[DATALAD] Recorded changes

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "rawdata/code/dandi-cli"]
+	path = rawdata/code/dandi-cli
+	url = https://github.com/dandi/dandi-cli.git
+[submodule "rawdata/code/python-neo"]
+	path = rawdata/code/python-neo
+	url = https://github.com/NeuralEnsemble/python-neo.git

rawdata/code/.gentoo/overlay/metadata/layout.conf

@@ -0,0 +1,2 @@
+masters = gentoo science
+auto-sync = false

rawdata/code/.gentoo/overlay/profiles/repo_name

@@ -0,0 +1 @@
+local

rawdata/code/.gentoo/overlay/sci-misc/mvmnda-study-code/metadata.xml

@@ -0,0 +1,11 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">TheChymera/mvmnda</remote-id>
+	</upstream>
+</pkgmetadata>

rawdata/code/.gentoo/overlay/sci-misc/mvmnda-study-code/mvmnda-study-code-99999.ebuild

@@ -0,0 +1,18 @@
+# Copyright 1999-2023 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Example data analysis code for NWB data converted from SpikeGLX"
+HOMEPAGE="https://github.com/TheChymera/mvmnda"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+
+DEPEND=""
+RDEPEND="
+	dev-python/spikeinterface
+	dev-python/python-dateutil
+	sci-biology/neuroconv
+"

rawdata/code/.gentoo/portage/make.conf

@@ -0,0 +1,19 @@
+COMMON_FLAGS="-O2 -pipe -march=native"
+# Comment the following out on systems with less than 8 threads
+MAKEOPTS="--jobs 8 --load-average 9"
+CFLAGS="${COMMON_FLAGS}"
+CXXFLAGS="${COMMON_FLAGS}"
+FCFLAGS="${COMMON_FLAGS}"
+FFLAGS="${COMMON_FLAGS}"
+
+# NOTE: This stage was built with the bindist Use flag enabled
+
+# This sets the language of build output to English.
+# Please keep this setting intact when reporting bugs.
+LC_MESSAGES=C
+
+USE="${USE} science"
+ACCEPT_LICENSE="*"
+
+# Needed in the container environment
+#FEATURES="-ipc-sandbox -network-sandbox -pid-sandbox"

rawdata/code/.gentoo/portage/package.accept_keywords/gen

@@ -0,0 +1,2 @@
+*/* ~amd64
+sci-misc/mvmnda-study-code **

rawdata/code/.gentoo/portage/package.mask/bugs

@@ -0,0 +1,2 @@
+# Not migrated to >=pandas-2.0.0 yet
+#>=dev-python/pandas-2.0.0

rawdata/code/.gentoo/portage/repos.conf/gentoo

@@ -0,0 +1,5 @@
+[gentoo]
+location = /var/db/repos/gentoo
+sync-type = git
+sync-uri = https://github.com/gentoo-mirror/gentoo.git
+sync-git-verify-commit-signature = yes

rawdata/code/.gentoo/portage/repos.conf/local

@@ -0,0 +1,2 @@
+[local]
+location = /var/db/repos/local

rawdata/code/.gentoo/portage/repos.conf/science

@@ -0,0 +1,5 @@
+[science]
+location = /var/db/repos/science
+sync-type = git
+sync-uri = https://anongit.gentoo.org/git/proj/sci.git
+priority = 7777

rawdata/code/Containerfile

@@ -0,0 +1,52 @@
+FROM docker.io/gentoo/portage:20240118 as portage
+FROM docker.io/gentoo/stage3:20240115
+
+# copy the entire portage volume in
+COPY --from=portage /var/db/repos/gentoo /var/db/repos/gentoo
+
+RUN emerge -v --noreplace dev-vcs/git
+RUN emerge -v1u portage
+
+# Pinned commits for the dependency tree state
+ARG gentoo_hash=3519e6c712f26cb361f43dc74bd96b27c6d04cac
+ARG science_hash=f9f093aa8035bb4656c98d054e00b5159e059153
+ARG FEATURES="-ipc-sandbox -network-sandbox -pid-sandbox"
+
+# This will be bound, and contents available outside of container
+RUN mkdir /outputs
+
+COPY .gentoo/portage/ /etc/portage/
+COPY .gentoo/overlay/ /var/db/repos/local/
+
+# Moving gentoo repo from default rsync to git
+RUN rm /var/db/repos/gentoo -rf
+
+# Disable auto-sync
+RUN sed -i /etc/portage/repos.conf/{gentoo,science} -e "s/sync-type *= *git/sync-type =/g"
+
+# Cloning manually to prevent vdb update, pinning state via git
+RUN REPO_URL=$(grep "^sync-uri" /etc/portage/repos.conf/gentoo | sed -e "s/sync-uri *= *//g"); mkdir -p /var/db/repos/gentoo; pushd /var/db/repos/gentoo; git clone ${REPO_URL} .; git fetch origin $gentoo_hash; git checkout $gentoo_hash; rm .git -rf; popd
+RUN REPO_URL=$(grep "^sync-uri" /etc/portage/repos.conf/science | sed -e "s/sync-uri *= *//g"); mkdir -p /var/db/repos/science; pushd /var/db/repos/science; git clone ${REPO_URL} .; git fetch origin $science_hash; git checkout $science_hash; rm .git -rf; popd
+
+# Remove sync-uri for consistency
+RUN sed -i /etc/portage/repos.conf/{gentoo,science} -e "/sync-uri/d"
+RUN sed -i /etc/portage/repos.conf/{gentoo,science} -e "/sync-git-verify-commit-signature/d"
+
+# Ensure Umask-safe permissions
+RUN chmod -R a+rX /var/db/repos/local*/
+
+# Make sure all CPU flags supported by the hardware are whitelisted
+# This only affects packages with handwritten assembly language optimizations, e.g. ffmpeg.
+# Removing it is safe, software will just not take full advantage of processor capabilities.
+#RUN emerge cpuid2cpuflags 
+#RUN echo "*/* $(cpuid2cpuflags)" > /etc/portage/package.use/00cpu-flags
+
+# Dynamically prepare manifest and go crazy.
+RUN my_ebuild=$(/bin/ls -1 /var/db/repos/local/sci-misc/*/*99999.ebuild) && \
+    ebuild "$my_ebuild"  manifest && \
+    emerge -v $(echo $my_ebuild | sed -e 's,.*/\([-_0-9a-zA-Z]*\)-99999.ebuild,\1,g') --autounmask-continue && \
+    rm -rf /var/cache/distfiles/
+
+#RUN my_ebuild=$(/bin/ls -1 /var/db/repos/local/sci-misc/*/*99999.ebuild) && \
+#    ebuild "$my_ebuild"  manifest
+#ENTRYPOINT ["/bin/bash"]

rawdata/code/Makefile

@@ -0,0 +1,91 @@
+# We must allow others exactly use our script without modification
+# Or its not replicable by others.
+#
+REGISTRY=docker.io
+REPOSITORY=centerforopenneuroscience
+
+IMAGE_NAME=mvmnda
+IMAGE_TAG=0.0.1
+
+FQDN_IMAGE=${REGISTRY}/${REPOSITORY}/${IMAGE_NAME}:${IMAGE_TAG}
+
+# PATH for scratch directory storing intermidiate results etc;
+# By default -- all data including intermediate results are under this folder (YODA!)
+#ifeq ($(SCRATCH_PATH),)
+#	SCRATCH_PATH = /var/tmp/mvmnda/
+#endif
+
+OCI_BINARY?=podman
+RELEASE_VERSION?=9999
+RESOLUTION?=9999 # specified in microns
+SING_BINARY?=singularity
+PACKAGE_NAME=mvmnda
+
+DISTFILE_CACHE_CMD :=
+
+check_defined = \
+    $(strip $(foreach 1,$1, \
+        $(call __check_defined,$1,$(strip $(value 2)))))
+__check_defined = \
+    $(if $(value $1),, \
+      $(error Undefined $1$(if $2, ($2))))
+
+ifeq ($(DISTFILE_CACHE_PATH),)
+    # If not set, don't add it as an option
+else
+    DISTFILE_CACHE_CMD =-v $(DISTFILE_CACHE_PATH):/var/cache/distfiles
+endif
+
+.PHONY: data
+data: clean
+	python reposit.py
+
+.PHONY: data-oci
+data-oci: clean
+	$(OCI_BINARY) run \
+		-it \
+		--rm \
+		-v ${PWD}/../..:/root/src/mvmnda \
+		--workdir /root/src/mvmnda/rawdata/code \
+		${FQDN_IMAGE} \
+		make data
+
+.PHONY: data-oci-interactive
+data-oci-interactive: clean
+	$(OCI_BINARY) run \
+		-it \
+		--rm \
+		-v ${PWD}/../..:/root/src/mvmnda \
+		--workdir /root/src/mvmnda/rawdata/code \
+		${FQDN_IMAGE} \
+		/bin/bash
+
+
+
+# Build data analysis container
+#.PHONY: oci-image-debug
+#oci-image:
+#	$(OCI_BINARY) build . $(DISTFILE_CACHE_CMD) \
+#		-it \
+#		-f Containerfile \
+#		-t ${FQDN_IMAGE}
+
+# Build data analysis container
+.PHONY: oci-image
+oci-image:
+	$(OCI_BINARY) build . $(DISTFILE_CACHE_CMD) \
+		-f Containerfile \
+		-t ${FQDN_IMAGE}
+
+# Push containers
+.PHONY: oci-push
+oci-push:
+	$(OCI_BINARY) push ${FQDN_IMAGE}
+
+# Push containers
+.PHONY: clean
+clean:
+	@rm -rf ABI-connectivity-data*
+
+
+

rawdata/code/bids_output/participants.json

@@ -0,0 +1,15 @@
+{
+    "subject_id": {
+        "Description": "Unique identifier of the subject"
+    },
+    "species": {
+        "Description": "The binomial species name from the NCBI Taxonomy"
+    },
+    "age": {
+        "Description": "Age of the participant at time of recording",
+        "Units": "days"
+    },
+    "sex": {
+        "Description": "Sex of participant"
+    }
+}

rawdata/code/bids_output/participants.tsv

@@ -0,0 +1,2 @@
+subject_id	species	age	sex
+sub-M388	Mus musculus	P90D	F

rawdata/code/bids_output/sub-M388/ses-20231120114021/ephys/channels.tsv

@@ -0,0 +1,394 @@
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rawdata/code/bids_output/sub-M388/ses-20231120114021/ephys/contacts.tsv

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+338	Neuropixel-Imec
+339	Neuropixel-Imec
+340	Neuropixel-Imec
+341	Neuropixel-Imec
+342	Neuropixel-Imec
+343	Neuropixel-Imec
+344	Neuropixel-Imec
+345	Neuropixel-Imec
+346	Neuropixel-Imec
+347	Neuropixel-Imec
+348	Neuropixel-Imec
+349	Neuropixel-Imec
+350	Neuropixel-Imec
+351	Neuropixel-Imec
+352	Neuropixel-Imec
+353	Neuropixel-Imec
+354	Neuropixel-Imec
+355	Neuropixel-Imec
+356	Neuropixel-Imec
+357	Neuropixel-Imec
+358	Neuropixel-Imec
+359	Neuropixel-Imec
+360	Neuropixel-Imec
+361	Neuropixel-Imec
+362	Neuropixel-Imec
+363	Neuropixel-Imec
+364	Neuropixel-Imec
+365	Neuropixel-Imec
+366	Neuropixel-Imec
+367	Neuropixel-Imec
+368	Neuropixel-Imec
+369	Neuropixel-Imec
+370	Neuropixel-Imec
+371	Neuropixel-Imec
+372	Neuropixel-Imec
+373	Neuropixel-Imec
+374	Neuropixel-Imec
+375	Neuropixel-Imec
+376	Neuropixel-Imec
+377	Neuropixel-Imec
+378	Neuropixel-Imec
+379	Neuropixel-Imec
+380	Neuropixel-Imec
+381	Neuropixel-Imec
+382	Neuropixel-Imec
+383	Neuropixel-Imec
+384	Neuropixel-Imec
+385	Neuropixel-Imec
+386	Neuropixel-Imec
+387	Neuropixel-Imec
+388	Neuropixel-Imec
+389	Neuropixel-Imec
+390	Neuropixel-Imec
+391	Neuropixel-Imec
+392	Neuropixel-Imec

rawdata/code/bids_output/sub-M388/ses-20231120114021/ephys/probes.tsv

@@ -0,0 +1,2 @@
+probe_id	type	description	manufacturer
+Neuropixel-Imec	unknown	"{""probe_type"": ""0"", ""probe_type_description"": ""NP1.0"", ""flex_part_number"": ""NP2_FLEX_0"", ""connected_base_station_part_number"": ""NP2_QBSC_00""}"	Imec

rawdata/code/bids_output/sub-M388/ses-20231120114021/ephys/sub-M388_ses-20231120114021.nwb

@@ -0,0 +1 @@
+../../../../../../.git/annex/objects/pF/1M/MD5E-s18608928083--27d8f877fbad3f65490eb2323fbc6603.nwb/MD5E-s18608928083--27d8f877fbad3f65490eb2323fbc6603.nwb

rawdata/code/bids_output/sub-M388/sessions.json

@@ -0,0 +1 @@
+{}

rawdata/code/bids_output/sub-M388/sessions.tsv

@@ -0,0 +1,2 @@
+session_id	comments
+ses-20231120114021	Auto-generated by neuroconv

rawdata/code/dandi-cli

@@ -0,0 +1 @@
+Subproject commit 96c395393eb4c1b1b04404445969e80e5e57bc2d

rawdata/code/nwb_to_bids.py

@@ -0,0 +1,213 @@
+from pynwb import NWBHDF5IO
+from pynwb.ecephys import ElectricalSeries
+from glob import glob
+import os
+import json
+import pandas as pd
+import shutil
+
+
+def extract_metadata(filepath: str) -> dict:
+
+    with NWBHDF5IO(filepath, load_namespaces=True) as io:
+        nwbfile = io.read()
+
+        subject = nwbfile.subject
+
+        probes = set([x.device for x in nwbfile.electrodes["group"][:]])
+
+
+        ess = [
+            x for x in nwbfile.objects.values()
+            if isinstance(x, ElectricalSeries)
+        ]
+
+        metadata = {
+            "general_ephys": {
+                "InstitutionName": nwbfile.institution,
+            },
+            "subject": {
+                "subject_id": "sub-" + subject.subject_id,
+                "species": subject.species,
+                "strain": subject.strain,
+                "birthday": subject.date_of_birth,
+                "age": subject.age,
+                "sex": subject.sex,
+            },
+            "session": {
+                "session_id": "ses-" + nwbfile.session_id,
+                "number_of_trials": len(nwbfile.trials) if nwbfile.trials else None,
+                "comments": nwbfile.session_description,
+            },
+            "probes": [
+                {
+                    "probe_id": probe.name,
+                    "type": "unknown",
+                    "description": probe.description,
+                    "manufacturer": probe.manufacturer,
+                }
+                for probe in probes
+            ],
+            "contacts": [
+                {
+                    "contact_id": contact.index[0],
+                    "probe_id": contact.group.iloc[0].device.name,
+                    #TODO "impedance": contact["imp"].iloc[0] if contact["imp"].iloc[0] > 0 else None,
+                    "location": contact["location"].iloc[0] if contact["location"].iloc[0] not in ("unknown",) else None,
+                }
+                for contact in nwbfile.electrodes
+            ],
+            "channels": [
+                {
+                    "channel_id": contact.index[0],
+                    "contact_id": contact.index[0],
+                    "type": "EXT",
+                    "unit": "V",
+                    "sampling_frequency": ess[0].rate,
+                    "gain": ess[0].conversion,
+                }
+                for contact in nwbfile.electrodes
+            ]
+        }
+    
+    return metadata
+
+def unique_list_of_dicts(data):
+    # Convert to set of tuples
+    unique_data = set(tuple(d.items()) for d in data)
+    
+    # Convert back to list of dictionaries
+    unique_list_of_dicts = [dict(t) for t in unique_data]
+    
+    return unique_list_of_dicts
+
+
+def drop_false_cols(df):
+    for col in df.columns:
+        if not any(df[col][:]):
+            df.drop(columns=[col], inplace=True)
+
+path = "../"
+#path = "/Volumes/Extreme Pro/neural_data/dandisets/000044"
+
+nwb_files = glob(path + "/sub-*/*.nwb")
+
+all_metadata = {x: extract_metadata(x) for x in nwb_files}
+
+# root
+
+out_path = "bids_output"
+
+#if not os.path.exists(out_path):
+#    os.mkdir(out_path)
+os.makedirs(out_path, exist_ok=True)
+
+# participants
+
+# create particiant table
+
+subjects = unique_list_of_dicts(
+    #[x["participant"] for x in all_metadata.values()]
+    [x["subject"] for x in all_metadata.values()]
+)
+
+df = pd.DataFrame(subjects)
+
+drop_false_cols(df)
+
+df.to_csv(os.path.join(out_path, "participants.tsv"), sep="\t", index=False)
+
+
+# create particiant json
+default_subjects_json = {
+    "subject_id": {"Description": "Unique identifier of the subject"},
+    "species": {"Description": "The binomial species name from the NCBI Taxonomy"},
+    "strain": {"Description": "Identifier of the strain"},
+    "birthdate": {"Description": "Day of birth of the participant in ISO8601 format"},
+    "age": {"Description": "Age of the participant at time of recording", "Units": "days"},
+    "sex": {"Description": "Sex of participant"},
+}
+
+subjects_json = {k: v for k, v in default_subjects_json.items() if k in df.columns}
+
+with open(os.path.join(out_path, "participants.json"), "w") as json_file:
+    json.dump(subjects_json, json_file, indent=4)
+
+
+# sessions
+
+default_session_json = {
+   "session_quality": {
+      "LongName": "General quality of the session",
+      "Description": "Quality of the session",
+      "Levels": {
+         "Bad": "Bad quality, should not be considered for further analysis",
+         "ok": "Ok quality, can be considered for further analysis with care",
+         "good": "Good quality, should be used for analysis",
+         "Excellent": "Excellent quality, extraordinarily good session",
+      }
+   },
+   "data_quality": {
+      "LongName": "Quality of the recorded signals",
+      "Description": "Quality of the recorded signals",
+      "Levels": {
+         "Bad": "Bad quality, should not be considered for further analysis",
+         "ok": "Ok quality, can be considered for further analysis with care",
+         "good": "Good quality, should be used for analysis",
+         "Excellent": "Excellent quality, extraordinarily good session",
+      },
+   },
+   "number_of_trials": {
+      "LongName": "Number of trials in this session",
+      "Description": "Count of attempted trials in the session (integer)",
+   },
+   "comment": {
+      "LongName": "General comments",
+      "Description": "General comments by the experimenter on the session",
+   },
+}
+
+for subject in subjects:
+    subject_id = subject["subject_id"]
+
+    os.makedirs(os.path.join(out_path, subject_id), exist_ok=True)
+
+    for metadata in all_metadata.values():
+        sessions = [
+            x["session"] for x in all_metadata.values() if
+            x["subject"]["subject_id"] == subject_id
+        ]
+
+        df = pd.DataFrame(sessions)
+        drop_false_cols(df)
+
+        df.to_csv(os.path.join(out_path, subject_id, "sessions.tsv"), sep="\t", index=False)
+
+        session_json = {k: v for k, v in default_session_json.items() if k in df.columns}
+
+        with open(os.path.join(out_path, subject_id, "sessions.json"), "w") as json_file:
+            json.dump(session_json, json_file, indent=4)
+
+# contacts, probes, and channels
+
+for metadata in all_metadata.values():
+
+    session_id = metadata["session"]["session_id"]
+    subject_id = metadata["subject"]["subject_id"]
+
+    os.makedirs(os.path.join(out_path, subject_id, session_id), exist_ok=True)
+    os.makedirs(os.path.join(out_path, subject_id, session_id, "ephys"), exist_ok=True)
+
+    for var in ("contacts", "probes", "channels"):
+        df = pd.DataFrame(metadata[var])
+        drop_false_cols(df)
+        df.to_csv(os.path.join(out_path, subject_id, session_id, "ephys", var + ".tsv"), sep="\t", index=False)
+
+
+# Actually copy the NWB files
+
+for nwb_file in nwb_files:
+    nwb_file_bids_path = f"{out_path}/{metadata['subject']['subject_id']}/{metadata['session']['session_id']}/ephys/{metadata['subject']['subject_id']}_{metadata['session']['session_id']}.nwb"
+    shutil.copyfile(nwb_file, nwb_file_bids_path)
+
+

rawdata/code/python-neo

@@ -0,0 +1 @@
+Subproject commit 4ef280130be875263878d5e55dbf7ee40f950c9b

rawdata/code/reposit.py

@@ -3,21 +3,52 @@ from dateutil import tz
 from pathlib import Path
 from neuroconv.converters import SpikeGLXConverterPipe
 import json
+import re
+import pynwb
+import datetime
 
-dir_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/Ach_DualPixel_7_14_23/Ach_DualPixel_7_14_23_g0"
+dir_path = "../../sourcedata/sub-M388/M388-2023-11-20_2_g0"
 #dir_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/sub-pixelfiber/M387-2023-10-20_g0"
 #dir_path = "../../sourcedata/M387-2023-10-20_g0"
 converter = SpikeGLXConverterPipe(folder_path=dir_path)
 
+m = re.match(".*?sub-(?P<subject>[a-zA-z0-9]+).*?","../../sourcedata/sub-M388/M388-2023-11-20_2_g0")
+# add logic to fall back on expkeys
+
+subject = m.groupdict()["subject"]
+
 # Extract what metadata we can from the source files
 metadata = converter.get_metadata()
 
-# The following doesn't work as per the guide ( https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/recording/spikeglx.html#single-stream ), apparently no session_start_time is read in:
-#session_start_time = metadata["NWBFile"]["session_start_time"].replace(tzinfo=tz.gettz("US/Pacific"))
-# So we do:
-session_start_time = datetime.now(tz.tzlocal())
+session_start_time = metadata["NWBFile"]["session_start_time"].replace(tzinfo=tz.gettz("US/Eastern"))
 metadata["NWBFile"].update(session_start_time=session_start_time)
+session = (metadata["NWBFile"]["session_start_time"]).strftime("%Y%m%d%H%M%S")
+
+print(session)
+
+# Maybe do data of birth rather than age
+metadata["Subject"] = dict(
+    subject_id=subject,
+    sex="F",
+    species="Mus musculus",
+    age="P90D",
+    #date_of_birth=session_start_time-age_delta,
+)
+# No idea why this needs to be done via `.update()`
+#metadata["NWBFile"].update(session_id=session)
+#metadata["session_id"] = session
+metadata["NWBFile"] = dict(session_id=session)
 
+print(metadata)
+
+#print(metadata)
+#print(metadata["NWBFile"])
+#
 # Choose a path for saving the nwb file and run the conversion
-nwbfile_path = "/mnt/DATA/data/studies/manish/mvmnda/rawdata/my_spikeglx_session.nwb"
+##nwbfile_path = "/mnt/DATA/data/studies/manish/mvmnda/rawdata/my_spikeglx_session.nwb"
+##converter.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
+
+
+
+nwbfile_path = "../_examplefile.nwb"
 converter.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

rawdata/code/requred_metadata.txt

@@ -0,0 +1,8 @@
+# Required by DANDI:
+Subject
+
+# Required by Manish:
+Date/Session — merged, sourced from metadata `...createtime...`
+Sex — sidecar
+Strain/genotype — sidecar
+Species

rawdata/dandiset.yaml

@@ -0,0 +1,49 @@
+# DO NOT EDIT THIS FILE LOCALLY. ALL LOCAL UPDATES WILL BE LOST.
+# It can be edited online at https://dandiarchive.org/dandiset/000876
+# and obtained from the dandiarchive.
+'@context': https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.4/context.json
+access:
+- schemaKey: AccessRequirements
+  status: dandi:OpenAccess
+assetsSummary:
+  numberOfBytes: 0
+  numberOfFiles: 0
+  schemaKey: AssetsSummary
+citation: Christian, Horea (2024) MVMNDA (Version draft) [Data set]. DANDI archive.
+  https://doi.org/10.80507/dandi.123456/0.123456.1234
+contributor:
+- affiliation: []
+  email: chr@chymera.eu
+  includeInCitation: true
+  name: Christian, Horea
+  roleName:
+  - dcite:ContactPerson
+  schemaKey: Person
+dateCreated: '2024-01-25T15:57:58.990029+00:00'
+datePublished: '2024-01-25T15:58:34.008145+00:00'
+description: Neuropixels SpikeGLX data for olfaction.
+doi: 10.80507/dandi.123456/0.123456.1234
+id: DANDI:000876/draft
+identifier: DANDI:000876
+license:
+- spdx:CC-BY-4.0
+manifestLocation:
+- https://api.dandiarchive.org/api/dandisets/000876/versions/draft/assets/
+name: MVMNDA
+publishedBy:
+  endDate: '2024-01-25T15:58:34.008145+00:00'
+  id: urn:uuid:1d0ab10e-bbc8-4059-9d81-4cce2184f32d
+  name: DANDI publish
+  schemaKey: PublishActivity
+  startDate: '2024-01-25T15:58:34.008145+00:00'
+  wasAssociatedWith:
+  - id: urn:uuid:14761d69-7aca-4a41-83f8-be522a85fa00
+    identifier: RRID:SCR_017571
+    name: DANDI API
+    schemaKey: Software
+    version: 0.1.0
+repository: https://dandiarchive.org
+schemaKey: Dandiset
+schemaVersion: 0.6.4
+url: https://dandiarchive.org/dandiset/000876/draft
+version: draft

rawdata/dataset_description.json

@@ -1,8 +0,0 @@
-{
-  "author": [
-    "Alice A",
-    " Bob B",
-    "Alice A",
-    " Bob B"
-  ]
-}

rawdata/environment_for_issue.txt

@@ -0,0 +1,154 @@
+Package                   Version
+------------------------- ------------
+aiohttp                   3.8.6
+aiosignal                 1.3.1
+altair                    5.2.0
+appdirs                   1.4.4
+arrow                     1.3.0
+asciitree                 0.3.3
+asttokens                 2.4.1
+async-timeout             4.0.3
+attrs                     23.1.0
+bidsschematools           0.7.2
+blessed                   1.20.0
+boto3                     1.28.76
+botocore                  1.31.76
+cbor2                     5.5.1
+certifi                   2023.7.22
+cffi                      1.16.0
+charset-normalizer        3.3.2
+ci-info                   0.3.0
+click                     8.1.7
+click-didyoumean          0.3.0
+cloudpickle               3.0.0
+comm                      0.2.0
+contourpy                 1.2.0
+cryptography              41.0.5
+cuda-python               12.3.0
+cycler                    0.12.1
+dandi                     0.57.0
+dandischema               0.8.4
+dask                      2023.12.0
+decorator                 5.1.1
+distinctipy               1.2.3
+distributed               2023.12.0
+dnspython                 2.4.2
+email-validator           2.1.0.post1
+etelemetry                0.3.1
+executing                 2.0.1
+fasteners                 0.19
+figurl                    0.2.18
+fonttools                 4.46.0
+fparse                    1.20.1
+fqdn                      1.5.1
+frozenlist                1.4.0
+fscacher                  0.4.0
+fsspec                    2023.10.0
+h5py                      3.10.0
+hdmf                      3.11.0
+humanize                  4.8.0
+idna                      3.4
+importlib-metadata        6.8.0
+interleave                0.2.1
+ipympl                    0.9.3
+ipython                   8.18.1
+ipython-genutils          0.2.0
+ipywidgets                8.1.1
+isodate                   0.6.1
+isoduration               20.11.0
+jaraco.classes            3.3.0
+jedi                      0.19.1
+jeepney                   0.8.0
+Jinja2                    3.1.2
+jmespath                  1.0.1
+joblib                    1.3.2
+jsonpointer               2.4
+jsonschema                4.19.2
+jsonschema-specifications 2023.7.1
+jupyterlab-widgets        3.0.9
+kachery-cloud             0.4.6
+keyring                   24.2.0
+keyrings.alt              5.0.0
+kiwisolver                1.4.5
+llvmlite                  0.41.1
+locket                    1.0.0
+MarkupSafe                2.1.3
+matplotlib                3.8.2
+matplotlib-inline         0.1.6
+more-itertools            10.1.0
+msgpack                   1.0.7
+multidict                 6.0.4
+natsort                   8.4.0
+neo                       0.12.0
+networkx                  3.2.1
+neuroconv                 0.4.4
+numba                     0.58.1
+numcodecs                 0.12.1
+numpy                     1.26.1
+nwbinspector              0.4.31
+packaging                 21.3
+pandas                    2.1.2
+parso                     0.8.3
+partd                     1.4.1
+pexpect                   4.9.0
+Pillow                    10.1.0
+pip                       23.0.1
+probeinterface            0.2.20
+prompt-toolkit            3.0.43
+psutil                    5.9.6
+ptyprocess                0.7.0
+pubnub                    7.3.2
+pure-eval                 0.2.2
+py-spy                    0.3.14
+pycparser                 2.21
+pycryptodomex             3.19.0
+pydantic                  1.10.13
+Pygments                  2.17.2
+pynwb                     2.5.0
+pyout                     0.7.3
+pyparsing                 3.1.1
+python-dateutil           2.8.2
+pytz                      2023.3.post1
+PyYAML                    6.0.1
+quantities                0.14.1
+referencing               0.30.2
+requests                  2.31.0
+rfc3339-validator         0.1.4
+rfc3987                   1.3.8
+rpds-py                   0.10.6
+ruamel.yaml               0.18.4
+ruamel.yaml.clib          0.2.8
+s3fs                      0.4.2
+s3transfer                0.7.0
+scikit-learn              1.3.2
+scipy                     1.11.3
+SecretStorage             3.3.3
+semantic-version          2.10.0
+setuptools                66.1.1
+simplejson                3.19.2
+six                       1.16.0
+sortedcontainers          2.4.0
+sortingview               0.12.0
+spikeinterface            0.99.1
+stack-data                0.6.3
+tblib                     3.0.0
+tenacity                  8.2.3
+threadpoolctl             3.2.0
+toolz                     0.12.0
+tornado                   6.4
+tqdm                      4.66.1
+traitlets                 5.14.0
+types-python-dateutil     2.8.19.14
+typing_extensions         4.8.0
+tzdata                    2023.3
+uri-template              1.3.0
+urllib3                   2.0.7
+wcwidth                   0.2.9
+webcolors                 1.13
+widgetsnbextension        4.0.9
+xarray                    2023.12.0
+yarl                      1.9.2
+zarr                      2.16.1
+zarr-checksum             0.2.9
+zict                      3.0.0
+zipp                      3.17.0

rawdata/my_spikeglx_session.nwb

@@ -1 +0,0 @@
-../.git/annex/objects/0W/JZ/MD5E-s181840--ab0823394beae190d1921dfdbbb07ff8.nwb/MD5E-s181840--ab0823394beae190d1921dfdbbb07ff8.nwb

rawdata/participants.tsv

@@ -1,2 +0,0 @@
-subject_id
-sub-pixelfiber

rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_contacts.tsv

@@ -1,385 +0,0 @@
-contact_id	1-indexed-contact_id	connected	shank_id	x	y
-0	1	1	1	43	20
-1	2	1	1	11	20
-2	3	1	1	59	40
-3	4	1	1	27	40
-4	5	1	1	43	60
-5	6	1	1	11	60
-6	7	1	1	59	80
-7	8	1	1	27	80
-8	9	1	1	43	100
-9	10	1	1	11	100
-10	11	1	1	59	120
-11	12	1	1	27	120
-12	13	1	1	43	140
-13	14	1	1	11	140
-14	15	1	1	59	160
-15	16	1	1	27	160
-16	17	1	1	43	180
-17	18	1	1	11	180
-18	19	1	1	59	200
-19	20	1	1	27	200
-20	21	1	1	43	220
-21	22	1	1	11	220
-22	23	1	1	59	240
-23	24	1	1	27	240
-24	25	1	1	43	260
-25	26	1	1	11	260
-26	27	1	1	59	280
-27	28	1	1	27	280
-28	29	1	1	43	300
-29	30	1	1	11	300
-30	31	1	1	59	320
-31	32	1	1	27	320
-32	33	1	1	43	340
-33	34	1	1	11	340
-34	35	1	1	59	360
-35	36	1	1	27	360
-36	37	0	1	43	380
-37	38	1	1	11	380
-38	39	1	1	59	400
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rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_ephys.json

@@ -1,3 +0,0 @@
-{
-  "PowerLineFrequency": 60
-}

rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_ephys.nwb

@@ -1 +0,0 @@
-../../../../.git/annex/objects/7P/mZ/MD5E-s189166911064--c8616e804722c783a2d6a548e0bdda3c.nwb/MD5E-s189166911064--c8616e804722c783a2d6a548e0bdda3c.nwb

rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_probes.tsv

@@ -1,2 +0,0 @@
-probe_id	type
-probe-None	Neuropixel

rawdata/sub-pixelfiber/sub-pixelfiber_sessions.tsv

@@ -1,2 +0,0 @@
-session_id
-ses-01