From b93eb6ded6106718d988fb4a10e331433e813190 Mon Sep 17 00:00:00 2001 From: Phil Date: Sat, 29 Jul 2023 19:15:33 -0700 Subject: [PATCH] yaml-validation --- README.md | 18 + environment.yml | 31 +- pyproject.toml | 19 + src/spikegadgets_to_nwb/convert_yaml.py | 6 + .../metadata_validation.py | 74 + src/spikegadgets_to_nwb/nwb_schema.json | 2797 +++++++++++++++++ .../__init__.py} | 0 .../test_metadata_validation.py | 190 ++ .../tests/test_data/test_metadata.yml | 21 +- .../test_data/test_metadata_dict_samples.py | 212 ++ .../test_metadata_probe_reconfig.yml | 21 +- .../__init__.py} | 0 .../tests/unit_tests/conftest.py | 31 + .../test_convert.py} | 0 .../test_convert_analog.py} | 0 .../test_convert_dios.py} | 0 .../{ => unit_tests}/test_convert_ephys.py | 13 +- .../unit_tests/test_convert_intervals.py | 0 .../tests/unit_tests/test_convert_position.py | 0 .../test_convert_rec_header.py | 38 +- .../{ => unit_tests}/test_convert_yaml.py | 32 +- .../unit_tests/test_metadata_validation.py | 25 + 22 files changed, 3436 insertions(+), 92 deletions(-) create mode 100644 src/spikegadgets_to_nwb/metadata_validation.py create mode 100644 src/spikegadgets_to_nwb/nwb_schema.json rename src/spikegadgets_to_nwb/tests/{test_convert.py => integration_tests/__init__.py} (100%) create mode 100644 src/spikegadgets_to_nwb/tests/integration_tests/test_metadata_validation.py create mode 100644 src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py rename src/spikegadgets_to_nwb/tests/{test_convert_analog.py => unit_tests/__init__.py} (100%) create mode 100644 src/spikegadgets_to_nwb/tests/unit_tests/conftest.py rename src/spikegadgets_to_nwb/tests/{test_convert_dios.py => unit_tests/test_convert.py} (100%) rename src/spikegadgets_to_nwb/tests/{test_convert_intervals.py => unit_tests/test_convert_analog.py} (100%) rename src/spikegadgets_to_nwb/tests/{test_convert_position.py => unit_tests/test_convert_dios.py} (100%) rename src/spikegadgets_to_nwb/tests/{ => unit_tests}/test_convert_ephys.py (95%) create mode 100644 src/spikegadgets_to_nwb/tests/unit_tests/test_convert_intervals.py create mode 100644 src/spikegadgets_to_nwb/tests/unit_tests/test_convert_position.py rename src/spikegadgets_to_nwb/tests/{ => unit_tests}/test_convert_rec_header.py (69%) rename src/spikegadgets_to_nwb/tests/{ => unit_tests}/test_convert_yaml.py (92%) create mode 100644 src/spikegadgets_to_nwb/tests/unit_tests/test_metadata_validation.py diff --git a/README.md b/README.md index 6f6bc9e..8513402 100644 --- a/README.md +++ b/README.md @@ -3,3 +3,21 @@ Converts data from SpikeGadgets to the NWB Data Format This will supersede [rec_to_nwb](https://github.com/LorenFrankLab/rec_to_nwb) once it is operational. + +## Notes + +### Unit Test + +Unit test are quick-running test to ensure that no code is broken as new code is added. It is recommended you run them frequently and before and after adding new code. To run the unit test, run - + +```bash +pytest src/spikegadgets_to_nwb/tests/unit_tests/ +``` + +### Integration Test + +Integration test are to ensure the system works. Functionality and third-party libraries are tested together and noting is mocked. They are best ran prior to pushing a commit as they can be slow. To run the test, run - + +```bash +pytest src/spikegadgets_to_nwb/tests/integration_tests/ +``` diff --git a/environment.yml b/environment.yml index 56ce96f..6098b95 100644 --- a/environment.yml +++ b/environment.yml @@ -1,18 +1,19 @@ name: spikegadgets_to_nwb channels: -- defaults -- conda-forge -- franklab + - defaults + - conda-forge + - franklab dependencies: -- numpy -- scipy -- pandas -- pynwb -- ipython -- black -- pytest -- pytest-cov -- pip -- pyyaml -- pip: - - ndx-franklab-novela \ No newline at end of file + - numpy + - scipy + - pandas + - pynwb + - ipython + - black + - pytest + - pytest-cov + - pip + - pyyaml + - jsonschema + - pip: + - ndx-franklab-novela diff --git a/pyproject.toml b/pyproject.toml index 166e2fc..3856cb2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,3 +50,22 @@ exclude = [".git_archival.txt"] [tool.hatch.build.targets.wheel] packages = ["src/spikegadgets_to_nwb"] exclude = ["src/spikegadgets_to_nwb/data/test_data"] + +[tool.black] +exclude = ''' + +( + /( + \.eggs # exclude a few common directories in the + | \.git # root of the project + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | _build + | buck-out + | build + | dist + )/ +) +''' diff --git a/src/spikegadgets_to_nwb/convert_yaml.py b/src/spikegadgets_to_nwb/convert_yaml.py index 1ffc133..179cddc 100644 --- a/src/spikegadgets_to_nwb/convert_yaml.py +++ b/src/spikegadgets_to_nwb/convert_yaml.py @@ -1,5 +1,6 @@ import yaml from xml.etree import ElementTree +from spikegadgets_to_nwb import metadata_validation from pynwb import NWBFile, TimeSeries from pynwb.file import Subject, ProcessingModule @@ -39,6 +40,11 @@ def load_metadata( """ with open(metadata_path, "r") as stream: metadata = yaml.safe_load(stream) + + is_metadata_valid, metadata_errors = metadata_validation.validate(metadata) + if not is_metadata_valid: + raise ValueError("".join(metadata_errors)) + probe_metadata = [] for path in probe_metadata_paths: with open(path, "r") as stream: diff --git a/src/spikegadgets_to_nwb/metadata_validation.py b/src/spikegadgets_to_nwb/metadata_validation.py new file mode 100644 index 0000000..dabbcb2 --- /dev/null +++ b/src/spikegadgets_to_nwb/metadata_validation.py @@ -0,0 +1,74 @@ +import jsonschema +import os +import yaml +import copy +import datetime + + +def _get_nwb_json_schema_path() -> str: + """Get the NWB JSON Schema file path + + Returns + ------- + str + NWB Schema file Path + """ + current_path = os.path.dirname(os.path.abspath(__file__)) + json_schema_file = "/./nwb_schema.json" + return f"{current_path}{os.path.normpath(json_schema_file)}" + + +def _get_json_schema() -> str: + """Get JSON Schema + + Returns + ------- + str + JSON Schema content + """ + json_schema = None + json_schema_path = _get_nwb_json_schema_path() + with open(json_schema_path, "r") as stream: + json_schema = yaml.safe_load(stream) + return json_schema + + +def validate(metadata: dict) -> tuple: + """Validates metadata + + Parameters + ---------- + metadata : dict + metadata documenting the particulars of a session + + Returns + ------- + tuple + information of the validity of the metadata data and any errors + """ + assert metadata is not None # metadata cannot be null + assert isinstance(metadata, dict) # cannot proceed if metadata is not a dictionary + + # date_of_birth is set to a datetime by the YAML-to-dict converter. + # This code converts date_of_birth to string + metadata_content = copy.deepcopy(metadata) or {} + if ( + metadata_content["subject"] + and metadata_content["subject"]["date_of_birth"] + and type(metadata_content["subject"]["date_of_birth"]) is datetime.datetime + ): + metadata_content["subject"]["date_of_birth"] = ( + metadata_content["subject"]["date_of_birth"].utcnow().isoformat() + ) + + schema = _get_json_schema() + validator = jsonschema.Draft202012Validator(schema) + metadata_validation_errors = validator.iter_errors(metadata_content) + errors = [] + + for metadata_validation_error in metadata_validation_errors: + errors.append(metadata_validation_error.message) + + is_valid = len(errors) == 0 + + return is_valid, errors diff --git a/src/spikegadgets_to_nwb/nwb_schema.json b/src/spikegadgets_to_nwb/nwb_schema.json new file mode 100644 index 0000000..ac97d28 --- /dev/null +++ b/src/spikegadgets_to_nwb/nwb_schema.json @@ -0,0 +1,2797 @@ +{ + "definitions": {}, + "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "https://lorenfranklab.github.io/rec_to_nwb_yaml_creator/v1.0.0", + "title": "Spikegadgets to NWB Validator", + "type": "object", + "description": "Spikegadgets to NWB Validator YAML schema version", + "required": ["experimenter_name", "lab", "institution", "data_acq_device", "times_period_multiplier", "raw_data_to_volts"], + "properties": { + "experimenter_name": { + "$id": "#root/experimenter_name", + "title": "experimenter_name", + "type": "array", + "default": [], + "examples": ["Jennifer Guidera", "Alison Comrie"], + "minItems": 1, + "uniqueItems": true, + "description": "Name of experimenter performing current session", + "items": { + "$id": "#root/experimenter_name/items", + "title": "items", + "type": "string", + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + }, + "lab": { + "$id": "#root/lab", + "title": "lab", + "type": "string", + "default": "", + "examples": ["Frank"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Laboratory where the experiment is conducted" + }, + "institution": { + "$id": "#root/institution", + "title": "institution", + "type": "string", + "default": "University of California, San Francisco", + "examples": [ + "Air Force Institute of Technology Graduate School of Engineering & Management", + "Albert Einstein College of Medicine", + "American University", + "Arizona State University Campus Immersion", + "Arizona State University Digital Immersion", + "Arkansas State University", + "Augusta University", + "Auburn University", + "Azusa Pacific University", + "Ball State University", + "Baylor College of Medicine", + "Baylor University", + "Binghamton University", + "Boise State University", + "Boston College", + "Boston University", + "Bowling Green State University", + "Brandeis University", + "Brigham Young University", + "Brown University", + "California Institute of Technology", + "California State University, East Bay", + "California State University, Fresno", + "California State University, Fullerton", + "California State University, Long Beach", + "California State University, San Bernardino", + "Carnegie Mellon University", + "Case Western Reserve University", + "Catholic University of America", + "Central Michigan University", + "Chapman University", + "Claremont Graduate University", + "Clark Atlanta University", + "Clark University", + "Clarkson University", + "Clemson University", + "Cleveland State University", + "College of William and Mary", + "Colorado School of Mines", + "Colorado State University", + "Columbia University", + "Cornell University", + "Creighton University", + "CUNY City College", + "Dartmouth College", + "DePaul University", + "Drexel University", + "Duke University", + "Duquesne University", + "East Carolina University", + "East Tennessee State University", + "Eastern Michigan University", + "Eastern Virginia Medical School", + "Emory University", + "Florida Agricultural and Mechanical University", + "Florida Atlantic University", + "Florida Institute of Technology", + "Florida International University", + "Florida State University", + "Fordham University", + "George Mason University", + "George Washington University", + "Georgetown University", + "Georgia Institute of Technology", + "Georgia Southern University", + "Georgia State University", + "Graduate Center, CUNY", + "Harvard University", + "Howard University", + "Icahn School of Medicine at Mount Sinai", + "Idaho State University", + "Illinois Institute of Technology", + "Illinois State University", + "Indiana University – Purdue University Indianapolis", + "Indiana University Bloomington", + "Indiana University of Pennsylvania", + "Iowa State University", + "Jackson State University", + "James Madison University", + "Johns Hopkins University", + "Kansas State University", + "Kennesaw State University", + "Kent State University", + "Lehigh University", + "Loma Linda University", + "Long Island University", + "Louisiana State University", + "Louisiana Tech University", + "Loyola Marymount University", + "Loyola University Chicago", + "Marquette University", + "Marshall University", + "Massachusetts Institute of Technology", + "Mayo Clinic College of Medicine and Science", + "Medical College of Wisconsin", + "Medical University of South Carolina", + "Mercer University", + "Miami University", + "Michigan State University", + "Michigan Technological University", + "Middle Tennessee State University", + "Mississippi State University", + "Missouri University of Science and Technology", + "Montana State University", + "Montclair State University", + "Morgan State University", + "New Jersey Institute of Technology", + "New Mexico State University", + "New York University", + "North Carolina A & T State University", + "North Carolina State University", + "North Dakota State University", + "Northeastern University", + "Northern Arizona University", + "Northern Illinois University", + "Northwestern University", + "Nova Southeastern University", + "Oakland University", + "Ohio State University", + "Ohio University", + "Oklahoma State University–Stillwater", + "Old Dominion University", + "Oregon Health & Science University", + "Oregon State University", + "Pennsylvania State University", + "Portland State University", + "Prairie View A&M University", + "Princeton University", + "Purdue University", + "Rensselaer Polytechnic Institute", + "Rice University", + "Rochester Institute of Technology", + "Rockefeller University", + "Rowan University", + "Rutgers University–Camden", + "Rutgers University–New Brunswick", + "Rutgers University–Newark", + "Saint Louis University", + "Sam Houston State University", + "San Diego State University", + "San Francisco State University", + "Seton Hall University", + "South Dakota State University", + "Southern Illinois University Carbondale", + "Southern Methodist University", + "Southern University", + "Stanford University", + "Stevens Institute of Technology", + "Stony Brook University", + "SUNY College of Environmental Science and Forestry", + "Syracuse University", + "Tarleton State University", + "Teachers College at Columbia University", + "Temple University", + "Tennessee State University", + "Tennessee Technological University", + "Texas A&M University", + "Texas A&M University–Corpus Christi", + "Texas A&M University–Kingsville", + "Texas Christian University", + "Texas Southern University", + "Texas State University", + "Texas Tech University", + "Texas Tech University Health Sciences Center", + "The New School", + "Thomas Jefferson University", + "Tufts University", + "Tulane University", + "Uniformed Services University of the Health Sciences", + "University at Albany, SUNY", + "University at Buffalo", + "University of Akron Main Campus", + "University of Alabama", + "University of Alabama at Birmingham", + "University of Alabama in Huntsville", + "University of Alaska Fairbanks", + "University of Arizona", + "University of Arkansas", + "University of Arkansas at Little Rock", + "University of Arkansas for Medical Sciences", + "University of California, Berkeley", + "University of California, Davis", + "University of California, Irvine", + "University of California, Los Angeles", + "University of California, Merced", + "University of California, Riverside", + "University of California, San Diego", + "University of California, San Francisco", + "University of California, Santa Barbara", + "University of California, Santa Cruz", + "University of Central Florida", + "University of Chicago", + "University of Cincinnati", + "University of Colorado Boulder", + "University of Colorado Colorado Springs", + "University of Colorado Denver", + "University of Connecticut", + "University of Dayton", + "University of Delaware", + "University of Denver", + "University of Florida", + "University of Georgia", + "University of Hawaii at Manoa", + "University of Houston", + "University of Idaho", + "University of Illinois Chicago", + "University of Illinois Urbana-Champaign", + "University of Iowa", + "University of Kansas", + "University of Kentucky", + "University of Louisiana at Lafayette", + "University of Louisville", + "University of Maine", + "University of Maryland, Baltimore", + "University of Maryland, Baltimore County", + "University of Maryland, College Park", + "University of Maryland, Eastern Shore", + "University of Massachusetts Amherst", + "University of Massachusetts Boston", + "University of Massachusetts Chan Medical School", + "University of Massachusetts Dartmouth", + "University of Massachusetts Lowell", + "University of Memphis", + "University of Miami", + "University of Michigan", + "University of Minnesota", + "University of Mississippi", + "University of Missouri", + "University of Missouri–Kansas City", + "University of Missouri–St. Louis", + "University of Montana", + "University of Nebraska at Omaha", + "University of Nebraska Medical Center", + "University of Nebraska–Lincoln", + "University of Nevada, Las Vegas", + "University of Nevada, Reno", + "University of New England", + "University of New Hampshire", + "University of New Mexico", + "University of New Orleans", + "University of North Carolina at Chapel Hill", + "University of North Carolina at Charlotte", + "University of North Carolina at Greensboro", + "University of North Carolina Wilmington", + "University of North Dakota", + "University of North Florida", + "University of North Texas", + "University of Notre Dame", + "University of Oklahoma", + "University of Oklahoma Health Sciences Center", + "University of Oregon", + "University of Pennsylvania", + "University of Pittsburgh", + "University of Puerto Rico at Río Piedras", + "University of Rhode Island", + "University of Rochester", + "University of San Diego", + "University of South Alabama", + "University of South Carolina", + "University of South Dakota", + "University of South Florida", + "University of Southern California", + "University of Southern Mississippi", + "University of Tennessee", + "University of Tennessee Health Science Center", + "University of Texas at Arlington", + "University of Texas at Austin", + "University of Texas at Dallas", + "University of Texas at El Paso", + "University of Texas at San Antonio", + "University of Texas Health Science Center at Houston", + "University of Texas Health Science Center at San Antonio", + "University of Texas Medical Branch", + "University of Texas Southwestern Medical Center", + "University of Toledo", + "University of Tulsa", + "University of Utah", + "University of Vermont", + "University of Virginia", + "University of Washington", + "University of Wisconsin–Madison", + "University of Wisconsin–Milwaukee", + "University of Wyoming", + "Utah State University", + "Vanderbilt University", + "Villanova University", + "Virginia Commonwealth University", + "Virginia Tech", + "Wake Forest University", + "Washington State University", + "Washington University in St. Louis", + "Wayne State University", + "Weill Cornell Medicine", + "West Chester University of Pennsylvania", + "West Virginia University", + "Western Michigan University", + "Wichita State University", + "Worcester Polytechnic Institute", + "Wright State University", + "Yale University" + ], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Type to search for institution ..." + }, + "experiment_description": { + "$id": "#root/experiment_description", + "title": "experiment_description", + "type": "string", + "default": "", + "examples": ["spatial alternation memory task"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Research work being conducted" + }, + "session_description": { + "$id": "#root/session_description", + "title": "session_description", + "type": "string", + "default": "", + "examples": ["spatial alternation memory task"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Aspect of research being conducted" + }, + "session_id": { + "$id": "#root/session_id", + "title": "session_id", + "type": "string", + "default": "", + "examples": ["J16_20210606"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Current session's identification code/number" + }, + "keywords": { + "$id": "#root/keywords", + "title": "keywords", + "type": "array", + "default": [], + "examples": ["J16_20210606"], + "minItems": 1, + "uniqueItems": true, + "description": "keywords", + "items": { + "$id": "#root/keywords/items", + "title": "items", + "type": "string", + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + }, + "subject": { + "$id": "#root/subject", + "title": "subject", + "type": "object", + "required": [ + "description", + "genotype", + "sex", + "species", + "subject_id", + "weight", + "date_of_birth" + ], + "properties": { + "description": { + "$id": "#root/subject/description", + "title": "description", + "type": "string", + "default": "", + "examples": ["Long Evans Rat"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Summary of animal model/patient/specimen being examined" + }, + "genotype": { + "$id": "#root/subject/genotype", + "title": "genotype", + "type": "string", + "default": "", + "examples": ["Wild Type"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Genetic summary of animal model/patient/specimen" + }, + "sex": { + "$id": "#root/subject/sex", + "title": "sex", + "type": "string", + "enum": ["M", "F", "U", "O"], + "default": "M", + "examples": ["M", "F", "U", "O"], + "description": "Gender of animal model/patient" + }, + "species": { + "$id": "#root/subject/species", + "title": "species", + "type": "string", + "default": "", + "examples": ["Rat"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Category of animal model/patient" + }, + "subject_id": { + "$id": "#root/subject/subject_id", + "title": "subject_id", + "type": "string", + "default": "", + "examples": ["J16"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Identification code/number of animal model/patient" + }, + "weight": { + "$id": "#root/subject/weight", + "title": "weight", + "type": "number", + "default": "100", + "minimum": 0, + "description": "Mass of animal model/patient in grams" + }, + "date_of_birth": { + "$id": "#root/subject/date_of_birth", + "title": "date_of_birth", + "type": "string", + "default": "", + "pattern": "(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d\\.\\d+)|(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d)|(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d)", + "description": "date of birth of animal model/patient, in ISO 8061 format" + } + } + }, + "data_acq_device": { + "$id": "#root/data_acq_device", + "title": "data_acq_device", + "type": "array", + "minItems": 1, + "default": [], + "items": { + "$id": "#root/data_acq_device/items", + "title": "items", + "type": "object", + "required": ["name", "system", "amplifier", "adc_circuit"], + "properties": { + "name": { + "$id": "#root/data_acq_device/items/name", + "title": "name", + "type": "string", + "default": "", + "description": "Data acquisition device name", + "examples": ["Spike Gadgets"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "system": { + "$id": "#root/data_acq_device/items/system", + "title": "system", + "type": "string", + "default": "", + "description": "Data acquisition information like version or id", + "examples": ["MCU"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "amplifier": { + "$id": "#root/data_acq_device/items/amplifier", + "title": "amplifier", + "type": "string", + "default": "", + "description": "Amplifier device", + "examples": ["intan"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "adc_circuit": { + "$id": "#root/data_acq_device/items/adc_circuit", + "title": "adc_circuit", + "type": "string", + "default": "", + "description": "adc circuit", + "examples": ["intan"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + } + } + }, + "associated_files": { + "$id": "#root/associated_files", + "title": "associated_files", + "type": "array", + "default": [], + "items": { + "$id": "#root/associated_files/items", + "title": "Items", + "type": "object", + "required": ["name", "description", "path", "task_epochs"], + "properties": { + "name": { + "$id": "#root/associated_files/items/name", + "title": "name", + "type": "string", + "default": "", + "description": "File name", + "examples": ["stateScriptLog_r1"], + "pattern": "(.|\\s)*\\S(.|\\s)*$" + }, + "description": { + "$id": "#root/associated_files/items/description", + "title": "description", + "type": "string", + "default": "", + "description": "Purpose of file", + "examples": ["stateScriptLog epoch r1"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "path": { + "$id": "#root/associated_files/items/path", + "title": "path", + "type": "string", + "default": "", + "description": "File location", + "examples": [ + "/nimbus/jguidera/J16/raw/20210606/20210606_J16_02_r1.stateScriptLog" + ], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "task_epochs": { + "$id": "#root/associated_files/items/task_epochs", + "title": "task_epochs", + "type": "integer", + "default": 0, + "description": "task epoch" + } + } + } + }, + "units": { + "$id": "#root/units", + "title": "units", + "type": "object", + "required": ["analog", "behavioral_events"], + "properties": { + "analog": { + "$id": "#root/units/analog", + "title": "analog", + "type": "string", + "default": "", + "description": "analog", + "examples": ["unspecified"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "behavioral_events": { + "$id": "#root/units/behavioral_events", + "title": "behavioral_events", + "type": "string", + "default": "", + "description": "behavioral_events", + "examples": ["unspecified"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + } + }, + "times_period_multiplier": { + "$id": "#root/times_period_multiplier", + "title": "times_period_multiplier", + "type": "number", + "examples": [1.5], + "default": 0.0 + }, + "raw_data_to_volts": { + "$id": "#root/raw_data_to_volts", + "title": "raw_data_to_volts", + "type": "number", + "examples": [1.95e-7], + "default": 0.0 + }, + "default_header_file_path": { + "$id": "#root/default_header_file_path", + "title": "default_header_file_path", + "type": "string", + "default": "", + "examples": ["default_header.xml"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "cameras": { + "$id": "#root/cameras", + "title": "cameras", + "type": "array", + "default": [], + "items": { + "$id": "#root/cameras/items", + "title": "Items", + "type": "object", + "required": [ + "id", + "meters_per_pixel", + "manufacturer", + "model", + "lens", + "camera_name" + ], + "properties": { + "id": { + "$id": "#root/cameras/items/id", + "title": "id", + "type": "integer", + "examples": [0], + "default": 0, + "description": "camera id" + }, + "meters_per_pixel": { + "$id": "#root/cameras/items/meters_per_pixel", + "title": "meters_per_pixel", + "type": "number", + "examples": [0.000842], + "default": 0.0, + "description": "meter per pixel" + }, + "manufacturer": { + "$id": "#root/cameras/items/manufacturer", + "title": "manufacturer", + "type": "string", + "default": "", + "examples": ["Manta"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Manufacturer" + }, + "model": { + "$id": "#root/cameras/items/model", + "title": "model", + "type": "string", + "default": "", + "examples": ["unknown"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Model" + }, + "lens": { + "$id": "#root/cameras/items/lens", + "title": "lens", + "type": "string", + "default": "", + "examples": ["unknown"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Len" + }, + "camera_name": { + "$id": "#root/cameras/items/camera_name", + "title": "camera_name", + "type": "string", + "default": "", + "examples": ["HomeBox_camera"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Camera Name" + } + } + } + }, + "tasks": { + "$id": "#root/tasks", + "title": "tasks", + "type": "array", + "default": [], + "items": { + "$id": "#root/tasks/items", + "title": "items", + "type": "object", + "required": [ + "task_name", + "task_description", + "task_environment", + "camera_id", + "task_epochs" + ], + "properties": { + "task_name": { + "$id": "#root/tasks/items/task_name", + "title": "task_name", + "type": "string", + "default": "", + "examples": ["home"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Task name" + }, + "task_description": { + "$id": "#root/tasks/items/task_description", + "title": "task_description", + "type": "string", + "default": "", + "examples": ["The animal rests in a box"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Task description" + }, + "task_environment": { + "$id": "#root/tasks/items/task_environment", + "title": "task_environment", + "type": "string", + "default": "", + "examples": ["HomeBox"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "description": "Task environment" + }, + "camera_id": { + "$id": "#root/tasks/items/camera_id", + "title": "camera_id", + "type": "array", + "description": "Comma separated camera ids, from camera list", + "examples": [], + "default": [], + "items": { + "$id": "#root/tasks/items/camera_id/items", + "title": "Items", + "uniqueItems": true, + "type": "integer", + "examples": [0], + "default": 0 + } + }, + "task_epochs": { + "$id": "#root/tasks/items/task_epochs", + "title": "task_epochs", + "type": "array", + "description": "Comma separated numbers of task epochs", + "examples": [], + "default": [], + "items": { + "$id": "#root/tasks/items/task_epochs/items", + "title": "Items", + "type": "integer", + "uniqueItems": true, + "examples": [18], + "default": 0 + } + } + } + } + }, + "associated_video_files": { + "$id": "#root/associated_video_files", + "title": "associated_video_files", + "type": "array", + "default": [], + "items": { + "$id": "#root/associated_video_files/items", + "title": "Items", + "type": "object", + "required": ["name", "camera_id", "task_epochs"], + "properties": { + "name": { + "$id": "#root/associated_video_files/items/name", + "title": "name", + "type": "string", + "default": "", + "description": "File name", + "examples": ["20210606_J16_01_s1.1.h264"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "camera_id": { + "$id": "#root/associated_video_files/items/camera_id", + "title": "camera_id", + "type": "integer", + "description": "camera id from camera list", + "default": 0 + }, + "task_epochs": { + "$id": "#root/associated_video_files/items/task_epochs", + "title": "task_epochs", + "type": "integer", + "default": 0, + "description": "task epoch" + } + } + } + }, + "behavioral_events": { + "$id": "#root/behavioral_events", + "title": "behavioral_events", + "type": "array", + "default": [], + "items": { + "$id": "#root/behavioral_events/items", + "title": "Items", + "type": "object", + "required": ["description", "name"], + "properties": { + "description": { + "$id": "#root/behavioral_events/items/description", + "title": "description", + "type": "string", + "default": "Din1", + "examples": ["Din", "Dout", "Accel", "Gyro", "Mag"], + "description": "Behavioral Events", + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "name": { + "$id": "#root/behavioral_events/items/name", + "title": "name", + "type": "string", + "default": "Home box camera", + "examples": [ + "Home box camera", + "Poke", "Light", + "Pump", + "Run Camera Ticks", + "Sleep" + ], + "description": "Type of behavioral events", + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + } + } + }, + "device": { + "$id": "#root/device", + "title": "device", + "type": "object", + "required": ["name"], + "properties": { + "name": { + "$id": "#root/device/items/name", + "title": "name", + "type": "array", + "minItems": 1, + "default": "Trodes", + "description": "Selected recording device", + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + } + }, + "electrode_groups": { + "$id": "#root/electrode_groups", + "title": "electrode_groups", + "type": "array", + "default": [], + "items": { + "$id": "#root/electrode_groups/items", + "title": "Items", + "type": "object", + "required": [ + "id", + "location", + "device_type", + "description", + "targeted_location", + "targeted_x", + "targeted_y", + "targeted_z", + "units" + ], + "properties": { + "id": { + "$id": "#root/electrode_groups/items/id", + "title": "id", + "type": "integer", + "examples": [0], + "default": 0, + "minimum": 0, + "description": "electrode/probe identification code/number" + }, + "location": { + "$id": "#root/electrode_groups/items/location", + "title": "location", + "type": "string", + "default": "Cornu ammonis 1 (CA1)", + "description": "Exact location of electrode/probe", + "examples": [ + "Brain (Brain)", + "White matter (wmt)", + "Olfactory white matter (olf)", + "lateral olfactory tract (lot)", + "corpus callosum and associated subcortical white matter (cc-ec-cing-dwm)", + "Anterior commissure (ac)", + "anterior commissure, anterior limb (aca)", + "anterior commissure, posterior limb (acp)", + "anterior commissure, intrabulbar part (aci)", + "Hippocampal white matter (hiw)", + "alveus of the hippocampus (alv)", + "ventral hippocampal commissure (vhc)", + "fornix (f)", + "fimbria of the hippocampus (fi)", + "Corticofugal pathways (cfp)", + "corticofugal tract and corona radiata (ic-cp-lfp-py)", + "pyramidal decussation (pyx)", + "Medial lemniscus (ml)", + "medial lemniscus, unspecified (ml-u)", + "medial lemniscus decussation (mlx)", + "Thalamic tracts (tht)", + "External medullary lamina (eml)", + "external medullary lamina, unspecified (eml-u)", + "external medullary lamina, auditory radiation (eml-ar)", + "internal medullary lamina (iml)", + "intramedullary thalamic area (ima)", + "superior cerebellar peduncle and prerubral field (scp-pr)", + "pretectothalamic lamina (ptl)", + "mammillotegmental tract (mtg)", + "commissural stria terminalis (cst)", + "fasciculus retroflexus (fr)", + "stria medullaris thalami (sm)", + "stria terminalis (st)", + "habenular commissure (hbc)", + "posterior commissure (pc)", + "Facial nerve (7n)", + "facial nerve, unspecified (7n-u)", + "ascending fibers of the facial nerve (asc7)", + "genu of the facial nerve (g7)", + "Optic fiber system and supraoptic decussation (ofs)", + "optic nerve (2n)", + "optic tract and optic chiasm (opt-och)", + "supraoptic decussation (sox)", + "White matter of the tectum (tew)", + "commissure of the superior colliculus (csc)", + "brachium of the superior colliculus (bsc)", + "inferior colliculus, commissure (cic)", + "inferior colliculus, brachium (bic)", + "Cerebellar and precerebellar white matter (cbt)", + "inferior cerebellar peduncle (icp)", + "middle cerebellar peduncle (mcp)", + "transverse fibers of the pons (tfp)", + "White matter of the brainstem (bsw)", + "Lateral lemniscus (ll)", + "lateral lemniscus, commissure (ll-c)", + "lateral lemniscus, unspecified (ll-u)", + "acoustic striae (as)", + "trapezoid body (tz)", + "spinal trigeminal tract (sp5t)", + "Gray matter (GM)", + "Telencephalon (Tel)", + "Laminated pallium (LamP)", + "Olfactory bulb (OB)", + "Glomerular layer of the accessory olfactory bulb (GlA)", + "Glomerular layer of the olfactory bulb (Gl)", + "Olfactory bulb, unspecified (OB-u)", + "Nucleus of the lateral olfactory tract (NLOT)", + "Cerebral cortex (Cx)", + "Hippocampal region (HR)", + "Hippocampal formation (HF)", + "Fasciola cinereum (FC)", + "Subiculum (SUB)", + "Cornu Ammonis (CA)", + "Cornu ammonis 1 (CA1)", + "Cornu ammonis 2 (CA2)", + "Cornu ammonis 3 (CA3)", + "Dentate gyrus (DG)", + "Parahippocampal region (PHR)", + "Postrhinal cortex (POR)", + "Presubiculum (PrS)", + "Parasubiculum (PaS)", + "Perirhinal cortex (PER)", + "Perirhinal area 35 (PER35)", + "Perirhinal area 36 (PER36)", + "Entorhinal cortex (EC)", + "Medial entorhinal cortex (MEC)", + "Lateral entorhinal cortex (LEC)", + "Piriform cortex (PIR)", + "Piriform cortex, layer 1 (PIR1)", + "Piriform cortex, layer 2 (PIR2)", + "Piriform cortex, layer 3 (PIR3)", + "Cingulate region (CgR)", + "Cingulate cortex (Cg)", + "Cingulate area 1 (Cg1)", + "Cingulate area 2 (Cg2)", + "Retrosplenial cortex (RS)", + "Retrosplenial dysgranular area (RSD)", + "Retrosplenial granular area (RSG)", + "Insular region (INS)", + "Agranular insular cortex (AI)", + "Agranular insular cortex, ventral area (AI-v)", + "Agranular insular cortex dorsal area (AI-d)", + "Agranular insular cortex, posterior area (AI-p)", + "Dysgranular insular cortex (DI)", + "Granular insular cortex (GI)", + "Frontal region (Front)", + "Frontal association cortex (FrA)", + "Orbitofrontal cortex (Orb)", + "Medial orbital area (MO)", + "Ventral orbital area (VO)", + "Ventrolateral orbital area (VLO)", + "Lateral orbital area (LO)", + "Dorsolateral orbital area (DLO)", + "Mediofrontal cortex (MFC)", + "Prelimbic area (PrL)", + "Infralimbic area (IL)", + "Motor cortex (M)", + "Primary motor area (M1)", + "Secondary motor area (M2)", + "Frontal association area 3 (Fr3)", + "Parietal region (Par)", + "Somatosensory cortex (SS)", + "Primary somatosensory area (S1)", + "Primary somatosensory area, face representation (S1-f)", + "Primary somatosensory area, barrel field (S1-bf)", + "Primary somatosensory area, dysgranular zone (S1-dz)", + "Primary somatosensory area, forelimb representation (S1-fl)", + "Primary somatosensory area, hindlimb representation (S1-hl)", + "Primary somatosensory area, trunk representation (S1-tr)", + "Secondary somatosensory area (S2)", + "Posterior parietal cortex (PPC)", + "Parietal association cortex, medial area (mPPC)", + "Parietal association cortex, lateral area (lPPC)", + "Parietal association cortex, posterior area (PtP)", + "Occipital region (Oc)", + "Visual cortex (Vis)", + "Primary visual area (V1)", + "Secondary visual area (V2)", + "Secondary visual area, medial part (V2M)", + "Secondary visual area, lateral part (V2L)", + "Temporal region (Te)", + "Temporal association cortex (TeA)", + "Auditory cortex (Au)", + "Primary auditory area (Au1)", + "Secondary auditory area (Au2)", + "Secondary auditory area, dorsal part (Au2-d)", + "Secondary auditory area, ventral part (Au2-v)", + "Non-laminated pallium (N-LamP)", + "Claustrum (CLA)", + "Endopiriform nucleus (Endo)", + "Amygdaloid area, unspecified (Am-u)", + " Subpallium (SubPAL)", + "Striatum (Str)", + "Caudate putamen (CPu)", + "Nucleus accumbens (NAc)", + "Nucleus accumbens, core (NAc-c)", + "Nucleus accumbens, shell (NAc-sh)", + "Ventral striatal region, unspecified (VSR-u)", + "Pallidum (PAL)", + "Globus pallidus external (GPe)", + "Globus pallidus external, medial part (GPe-m)", + "Globus pallidus external, lateral part (GPe-l)", + "Entopeduncular nucleus (EP)", + "Ventral pallidum (VP)", + "Basal forebrain region (BRF)", + "Basal forebrain region, unspecified (BFR-u)", + "Bed nucleus of the stria terminalis (BNST)", + "Septal region (Sep)", + "Subthalamic nucleus (STh)", + "Diencephalon (Dien)", + "Prethalamus (Thal-Pre)", + "Reticular (pre)thalamic nucleus (RT)", + "Reticular (pre)thalamic nucleus, unspecified (RT-u)", + "Reticular (pre)thalamic nucleus, auditory segment (RT-a)", + "Zona incerta (ZI)", + "Zona incerta, dorsal part (ZI-d)", + "Zona incerta, ventral part (ZI-v)", + "Zona incerta, rostral part (ZI-r)", + "Zona incerta, caudal part (ZI-c)", + "Zona incerta, A13 dopamine cells (ZI-A13)", + "Zona incerta, A11 dopamine cells (ZI-A11)", + "Fields of Forel (FoF)", + "Pregeniculate nucleus (PrG)", + "Subgeniculate nucleus (SubG)", + "Intergeniculate leaflet (IGL)", + "Epithalamus (Thal-EPI)", + "Lateral habenular nucleus (LHb)", + "Medial habenular nucleus (MHb)", + "Nucleus of the stria medullaris (SMn)", + "Pineal gland (PG)", + "Dorsal thalamus (Thal-D)", + "Anterior nuclei of the dorsal thalamus (ANT)", + "Anterodorsal thalamic nucleus (AD)", + "Anteroventral thalamic nucleus (AV)", + "Anteroventral thalamic nucleus, dorsomedial part (AV-dm)", + "Anteroventral thalamic nucleus, ventrolateral part (AV-vl)", + "Anteromedial thalamic nucleus (AM)", + "Interanteromedial thalamic nucleus (IAM)", + "Paraventricular thalamic nuclei (anterior and posterior) (PV)", + "Intermediodorsal thalamic nucleus (IMD)", + "Parataenial thalamic nucleus (PT)", + "Subparafascicular nucleus (SPF)", + "Posterior intralaminar nucleus (PIL)", + "Ventral midline group of the dorsal thalamus (V-MID)", + "Rhomboid thalamic nucleus (Rh)", + "Reuniens thalamic nucleus (Re)", + "Retroreuniens thalamic nucleus (RRe)", + "Xiphoid thalamic nucleus (Xi)", + "Mediodorsal nucleus of the dorsal thalamus (MD)", + "Mediodorsal thalamic nucleus, lateral part (MD-l)", + "Mediodorsal thalamic nucleus, central part (MD-c)", + "Mediodorsal thalamic nucleus, medial part (MD-m)", + "Ventral nuclei of the dorsal thalamus (VENT)", + "Ventral anterior thalamic nucleus (VA)", + "Ventromedial thalamic nucleus (VM)", + "Ventrolateral thalamic nucleus (VL)", + "Angular thalamic nucleus (Ang)", + "Ventral posterior thalamic nucleus (VPN)", + "Ventral posteromedial thalamic nucleus (VPM)", + "Ventral posterolateral thalamic nucleus (VPL)", + "Ventral posterior nucleus of the thalamus, parvicellular part (VP-pc)", + "Submedius thalamic nucleus (SMT)", + "Intralaminar nuclei of the dorsal thalamus (ILM)", + "Paracentral thalamic nucleus (PCN)", + "Central medial thalamic nucleus (CM)", + "Central lateral thalamic nucleus (CL)", + "Parafascicular thalamic nucleus (PF)", + "Ethmoid-Limitans nucleus (Eth)", + "Posterior complex of the dorsal thalamus (PoC)", + "Posterior thalamic nucleus (Po)", + "Posterior thalamic nuclear group, triangular part (Po-t)", + "Lateral posterior (pulvinar) complex of the dorsal thalamus (LP)", + "Lateral posterior thalamic nucleus, mediorostral part (LP-mr)", + "Lateral posterior thalamic nucleus, mediocaudal part (LP-mc)", + "Lateral posterior thalamic nucleus, lateral part (LP-l)", + "Laterodorsal thalamic nuclei of the dorsal thalamus (LD)", + "Laterodorsal thalamic nucleus, dorsomedial part (LD-dm)", + "Laterodorsal thalamic nucleus, ventrolateral part (LD-vl)", + "Dorsal lateral geniculate nucleus (DLG)", + "Medial geniculate complex of the dorsal thalamus (MG)", + "Medial geniculate body, ventral division (MG-v)", + "Medial geniculate body, dorsal division (MG-d)", + "Medial geniculate body, marginal zone (MG-mz)", + "Medial geniculate body, medial division (MG-m)", + "Medial geniculate body, suprageniculate nucleus (MG-sg)", + "Hypothalamus (HY)", + "Hypothalamic region, unspecified (HTh-u)", + "Pretectum (PreT)", + "Pretectal region (PRT)", + "Nucleus sagulum (Sag)", + "Mesencephalon (Mes)", + "Midbrain (MB)", + "Tectum (Tc)", + "Inferior colliculus (IC)", + "Inferior colliculus, dorsal cortex (DCIC)", + "Inferior colliculus, central nucleus (CNIC)", + "Inferior colliculus, external cortex (ECIC)", + "Superior colliculus (Su)", + "Superficial gray layer of the superior colliculus (SuG)", + "Deeper layers of the superior colliculus (SuD)", + "Tegmentum (Tg)", + "Substantia nigra (SN)", + "Substantia nigra, reticular part (SN-r)", + "Substantia nigra, compact part (SN-c)", + "Substantia nigra, lateral part (SN-l)", + "Ventral tegmental area (VTA)", + "Peripeduncular nucleus (PP)", + "Interpeduncular nucleus (IP)", + "Periaqueductal gray (PAG)", + "Brainstem, unspecified (BS-u)", + "Rhombencephalon (Rho)", + "Metencephalon (Met)", + "Pontine nuclei (Pn)", + "Cerebellum (Cb)", + "Molecular cell layer of the cerebellum (Cb-m)", + "Cerebellum, unspecified (Cb-u)", + "Myelencephalon (Myel)", + "Cochlear nucleus, ventral part (VCN)", + "Ventral cochlear nucleus, anterior part (AVCN)", + "Ventral cochlear nucleus, posterior part (PVCN)", + "Ventral cochlear nucleus, cap area (Cap)", + "Ventral cochlear nucleus, granule cell layer (GCL)", + "Cochlear nucleus, dorsal part (DCN)", + "Dorsal cochlear nucleus, molecular layer (DCNM)", + "Dorsal cochlear nucleus, fusiform and granule layer (DCNFG)", + "Dorsal cochlear nucleus, deep core (DCND)", + "Spinal trigeminal nucleus (Sp5n)", + "Periventricular gray (PVG)", + "Superior olivary complex (SO)", + "Nucleus of the trapezoid body (NTB)", + "Superior paraolivary nucleus (SPN)", + "Medial superior olive (MSO)", + "Lateral superior olive (LSO)", + "Superior periolivary region (SPR)", + "Ventral periolivary nuclei (VPO)", + "Nuclei of the lateral lemniscus (NLL)", + "Lateral lemniscus, ventral nucleus (VLL)", + "Lateral lemniscus, intermediate nucleus (ILL)", + "Lateral lemniscus, dorsal nucleus (DLL)", + "Inferior olive (IO)", + "Ventricular system (V)", + "ventricular system, unspecified (V-u)", + "4th ventricle (4V)", + "central canal (CC)", + "spinal cord (SpC)", + "Inner ear (IE)", + "vestibular apparatus (VeA)", + "cochlea (Co)", + "cochlear nerve (8cn)", + "vestibular nerve (8vn)", + "spiral ganglion (SpG)" + ], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "device_type": { + "$id": "#root/electrode_groups/items/device_type", + "title": "device_type", + "type": "string", + "default": "", + "examples": ["", "tetrode_12.5", "A1x32-6mm-50-177-H32_21mm", "128c-4s8mm6cm-20um-40um-sl", "128c-4s6mm6cm-15um-26um-sl", "32c-2s8mm6cm-20um-40um-dl", "64c-4s6mm6cm-20um-40um-dl", "64c-3s6mm6cm-20um-40um-sl"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$", + "enum": ["tetrode_12.5", "A1x32-6mm-50-177-H32_21mm", "128c-4s8mm6cm-20um-40um-sl", "128c-4s6mm6cm-15um-26um-sl", "32c-2s8mm6cm-20um-40um-dl", "64c-4s6mm6cm-20um-40um-dl", "64c-3s6mm6cm-20um-40um-sl"] + }, + "description": { + "$id": "#root/electrode_groups/items/description", + "title": "description", + "type": "string", + "default": "", + "description": "electrode groups description", + "examples": ["tetrode"], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "targeted_location": { + "$id": "#root/electrode_groups/items/targeted_location", + "title": "targeted_location", + "type": "string", + "default": "Cornu ammonis 1 (CA1)", + "description": "Planned location of electrode/probe", + "examples": [ + "Brain (Brain)", + "White matter (wmt)", + "Olfactory white matter (olf)", + "lateral olfactory tract (lot)", + "corpus callosum and associated subcortical white matter (cc-ec-cing-dwm)", + "Anterior commissure (ac)", + "anterior commissure, anterior limb (aca)", + "anterior commissure, posterior limb (acp)", + "anterior commissure, intrabulbar part (aci)", + "Hippocampal white matter (hiw)", + "alveus of the hippocampus (alv)", + "ventral hippocampal commissure (vhc)", + "fornix (f)", + "fimbria of the hippocampus (fi)", + "Corticofugal pathways (cfp)", + "corticofugal tract and corona radiata (ic-cp-lfp-py)", + "pyramidal decussation (pyx)", + "Medial lemniscus (ml)", + "medial lemniscus, unspecified (ml-u)", + "medial lemniscus decussation (mlx)", + "Thalamic tracts (tht)", + "External medullary lamina (eml)", + "external medullary lamina, unspecified (eml-u)", + "external medullary lamina, auditory radiation (eml-ar)", + "internal medullary lamina (iml)", + "intramedullary thalamic area (ima)", + "superior cerebellar peduncle and prerubral field (scp-pr)", + "pretectothalamic lamina (ptl)", + "mammillotegmental tract (mtg)", + "commissural stria terminalis (cst)", + "fasciculus retroflexus (fr)", + "stria medullaris thalami (sm)", + "stria terminalis (st)", + "habenular commissure (hbc)", + "posterior commissure (pc)", + "Facial nerve (7n)", + "facial nerve, unspecified (7n-u)", + "ascending fibers of the facial nerve (asc7)", + "genu of the facial nerve (g7)", + "Optic fiber system and supraoptic decussation (ofs)", + "optic nerve (2n)", + "optic tract and optic chiasm (opt-och)", + "supraoptic decussation (sox)", + "White matter of the tectum (tew)", + "commissure of the superior colliculus (csc)", + "brachium of the superior colliculus (bsc)", + "inferior colliculus, commissure (cic)", + "inferior colliculus, brachium (bic)", + "Cerebellar and precerebellar white matter (cbt)", + "inferior cerebellar peduncle (icp)", + "middle cerebellar peduncle (mcp)", + "transverse fibers of the pons (tfp)", + "White matter of the brainstem (bsw)", + "Lateral lemniscus (ll)", + "lateral lemniscus, commissure (ll-c)", + "lateral lemniscus, unspecified (ll-u)", + "acoustic striae (as)", + "trapezoid body (tz)", + "spinal trigeminal tract (sp5t)", + "Gray matter (GM)", + "Telencephalon (Tel)", + "Laminated pallium (LamP)", + "Olfactory bulb (OB)", + "Glomerular layer of the accessory olfactory bulb (GlA)", + "Glomerular layer of the olfactory bulb (Gl)", + "Olfactory bulb, unspecified (OB-u)", + "Nucleus of the lateral olfactory tract (NLOT)", + "Cerebral cortex (Cx)", + "Hippocampal region (HR)", + "Hippocampal formation (HF)", + "Fasciola cinereum (FC)", + "Subiculum (SUB)", + "Cornu Ammonis (CA)", + "Cornu ammonis 1 (CA1)", + "Cornu ammonis 2 (CA2)", + "Cornu ammonis 3 (CA3)", + "Dentate gyrus (DG)", + "Parahippocampal region (PHR)", + "Postrhinal cortex (POR)", + "Presubiculum (PrS)", + "Parasubiculum (PaS)", + "Perirhinal cortex (PER)", + "Perirhinal area 35 (PER35)", + "Perirhinal area 36 (PER36)", + "Entorhinal cortex (EC)", + "Medial entorhinal cortex (MEC)", + "Lateral entorhinal cortex (LEC)", + "Piriform cortex (PIR)", + "Piriform cortex, layer 1 (PIR1)", + "Piriform cortex, layer 2 (PIR2)", + "Piriform cortex, layer 3 (PIR3)", + "Cingulate region (CgR)", + "Cingulate cortex (Cg)", + "Cingulate area 1 (Cg1)", + "Cingulate area 2 (Cg2)", + "Retrosplenial cortex (RS)", + "Retrosplenial dysgranular area (RSD)", + "Retrosplenial granular area (RSG)", + "Insular region (INS)", + "Agranular insular cortex (AI)", + "Agranular insular cortex, ventral area (AI-v)", + "Agranular insular cortex dorsal area (AI-d)", + "Agranular insular cortex, posterior area (AI-p)", + "Dysgranular insular cortex (DI)", + "Granular insular cortex (GI)", + "Frontal region (Front)", + "Frontal association cortex (FrA)", + "Orbitofrontal cortex (Orb)", + "Medial orbital area (MO)", + "Ventral orbital area (VO)", + "Ventrolateral orbital area (VLO)", + "Lateral orbital area (LO)", + "Dorsolateral orbital area (DLO)", + "Mediofrontal cortex (MFC)", + "Prelimbic area (PrL)", + "Infralimbic area (IL)", + "Motor cortex (M)", + "Primary motor area (M1)", + "Secondary motor area (M2)", + "Frontal association area 3 (Fr3)", + "Parietal region (Par)", + "Somatosensory cortex (SS)", + "Primary somatosensory area (S1)", + "Primary somatosensory area, face representation (S1-f)", + "Primary somatosensory area, barrel field (S1-bf)", + "Primary somatosensory area, dysgranular zone (S1-dz)", + "Primary somatosensory area, forelimb representation (S1-fl)", + "Primary somatosensory area, hindlimb representation (S1-hl)", + "Primary somatosensory area, trunk representation (S1-tr)", + "Secondary somatosensory area (S2)", + "Posterior parietal cortex (PPC)", + "Parietal association cortex, medial area (mPPC)", + "Parietal association cortex, lateral area (lPPC)", + "Parietal association cortex, posterior area (PtP)", + "Occipital region (Oc)", + "Visual cortex (Vis)", + "Primary visual area (V1)", + "Secondary visual area (V2)", + "Secondary visual area, medial part (V2M)", + "Secondary visual area, lateral part (V2L)", + "Temporal region (Te)", + "Temporal association cortex (TeA)", + "Auditory cortex (Au)", + "Primary auditory area (Au1)", + "Secondary auditory area (Au2)", + "Secondary auditory area, dorsal part (Au2-d)", + "Secondary auditory area, ventral part (Au2-v)", + "Non-laminated pallium (N-LamP)", + "Claustrum (CLA)", + "Endopiriform nucleus (Endo)", + "Amygdaloid area, unspecified (Am-u)", + " Subpallium (SubPAL)", + "Striatum (Str)", + "Caudate putamen (CPu)", + "Nucleus accumbens (NAc)", + "Nucleus accumbens, core (NAc-c)", + "Nucleus accumbens, shell (NAc-sh)", + "Ventral striatal region, unspecified (VSR-u)", + "Pallidum (PAL)", + "Globus pallidus external (GPe)", + "Globus pallidus external, medial part (GPe-m)", + "Globus pallidus external, lateral part (GPe-l)", + "Entopeduncular nucleus (EP)", + "Ventral pallidum (VP)", + "Basal forebrain region (BRF)", + "Basal forebrain region, unspecified (BFR-u)", + "Bed nucleus of the stria terminalis (BNST)", + "Septal region (Sep)", + "Subthalamic nucleus (STh)", + "Diencephalon (Dien)", + "Prethalamus (Thal-Pre)", + "Reticular (pre)thalamic nucleus (RT)", + "Reticular (pre)thalamic nucleus, unspecified (RT-u)", + "Reticular (pre)thalamic nucleus, auditory segment (RT-a)", + "Zona incerta (ZI)", + "Zona incerta, dorsal part (ZI-d)", + "Zona incerta, ventral part (ZI-v)", + "Zona incerta, rostral part (ZI-r)", + "Zona incerta, caudal part (ZI-c)", + "Zona incerta, A13 dopamine cells (ZI-A13)", + "Zona incerta, A11 dopamine cells (ZI-A11)", + "Fields of Forel (FoF)", + "Pregeniculate nucleus (PrG)", + "Subgeniculate nucleus (SubG)", + "Intergeniculate leaflet (IGL)", + "Epithalamus (Thal-EPI)", + "Lateral habenular nucleus (LHb)", + "Medial habenular nucleus (MHb)", + "Nucleus of the stria medullaris (SMn)", + "Pineal gland (PG)", + "Dorsal thalamus (Thal-D)", + "Anterior nuclei of the dorsal thalamus (ANT)", + "Anterodorsal thalamic nucleus (AD)", + "Anteroventral thalamic nucleus (AV)", + "Anteroventral thalamic nucleus, dorsomedial part (AV-dm)", + "Anteroventral thalamic nucleus, ventrolateral part (AV-vl)", + "Anteromedial thalamic nucleus (AM)", + "Interanteromedial thalamic nucleus (IAM)", + "Paraventricular thalamic nuclei (anterior and posterior) (PV)", + "Intermediodorsal thalamic nucleus (IMD)", + "Parataenial thalamic nucleus (PT)", + "Subparafascicular nucleus (SPF)", + "Posterior intralaminar nucleus (PIL)", + "Ventral midline group of the dorsal thalamus (V-MID)", + "Rhomboid thalamic nucleus (Rh)", + "Reuniens thalamic nucleus (Re)", + "Retroreuniens thalamic nucleus (RRe)", + "Xiphoid thalamic nucleus (Xi)", + "Mediodorsal nucleus of the dorsal thalamus (MD)", + "Mediodorsal thalamic nucleus, lateral part (MD-l)", + "Mediodorsal thalamic nucleus, central part (MD-c)", + "Mediodorsal thalamic nucleus, medial part (MD-m)", + "Ventral nuclei of the dorsal thalamus (VENT)", + "Ventral anterior thalamic nucleus (VA)", + "Ventromedial thalamic nucleus (VM)", + "Ventrolateral thalamic nucleus (VL)", + "Angular thalamic nucleus (Ang)", + "Ventral posterior thalamic nucleus (VPN)", + "Ventral posteromedial thalamic nucleus (VPM)", + "Ventral posterolateral thalamic nucleus (VPL)", + "Ventral posterior nucleus of the thalamus, parvicellular part (VP-pc)", + "Submedius thalamic nucleus (SMT)", + "Intralaminar nuclei of the dorsal thalamus (ILM)", + "Paracentral thalamic nucleus (PCN)", + "Central medial thalamic nucleus (CM)", + "Central lateral thalamic nucleus (CL)", + "Parafascicular thalamic nucleus (PF)", + "Ethmoid-Limitans nucleus (Eth)", + "Posterior complex of the dorsal thalamus (PoC)", + "Posterior thalamic nucleus (Po)", + "Posterior thalamic nuclear group, triangular part (Po-t)", + "Lateral posterior (pulvinar) complex of the dorsal thalamus (LP)", + "Lateral posterior thalamic nucleus, mediorostral part (LP-mr)", + "Lateral posterior thalamic nucleus, mediocaudal part (LP-mc)", + "Lateral posterior thalamic nucleus, lateral part (LP-l)", + "Laterodorsal thalamic nuclei of the dorsal thalamus (LD)", + "Laterodorsal thalamic nucleus, dorsomedial part (LD-dm)", + "Laterodorsal thalamic nucleus, ventrolateral part (LD-vl)", + "Dorsal lateral geniculate nucleus (DLG)", + "Medial geniculate complex of the dorsal thalamus (MG)", + "Medial geniculate body, ventral division (MG-v)", + "Medial geniculate body, dorsal division (MG-d)", + "Medial geniculate body, marginal zone (MG-mz)", + "Medial geniculate body, medial division (MG-m)", + "Medial geniculate body, suprageniculate nucleus (MG-sg)", + "Hypothalamus (HY)", + "Hypothalamic region, unspecified (HTh-u)", + "Pretectum (PreT)", + "Pretectal region (PRT)", + "Nucleus sagulum (Sag)", + "Mesencephalon (Mes)", + "Midbrain (MB)", + "Tectum (Tc)", + "Inferior colliculus (IC)", + "Inferior colliculus, dorsal cortex (DCIC)", + "Inferior colliculus, central nucleus (CNIC)", + "Inferior colliculus, external cortex (ECIC)", + "Superior colliculus (Su)", + "Superficial gray layer of the superior colliculus (SuG)", + "Deeper layers of the superior colliculus (SuD)", + "Tegmentum (Tg)", + "Substantia nigra (SN)", + "Substantia nigra, reticular part (SN-r)", + "Substantia nigra, compact part (SN-c)", + "Substantia nigra, lateral part (SN-l)", + "Ventral tegmental area (VTA)", + "Peripeduncular nucleus (PP)", + "Interpeduncular nucleus (IP)", + "Periaqueductal gray (PAG)", + "Brainstem, unspecified (BS-u)", + "Rhombencephalon (Rho)", + "Metencephalon (Met)", + "Pontine nuclei (Pn)", + "Cerebellum (Cb)", + "Molecular cell layer of the cerebellum (Cb-m)", + "Cerebellum, unspecified (Cb-u)", + "Myelencephalon (Myel)", + "Cochlear nucleus, ventral part (VCN)", + "Ventral cochlear nucleus, anterior part (AVCN)", + "Ventral cochlear nucleus, posterior part (PVCN)", + "Ventral cochlear nucleus, cap area (Cap)", + "Ventral cochlear nucleus, granule cell layer (GCL)", + "Cochlear nucleus, dorsal part (DCN)", + "Dorsal cochlear nucleus, molecular layer (DCNM)", + "Dorsal cochlear nucleus, fusiform and granule layer (DCNFG)", + "Dorsal cochlear nucleus, deep core (DCND)", + "Spinal trigeminal nucleus (Sp5n)", + "Periventricular gray (PVG)", + "Superior olivary complex (SO)", + "Nucleus of the trapezoid body (NTB)", + "Superior paraolivary nucleus (SPN)", + "Medial superior olive (MSO)", + "Lateral superior olive (LSO)", + "Superior periolivary region (SPR)", + "Ventral periolivary nuclei (VPO)", + "Nuclei of the lateral lemniscus (NLL)", + "Lateral lemniscus, ventral nucleus (VLL)", + "Lateral lemniscus, intermediate nucleus (ILL)", + "Lateral lemniscus, dorsal nucleus (DLL)", + "Inferior olive (IO)", + "Ventricular system (V)", + "ventricular system, unspecified (V-u)", + "4th ventricle (4V)", + "central canal (CC)", + "spinal cord (SpC)", + "Inner ear (IE)", + "vestibular apparatus (VeA)", + "cochlea (Co)", + "cochlear nerve (8cn)", + "vestibular nerve (8vn)", + "spiral ganglion (SpG)" + ], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + }, + "targeted_x": { + "$id": "#root/electrode_groups/items/targeted_x", + "title": "targeted_x", + "type": "number", + "description": "Medial/Latetal", + "examples": [2.6], + "default": 0.0 + }, + "targeted_y": { + "$id": "#root/electrode_groups/items/targeted_y", + "title": "targeted_y", + "type": "number", + "description": "Anterior/Posterior", + "examples": [-3.8], + "default": 0.0 + }, + "targeted_z": { + "$id": "#root/electrode_groups/items/targeted_z", + "title": "targeted_z", + "type": "number", + "description": "Ventral/Dorsal", + "examples": [0], + "default": 0 + }, + "units": { + "$id": "#root/electrode_groups/items/units", + "title": "units", + "type": "string", + "default": "mm", + "examples": [ + "pm", + "nm", + "μm", + "mm", + "cm", + "in", + "yd", + "ft" + ], + "pattern": "^(.|\\s)*\\S(.|\\s)*$" + } + } + } + }, + "ntrode_electrode_group_channel_map": { + "$id": "#root/ntrode_electrode_group_channel_map", + "title": "ntrode_electrode_group_channel_map", + "type": "array", + "default": [], + "items": { + "$id": "#root/ntrode_electrode_group_channel_map/items", + "title": "Items", + "type": "object", + "required": ["ntrode_id", "electrode_group_id", "bad_channels", "map"], + "properties": { + "ntrode_id": { + "$id": "#root/ntrode_electrode_group_channel_map/items/ntrode_id", + "title": "ntrode_id", + "type": "integer", + "examples": [1], + "default": 0 + }, + "electrode_group_id": { + "$id": "#root/ntrode_electrode_group_channel_map/items/electrode_group_id", + "title": "electrode_group_id", + "type": "integer", + "examples": [0], + "default": 0 + }, + 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42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127], + "enum": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127], + "minimum": 0, + "default": 126 + }, + "127": { + "$id": "#root/ntrode_electrode_group_channel_map/items/map/127", + "title": "127", + "type": "integer", + "examples": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127], + "enum": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127], + "minimum": 0, + "default": 127 + } + } + } + } + } + } + } + } + \ No newline at end of file diff --git a/src/spikegadgets_to_nwb/tests/test_convert.py b/src/spikegadgets_to_nwb/tests/integration_tests/__init__.py similarity index 100% rename from src/spikegadgets_to_nwb/tests/test_convert.py rename to src/spikegadgets_to_nwb/tests/integration_tests/__init__.py diff --git a/src/spikegadgets_to_nwb/tests/integration_tests/test_metadata_validation.py b/src/spikegadgets_to_nwb/tests/integration_tests/test_metadata_validation.py new file mode 100644 index 0000000..4d9d904 --- /dev/null +++ b/src/spikegadgets_to_nwb/tests/integration_tests/test_metadata_validation.py @@ -0,0 +1,190 @@ +import pytest +import os +from spikegadgets_to_nwb.metadata_validation import ( + validate, +) +from spikegadgets_to_nwb.tests.test_data.test_metadata_dict_samples import ( + basic_data, + basic_data_with_optional_arrays, + empty_experimenter_name, + string_as_experimenter_name, + empty_lab, + empty_institution, + empty_experiment_description, + empty_session_description, + empty_session_id, + empty_keywords, + keywords_array_with_empty_item, + not_array_keywords, + empty_subject, + subject_with_empty_values, + subject_with_invalid_sex, + subject_with_invalid_date, + empty_data_acq_device, + data_acq_device_with_no_values, + empty_units, + invalid_times_period_multiplier, + invalid_raw_data_to_volts, + invalid_default_header_file_path, + empty_device_name, + basic_ntrode_electrode_group_channel_map, +) + + +@pytest.mark.parametrize("metadata", [(None), ("")]) +def test_metadata_validation_only_accepts_right_data_type(metadata): + with pytest.raises(AssertionError) as e: + validate(metadata) + + +@pytest.mark.parametrize("metadata", [(basic_data), (basic_data_with_optional_arrays)]) +def test_metadata_validation_verification_on_valid_data(metadata): + is_valid, errors = validate(metadata) + + assert is_valid, "".join(errors) + + +@pytest.mark.parametrize( + "metadata, key, expected", + [ + (empty_experimenter_name, "experimenter_name", ["[] is too short"]), + ( + string_as_experimenter_name, + "experimenter_name", + [ + "'' is not of type 'array'", + ], + ), + (empty_lab, "lab", ["does not match"]), + (empty_institution, "institution", ["does not match"]), + ( + empty_experiment_description, + "experiment_description", + ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"], + ), + ( + empty_session_description, + "session_description", + ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"], + ), + ( + empty_session_id, + "session_id", + ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"], + ), + ( + empty_keywords, + "keywords", + [ + "[] is too short", + ], + ), + ( + keywords_array_with_empty_item, + "keywords", + [ + "", + ], + ), + (not_array_keywords, "keywords", ["is not of type 'array'"]), + ( + subject_with_empty_values, + "subject1", + [ + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "is not one of ['M', 'F', 'U', 'O']", + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "-1 is less than the minimum of 0", + "does not match '(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d\\\\.\\\\d+)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d)'", + ], + ), + ( + empty_subject, + "subject", + [ + "'description' is a required property", + "'genotype' is a required property", + "'sex' is a required property", + "'species' is a required property", + "'subject_id' is a required property", + "'weight' is a required property", + "'date_of_birth' is a required property", + ], + ), + (subject_with_invalid_sex, "subject", ["is not one of ['M', 'F', 'U', 'O']"]), + ( + subject_with_invalid_date, + "subject", + [ + "'2023-01-04' does not match '(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d\\\\.\\\\d+)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d)'" + ], + ), + ( + data_acq_device_with_no_values, + "data_acq_device1", + [ + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'", + ], + ), + (empty_data_acq_device, "data_acq_device", ["[] is too short"]), + ( + empty_units, + "units", + [ + "'analog' is a required property", + "'behavioral_events' is a required property", + ], + ), + ( + invalid_times_period_multiplier, + "times_period_multiplier", + [ + "'a' is not of type 'number'", + ], + ), + ( + invalid_raw_data_to_volts, + "raw_data_to_volts", + ["'a' is not of type 'number'"], + ), + ( + invalid_default_header_file_path, + "default_header_file_path", + ["None is not of type 'string'"], + ), + (empty_device_name, "device_name", ["'name' is a required property"]), + ( + basic_ntrode_electrode_group_channel_map, + "ntrode_electrode_group_channel_map", + ( + [ + "'a' is not of type 'integer'", + "'z' is not of type 'integer'", + "'z' is not of type 'integer'", + "'0' is not of type 'integer'", + "'0' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]", + "'t' is not of type 'integer'", + "'t' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]", + "'a' is not of type 'integer'", + "'a' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]", + "-3 is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]", + "-3 is less than the minimum of 0", + ] + ), + ), + ], +) +def test_metadata_validation_verification_on_invalid_data(metadata, key, expected): + is_valid, errors = validate(metadata) + + assert len(errors) == len(expected), f"Not all the errors are occurring in - {key}" + assert not is_valid, f"{key} should be invalid" + for index, error in enumerate(errors): + assert ( + expected[index] in error + ), f"Expected error not found - ${expected[index]}" diff --git a/src/spikegadgets_to_nwb/tests/test_data/test_metadata.yml b/src/spikegadgets_to_nwb/tests/test_data/test_metadata.yml index 21ec96b..f56fa4f 100644 --- a/src/spikegadgets_to_nwb/tests/test_data/test_metadata.yml +++ b/src/spikegadgets_to_nwb/tests/test_data/test_metadata.yml @@ -56,34 +56,27 @@ associated_files: - name: associated1.txt description: good file path: path/ - task_epochs: - - 1 + task_epochs: 1 - name: associated2.txt description: good file path: path/ - task_epochs: - - 2 + task_epochs: 2 associated_video_files: - name: video1 camera_id: 0 - task_epochs: - - 1 + task_epochs: 1 - name: video3 camera_id: 0 - task_epochs: - - 3 + task_epochs: 3 - name: video5 camera_id: 0 - task_epochs: - - 5 + task_epochs: 5 - name: video2 camera_id: 1 - task_epochs: - - 2 + task_epochs: 2 - name: video4 camera_id: 1 - task_epochs: - - 2 + task_epochs: 2 units: analog: "-1" behavioral_events: "-1" diff --git a/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py new file mode 100644 index 0000000..6cad848 --- /dev/null +++ b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py @@ -0,0 +1,212 @@ +import pytest +import copy + +basic_data = { + "experimenter_name": ["michael jackson"], + "lab": "Loren Frank Lab", + "institution": "University of California, San Francisco", + "experiment_description": "making of thriller", + "session_description": "make an album like the nutcracker", + "session_id": "6", + "keywords": ["best"], + "subject": { + "description": "Long-Evans Rat", + "genotype": "Wild Type", + "sex": "M", + "species": "Rattus norvegicus", + "subject_id": "1", + "date_of_birth": "2023-07-24T00:00:00.000Z", + "weight": 100, + }, + "data_acq_device": [ + { + "name": "SpikeGadgets", + "system": "SpikeGadgets", + "amplifier": "Intan", + "adc_circuit": "Intan", + } + ], + "cameras": [], + "tasks": [], + "associated_files": [], + "associated_video_files": [], + "units": {"analog": "1", "behavioral_events": "1"}, + "times_period_multiplier": 1, + "raw_data_to_volts": 1, + "default_header_file_path": "epic/michaeljackson/thriller", + "behavioral_events": [], + "device": {"name": ["Trodes"]}, + "electrode_groups": [], + "ntrode_electrode_group_channel_map": [], +} + +basic_data_with_optional_arrays = { + "experimenter_name": ["michael jackson"], + "lab": "Loren Frank Lab", + "institution": "University of California, San Francisco", + "experiment_description": "making of thriller", + "session_description": "make an album like the nutcracker", + "session_id": "6", + "keywords": ["best"], + "subject": { + "description": "Long-Evans Rat", + "genotype": "Wild Type", + "sex": "M", + "species": "Rattus norvegicus", + "subject_id": "1", + "date_of_birth": "2023-07-24T00:00:00.000Z", + "weight": 100, + }, + "data_acq_device": [ + { + "name": "SpikeGadgets", + "system": "SpikeGadgets", + "amplifier": "Intan", + "adc_circuit": "Intan", + } + ], + "cameras": [ + { + "id": 10, + "meters_per_pixel": 1, + "manufacturer": "Epic Record", + "model": "555", + "lens": "MJ lens", + "camera_name": "MJ cam", + }, + ], + "tasks": [], + "associated_files": [ + { + "name": "Michael Jackson", + "description": "Thriller25", + "path": "Hard work", + "task_epochs": 0, + }, + { + "name": "Michael Jackson2", + "description": "HIStory", + "path": "Making/a/statement", + "task_epochs": 1, + }, + ], + "associated_video_files": [ + { + "name": "Michael Jackson", + "camera_id": 1, + "task_epochs": 1, + } + ], + "units": {"analog": "1", "behavioral_events": "1"}, + "times_period_multiplier": 1, + "raw_data_to_volts": 1, + "default_header_file_path": "epic/michaeljackson/thriller", + "behavioral_events": [ + { + "description": "Din555", + "name": "M. Joe Jackson", + } + ], + "device": {"name": ["Trodes"]}, + "electrode_groups": [], + "ntrode_electrode_group_channel_map": [], +} + +empty_experimenter_name = copy.deepcopy(basic_data) +empty_experimenter_name["experimenter_name"] = [] + +string_as_experimenter_name = copy.deepcopy(basic_data) +string_as_experimenter_name["experimenter_name"] = "" + +empty_lab = copy.deepcopy(basic_data) +empty_lab["lab"] = "" + +empty_institution = copy.deepcopy(basic_data) +empty_institution["institution"] = "" + +empty_experiment_description = copy.deepcopy(basic_data) +empty_experiment_description["experiment_description"] = "" + +empty_session_description = copy.deepcopy(basic_data) +empty_session_description["session_description"] = "" + +empty_session_id = copy.deepcopy(basic_data) +empty_session_id["session_id"] = "" + +empty_keywords = copy.deepcopy(basic_data) +empty_keywords["keywords"] = [] + +keywords_array_with_empty_item = copy.deepcopy(basic_data) +keywords_array_with_empty_item["keywords"] = [""] + +not_array_keywords = copy.deepcopy(basic_data) +not_array_keywords["keywords"] = "test" + +subject_with_empty_values = copy.deepcopy(basic_data) +subject_with_empty_values["subject"] = { + "description": "", + "genotype": "", + "sex": "", + "species": "", + "subject_id": "", + "date_of_birth": "", + "weight": -1, +} + +empty_subject = copy.deepcopy(basic_data) +empty_subject["subject"] = {} + +subject_with_invalid_sex = copy.deepcopy(basic_data) +subject_with_invalid_sex["subject"] = { + "description": "Long-Evans Rat", + "genotype": "Wild Type", + "sex": "m", + "species": "Rattus norvegicus", + "subject_id": "1", + "date_of_birth": "2023-07-24T00:00:00.000Z", + "weight": 100, +} + +subject_with_invalid_date = copy.deepcopy(basic_data) +subject_with_invalid_date["subject"] = { + "description": "Long-Evans Rat", + "genotype": "Wild Type", + "sex": "M", + "species": "Rattus norvegicus", + "subject_id": "1", + "date_of_birth": "2023-01-04", + "weight": 100, +} + +data_acq_device_with_no_values = copy.deepcopy(basic_data) +data_acq_device_with_no_values["data_acq_device"] = [ + {"name": "", "system": "", "amplifier": "", "adc_circuit": ""} +] + +empty_data_acq_device = copy.deepcopy(basic_data) +empty_data_acq_device["data_acq_device"] = [] + +empty_units = copy.deepcopy(basic_data) +empty_units["units"] = {} + +invalid_times_period_multiplier = copy.deepcopy(basic_data) +invalid_times_period_multiplier["times_period_multiplier"] = "a" + +invalid_raw_data_to_volts = copy.deepcopy(basic_data) +invalid_raw_data_to_volts["raw_data_to_volts"] = "a" + +invalid_default_header_file_path = copy.deepcopy(basic_data) +invalid_default_header_file_path["default_header_file_path"] = None + +empty_device_name = copy.deepcopy(basic_data) +empty_device_name["device"] = {} + +basic_ntrode_electrode_group_channel_map = copy.deepcopy(basic_data) +basic_ntrode_electrode_group_channel_map["ntrode_electrode_group_channel_map"] = [ + { + "ntrode_id": "a", + "electrode_group_id": "z", + "bad_channels": ["z"], + "map": {"0": "0", "1": "t", "2": "a", "3": -3}, + } +] diff --git a/src/spikegadgets_to_nwb/tests/test_data/test_metadata_probe_reconfig.yml b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_probe_reconfig.yml index eaec1b9..9f731d5 100644 --- a/src/spikegadgets_to_nwb/tests/test_data/test_metadata_probe_reconfig.yml +++ b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_probe_reconfig.yml @@ -56,34 +56,27 @@ associated_files: - name: associated1.txt description: good file path: path/ - task_epochs: - - 1 + task_epochs: 1 - name: associated2.txt description: good file path: path/ - task_epochs: - - 2 + task_epochs: 2 associated_video_files: - name: video1 camera_id: 0 - task_epochs: - - 1 + task_epochs: 1 - name: video3 camera_id: 0 - task_epochs: - - 3 + task_epochs: 3 - name: video5 camera_id: 0 - task_epochs: - - 5 + task_epochs: 5 - name: video2 camera_id: 1 - task_epochs: - - 2 + task_epochs: 2 - name: video4 camera_id: 1 - task_epochs: - - 2 + task_epochs: 2 units: analog: "-1" behavioral_events: "-1" diff --git a/src/spikegadgets_to_nwb/tests/test_convert_analog.py b/src/spikegadgets_to_nwb/tests/unit_tests/__init__.py similarity index 100% rename from src/spikegadgets_to_nwb/tests/test_convert_analog.py rename to src/spikegadgets_to_nwb/tests/unit_tests/__init__.py diff --git a/src/spikegadgets_to_nwb/tests/unit_tests/conftest.py b/src/spikegadgets_to_nwb/tests/unit_tests/conftest.py new file mode 100644 index 0000000..e2669e4 --- /dev/null +++ b/src/spikegadgets_to_nwb/tests/unit_tests/conftest.py @@ -0,0 +1,31 @@ +import pytest +import os +from xml.etree import ElementTree +from spikegadgets_to_nwb import convert_rec_header + + +# fixtures +@pytest.fixture +def path() -> str: + path = os.path.dirname(os.path.abspath(__file__)) + return path + + +@pytest.fixture +def default_test_xml_tree() -> ElementTree: + """Function to return a default xml tree for initial nwb generation + + Returns + ------- + ElementTree + root xml tree for initial nwb generation + """ + # running in a git action if DOWNLOAD_DIR' in os.environ == true; else running locally + rec_path = ( + os.environ.get("DOWNLOAD_DIR") + if "DOWNLOAD_DIR" in os.environ + else f"{path}../test_data" + ) + trodesconf_file = f"{rec_path}/20230622_155936.rec" + rec_header = convert_rec_header.read_header(trodesconf_file) + return rec_header diff --git a/src/spikegadgets_to_nwb/tests/test_convert_dios.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert.py similarity index 100% rename from src/spikegadgets_to_nwb/tests/test_convert_dios.py rename to src/spikegadgets_to_nwb/tests/unit_tests/test_convert.py diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_analog.py similarity index 100% rename from src/spikegadgets_to_nwb/tests/test_convert_intervals.py rename to src/spikegadgets_to_nwb/tests/unit_tests/test_convert_analog.py diff --git a/src/spikegadgets_to_nwb/tests/test_convert_position.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_dios.py similarity index 100% rename from src/spikegadgets_to_nwb/tests/test_convert_position.py rename to src/spikegadgets_to_nwb/tests/unit_tests/test_convert_dios.py diff --git a/src/spikegadgets_to_nwb/tests/test_convert_ephys.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_ephys.py similarity index 95% rename from src/spikegadgets_to_nwb/tests/test_convert_ephys.py rename to src/spikegadgets_to_nwb/tests/unit_tests/test_convert_ephys.py index 5ccb89a..419e042 100644 --- a/src/spikegadgets_to_nwb/tests/test_convert_ephys.py +++ b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_ephys.py @@ -1,14 +1,15 @@ import os import pynwb +import pytest + from spikegadgets_to_nwb.convert_ephys import add_raw_ephys from spikegadgets_to_nwb import convert_yaml, convert_rec_header -from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree MICROVOLTS_PER_VOLT = 1e6 -path = os.path.dirname(os.path.abspath(__file__)) -def test_add_raw_ephys_single_rec(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_add_raw_ephys_single_rec(path, default_test_xml_tree): # load metadata yml and make nwb file metadata_path = ( path + "/test_data/test_metadata.yml" @@ -101,7 +102,8 @@ def test_add_raw_ephys_single_rec(): os.remove(filename) -def test_add_raw_ephys_single_rec_probe_configuration(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_add_raw_ephys_single_rec_probe_configuration(path, default_test_xml_tree): # load metadata yml and make nwb file metadata_path = path + "/test_data/test_metadata_probe_reconfig.yml" probe_metadata = [ @@ -183,7 +185,8 @@ def test_add_raw_ephys_single_rec_probe_configuration(): os.remove(filename) -def test_add_raw_ephys_two_epoch(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_add_raw_ephys_two_epoch(path, default_test_xml_tree): # load metadata yml and make nwb file metadata_path = path + "/test_data/test_metadata.yml" probe_metadata = [ diff --git a/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_intervals.py new file mode 100644 index 0000000..e69de29 diff --git a/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_position.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_position.py new file mode 100644 index 0000000..e69de29 diff --git a/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_rec_header.py similarity index 69% rename from src/spikegadgets_to_nwb/tests/test_convert_rec_header.py rename to src/spikegadgets_to_nwb/tests/unit_tests/test_convert_rec_header.py index 441c202..cdf1953 100644 --- a/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py +++ b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_rec_header.py @@ -1,40 +1,16 @@ -from spikegadgets_to_nwb import convert_yaml, convert_rec_header +import pytest +import os +from spikegadgets_to_nwb import convert_yaml, convert_rec_header from pynwb.file import NWBFile from ndx_franklab_novela import HeaderDevice from xml.etree import ElementTree -import os - -path = os.path.dirname(os.path.abspath(__file__)) - - -def default_test_xml_tree() -> ElementTree: - """Function to return a default xml tree for intial nwb generation - - Returns - ------- - ElementTree - root xml tree for intial nwb generation - """ - try: - # running on github - trodesconf_file = ( - os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.rec" - ) # "/test_data/reconfig_probeDevice.trodesconf" - rec_header = convert_rec_header.read_header(trodesconf_file) - except: - # running locally - trodesconf_file = ( - path + "/test_data/20230622_155936.rec" - ) # "/test_data/reconfig_probeDevice.trodesconf" - rec_header = convert_rec_header.read_header(trodesconf_file) - return rec_header - -def test_add_header_device(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_add_header_device(path, default_test_xml_tree): # Set up test data - metadata_path = path + "/test_data/test_metadata.yml" + metadata_path = path + "/../test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree()) # Call the function to be tested @@ -44,7 +20,7 @@ def test_add_header_device(): convert_rec_header.add_header_device(nwbfile, recfile) except (TypeError, FileNotFoundError): # running locally - recfile = path + "/test_data/20230622_155936.rec" + recfile = path + "/../test_data/20230622_155936.rec" convert_rec_header.add_header_device(nwbfile, recfile) # Perform assertions to check the results diff --git a/src/spikegadgets_to_nwb/tests/test_convert_yaml.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_yaml.py similarity index 92% rename from src/spikegadgets_to_nwb/tests/test_convert_yaml.py rename to src/spikegadgets_to_nwb/tests/unit_tests/test_convert_yaml.py index 97370aa..ca66e2d 100644 --- a/src/spikegadgets_to_nwb/tests/test_convert_yaml.py +++ b/src/spikegadgets_to_nwb/tests/unit_tests/test_convert_yaml.py @@ -1,16 +1,15 @@ +import os +import pytest + from spikegadgets_to_nwb import convert_yaml, convert_rec_header from datetime import datetime from pynwb.file import Subject, ProcessingModule from ndx_franklab_novela import Probe, Shank, ShanksElectrode from hdmf.common.table import DynamicTable, VectorData -from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree - -import os - -path = os.path.dirname(os.path.abspath(__file__)) -def test_initial_nwb_creation(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_initial_nwb_creation(path, default_test_xml_tree): metadata_path = path + "/test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree()) @@ -31,7 +30,8 @@ def test_initial_nwb_creation(): assert len(nwb_file.devices) == 0 -def test_subject_creation(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_subject_creation(path, default_test_xml_tree): metadata_path = path + "/test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree()) @@ -47,7 +47,8 @@ def test_subject_creation(): assert isinstance(subject.date_of_birth, datetime) -def test_camera_creation(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_camera_creation(path, default_test_xml_tree): metadata_path = path + "/test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree()) @@ -61,7 +62,8 @@ def test_camera_creation(): assert cameras[name].manufacturer == "Allied Vision" -def test_acq_device_creation(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_acq_device_creation(path, default_test_xml_tree): metadata_path = path + "/test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree()) @@ -74,7 +76,8 @@ def test_acq_device_creation(): assert devices[name].adc_circuit == "Intan" -def test_electrode_creation(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_electrode_creation(path, default_test_xml_tree): # load metadata yml and make nwb file metadata_path = path + "/test_data/test_metadata.yml" probe_metadata = [ @@ -152,7 +155,8 @@ def test_electrode_creation(): assert list(nwbfile.electrodes.to_dataframe()["ref_elect_id"][:4]) == [0, 0, 0, 0] -def test_electrode_creation_reconfigured(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_electrode_creation_reconfigured(path, default_test_xml_tree): # load metadata yml and make nwb file metadata_path = path + "/test_data/test_metadata_probe_reconfig.yml" probe_metadata = [ @@ -231,7 +235,8 @@ def test_electrode_creation_reconfigured(): assert list(nwbfile.electrodes.to_dataframe()["hwChan"][-2:]) == ["115", "107"] -def test_add_tasks(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_add_tasks(path, default_test_xml_tree): # Set up test data metadata_path = path + "/test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) @@ -283,7 +288,8 @@ def test_add_tasks(): assert task_df["task_environment"][0] == task_metadata["task_environment"] -def test_add_associated_files(): +@pytest.mark.skip(reason="Sam needs add rec file access across all machine") +def test_add_associated_files(path, default_test_xml_tree): # Set up test data metadata_path = path + "/test_data/test_metadata.yml" metadata, _ = convert_yaml.load_metadata(metadata_path, []) diff --git a/src/spikegadgets_to_nwb/tests/unit_tests/test_metadata_validation.py b/src/spikegadgets_to_nwb/tests/unit_tests/test_metadata_validation.py new file mode 100644 index 0000000..003e858 --- /dev/null +++ b/src/spikegadgets_to_nwb/tests/unit_tests/test_metadata_validation.py @@ -0,0 +1,25 @@ +import copy +import datetime +from unittest.mock import MagicMock, patch +from spikegadgets_to_nwb.metadata_validation import ( + validate, + _get_nwb_json_schema_path, +) +from spikegadgets_to_nwb.tests.test_data import test_metadata_dict_samples + + +def test_path_to_json_schema_is_correct(): + path = _get_nwb_json_schema_path() + json_schema_file = "nwb_schema.json" + + assert json_schema_file in path + + +@patch("spikegadgets_to_nwb.metadata_validation._get_json_schema") +@patch("jsonschema.Draft202012Validator") +def test_verify_validation_called(jsonValidator, getSchema): + basic_test_data = copy.deepcopy(test_metadata_dict_samples.basic_data) + basic_test_data["subject"]["date_of_birth"] = datetime.datetime.now().isoformat() + validate(basic_test_data) + assert getSchema.call_count == 1 + assert jsonValidator.call_count == 1