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Pare down giant comment blocks that largely do what Git already does #363

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May 5, 2023
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Pare down giant comment blocks that largely do what Git already does #363

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32 changes: 2 additions & 30 deletions src/nidm/experiment/Query.py
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@@ -1,33 +1,5 @@
# *****************************************************************************
# *****************************************************************************
# nidm_query.py
# License: GPL
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@yarikoptic yarikoptic May 5, 2023 •
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@dbkeator Please confirm that it is Ok to assume that this file is also under Apache 2 license (per https://github.com/incf-nidash/PyNIDM/blob/master/LICENSE) as the rest of the codebase, or it has to be GPL?

# *****************************************************************************
# *****************************************************************************
# Date: 8-1-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: nidm_query.py
#
# Program description: This program provides query functionality for NIDM-Experiment files
#
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: os, sys, rdflib, pandas, argparse, logging
# *****************************************************************************
# Start date: 8-1-18
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""This program provides query functionality for NIDM-Experiment files"""

import functools
import hashlib
import json
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32 changes: 5 additions & 27 deletions src/nidm/experiment/tools/bidsmri2nidm.py
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# !/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# bidsmri2nidm.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 10-2-17 Coded by: David Keator (dbkeator@gmail.com)
# Filename: bidsmri2nidm.py
#
# Program description: This program will convert a BIDS MRI dataset to a NIDM-Experiment
# RDF document. It will parse phenotype information and simply store variables/values
# and link to the associated json data dictionary file.
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""
This program will convert a BIDS MRI dataset to a NIDM-Experiment RDF document.
It will parse phenotype information and simply store variables/values and link
to the associated json data dictionary file.
"""

from argparse import ArgumentParser, RawTextHelpFormatter
import csv
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37 changes: 7 additions & 30 deletions src/nidm/experiment/tools/csv2nidm.py
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#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# csv2nidm.py
# License:Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 01-19-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: csv2nidm.py
#
# Program description: This program will load in a CSV file and iterate over the header
# variable names performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim
# tagged terms that fuzzy match the variable names. The user will then interactively pick
# a term to associate with the variable name. The resulting annotated CSV data will
# then be written to a NIDM data file.
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""
This program will load in a CSV file and iterate over the header variable names
performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim tagged
terms that fuzzy match the variable names. The user will then interactively
pick a term to associate with the variable name. The resulting annotated CSV
data will then be written to a NIDM data file.
"""

from argparse import ArgumentParser
from io import StringIO
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43 changes: 8 additions & 35 deletions src/nidm/experiment/tools/nidm2bids.py
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@@ -1,38 +1,11 @@
#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# NIDM2BIDSMRI.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 10-2-17 Coded by: David Keator (dbkeator@gmail.com)
# Filename: NIDM2BIDSMRI.py
#
# Program description: This program will convert a NIDM-Experiment RDF document
# to a BIDS dataset. The program will query the NIDM-Experiment document for subjects,
# MRI scans, and associated assessments saving the MRI data to disk in an organization
# according to the BIDS specification, the demographics metadata to a participants.tsv
# file, the project-level metadata to a dataset_description.json file, and the
# assessments to *.tsv/*.json file pairs in a phenotypes directory.
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# Start date: 10-2-17
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""
This program will convert a NIDM-Experiment RDF document to a BIDS dataset.
The program will query the NIDM-Experiment document for subjects, MRI scans,
and associated assessments saving the MRI data to disk in an organization
according to the BIDS specification, the demographics metadata to a
participants.tsv file, the project-level metadata to a dataset_description.json
file, and the assessments to *.tsv/*.json file pairs in a phenotypes directory.
"""

from argparse import ArgumentParser
from io import StringIO
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32 changes: 1 addition & 31 deletions src/nidm/experiment/tools/nidm_concat.py
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#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# nidm_utils.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 11-28-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: nidm_utils.py
#
# Program description: Tools for working with NIDM-Experiment files
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# Start date: 11-28-18
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""Tools for working with NIDM-Experiment files"""

import click
from nidm.experiment.Query import GetMergedGraph
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32 changes: 1 addition & 31 deletions src/nidm/experiment/tools/nidm_convert.py
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#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# nidm_utils.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 11-28-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: nidm_utils.py
#
# Program description: Tools for working with NIDM-Experiment files
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# Start date: 11-28-18
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
""" Tools for working with NIDM-Experiment files """

from os.path import basename, join, splitext
import click
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33 changes: 1 addition & 32 deletions src/nidm/experiment/tools/nidm_linreg.py
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# coding=utf-8
# !/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# nidm_linreg.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 07-26-22 Coded by: Ashmita Kumar (ashmita.kumar@gmail.com)
# Filename: nidm_linreg.py
#
# Program description: This program provides a tool to complete a linear regression on nidm files
#
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: os, sys, tempfile, pandas, click, nidm, csv, sklearn, numpy, statsmodel.api, patsy.contrasts
# *****************************************************************************
# Start date: 6-15-20
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""This program provides a tool to complete a linear regression on nidm files"""

import csv
import os
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32 changes: 1 addition & 31 deletions src/nidm/experiment/tools/nidm_merge.py
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#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# nidm_utils.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 11-28-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: nidm_utils.py
#
# Program description: Tools for working with NIDM-Experiment files
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# Start date: 11-28-18
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""Tools for working with NIDM-Experiment files"""

import click
from rdflib import Graph, util
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32 changes: 1 addition & 31 deletions src/nidm/experiment/tools/nidm_query.py
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@@ -1,34 +1,4 @@
#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# nidm_query.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 8-1-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: nidm_query.py
#
# Program description: This program provides query functionality for NIDM-Experiment files
#
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: os, sys, rdflib, pandas, argparse, logging
# *****************************************************************************
# Start date: 8-1-18
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
"""This program provides query functionality for NIDM-Experiment files"""

from json import dumps
import os
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32 changes: 1 addition & 31 deletions src/nidm/experiment/tools/nidm_utils.py
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@@ -1,34 +1,4 @@
#!/usr/bin/env python
# *****************************************************************************
# *****************************************************************************
# nidm_utils.py
# License: Apache License, Version 2.0
# *****************************************************************************
# *****************************************************************************
# Date: 11-28-18 Coded by: David Keator (dbkeator@gmail.com)
# Filename: nidm_utils.py
#
# Program description: Tools for working with NIDM-Experiment files
#
# *****************************************************************************
# Development environment: Python - PyCharm IDE
#
# *****************************************************************************
# System requirements: Python 3.X
# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
# os,sys,getopt,csv
# *****************************************************************************
# Start date: 11-28-18
# Update history:
# DATE MODIFICATION Who
#
#
# *****************************************************************************
# Programmer comments:
#
#
# *****************************************************************************
# *****************************************************************************
""" Tools for working with NIDM-Experiment files """

from argparse import ArgumentParser
import os.path
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