": "Script file used to create this NWB file."
},
"notes": {
"type": "string",
"description": "Notes about the experiment."
},
"virus": {
"type": "string",
"description": "Narrative description about surgery/surgeries, including date(s) and who performed surgery."
},
"data_collection": {
"type": "string",
"description": "Notes about data collection and analysis."
},
"stimulus_notes": {
"type": "string",
"description": "Notes about data collection and analysis."
}
}
},
"Subject": {
"type": "object",
"required": [
"subject_id",
"sex",
"species"
],
"additionalProperties": false,
"properties": {
"age": {
"type": "string",
"description": "The age of the subject. The ISO 8601 Duration format is recommended, e.g., 'P90D' for 90 days old, 'P2W' for 2 weeks old, 'P18Y' for 18 years old.",
"pattern": "^P((\\d+Y)?(\\d+M)?(\\d+D)?(T(\\d+H)?(\\d+M)?(\\d+S)?))|(\\d+W)?$"
},
"age__reference": {
"type": "string",
"enum": ["birth", "gestational"],
"description": "Age is with reference to this event. Can be 'birth' or 'gestational'.",
"default": "birth"
},
"description": {
"type": "string",
"description": "Description of subject and where subject came from (e.g., breeder, if animal)."
},
"genotype": {
"type": "string",
"description": "Genetic strain. If absent, assume Wild Type (WT)"
},
"sex": {
"type": "string",
"enum": [
"M",
"F",
"U",
"O"
]
},
"species": {
"type": "string",
"description": "Species of subject. Use latin name.",
"pattern": "^[A-Z][a-z]+ [a-z]+"
},
"subject_id": {
"type": "string",
"description": "ID of animal/person used/participating in experiment (lab convention)"
},
"weight": {
"type": "string",
"description": "Weight at time of experiment, at time of surgery and at other important times."
},
"date_of_birth": {
"type": "string",
"format": "date-time",
"description": "Date of birth of subject. Can be supplied instead of 'age'."
},
"strain": {
"type": "string",
"description": "The strain of the subject, e.g., 'C57BL/6J'"
}
}
}
}
}
35 changes: 0 additions & 35 deletions schemas/json/project/subject.json
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