This package aims to provide some tools to facilitate working with the Open Humans APIs.
In particular, this package provides some command line tools for data file downloads and uploads. These tools are listed below.
This package is distributed via PyPI. We recommend you install it using
pip, e.g. pip install open-humans-api.
Command line tools aim to facilitate one-off operations by users (for example, one-off data upload by a project).
These tools might also be helpful for programmers seeking to use the API in non-Python programmatic contexts.
Usage: ohpub-download [OPTIONS]
Download public data from Open Humans.
Options:
-s, --source TEXT the source to download files from
-u, --username TEXT the user to download files from
-d, --directory TEXT the directory for downloaded files
-m, --max-size TEXT the maximum file size to download
--help Show this message and exit.
# download all 23andMe files to 23andme/
$ mkdir 23andme
$ ohpub-download --source twenty_three_and_me --directory 23andme
# download all of beau's files to the current directory
$ ohpub-download --username beau
Usage: ohproj-download [OPTIONS]
Download data from project members to the target directory.
Unless this is a member-specific download, directories will be created for
each project member ID. Also, unless a source is specified, all shared
sources are downloaded and data is sorted into subdirectories according to
source.
Projects can optionally return data to Open Humans member accounts. If
project_data is True (or the "--project-data" flag is used), this data
(the project's own data files, instead of data from other sources) will be
downloaded for each member.
Options:
-d, --directory TEXT Target directory for downloaded files. [required]
-T, --master-token TEXT Project master access token.
-m, --member TEXT Project member ID.
-t, --access-token TEXT OAuth2 user access token.
-s, --source TEXT Only download files from this source.
--project-data TEXT Download this project's own data.
--max-size TEXT Maximum file size to download. [default: 128m]
-v, --verbose Report INFO level logging to stdout
--debug Report DEBUG level logging to stdout.
--memberlist TEXT Text file with whitelist IDs to retrieve
--excludelist TEXT Text file with blacklist IDs to avoid
--help Show this message and exit.
Usage: ohproj-download-metadata [OPTIONS]
Output CSV with metadata for a project's downloadable files in Open
Humans.
Options:
-T, --master-token TEXT Project master access token. [required]
-v, --verbose Show INFO level logging
--debug Show DEBUG level logging.
--output-csv TEXT Output project metedata CSV [required]
--help Show this message and exit.
Usage: ohproj-upload-metadata [OPTIONS]
Draft or review metadata files for uploading files to Open Humans.
The target directory should either represent files for a single member (no
subdirectories), or contain a subdirectory for each project member ID.
Options:
-d, --directory TEXT Target directory [required]
--create-csv TEXT Create draft CSV metadata [required]
--max-size TEXT Maximum file size to consider. [default: 128m]
-v, --verbose Show INFO level logging
--debug Show DEBUG level logging.
--help Show this message and exit.
Create directory containing data for project members. For example it might look like the following example (two project members with IDs '01234567' and '12345678').
- member_data/
- 01234567/
- testdata.json
- testdata.txt
- 12345678/
- testdata.json
- testdata.txt
- 01234567/
Draft metadata file:
$ ohproj-metadata -d member_data --create-csv member_data_metadata.csv
Initially it looks like this:
project_member_id,filename,tags,description,md5,creation_date
01234567,testdata.txt,,,fa61a92e21a2597900cbde09d8ddbc1a,2016-08-23T15:23:22.277060+00:00
01234567,testdata.json,json,,577da9879649acaf17226a6461bd19c8,2016-08-23T16:06:16.415039+00:00
12345678,testdata.txt,,,fa61a92e21a2597900cbde09d8ddbc1a,2016-09-20T10:10:59.863201+00:00
12345678,testdata.json,json,,577da9879649acaf17226a6461bd19c8,2016-09-20T10:10:59.859201+00:00
You can use a spreadsheet editor to edit it. Make sure to save the result as CSV! For example, it might look like this if you add descriptions and more tags:
1234567,testdata.txt,"txt, verbose-data",Complete test data in text format.,fa61a92e21a2597900cbde09d8ddbc1a,2016-08-23T15:23:22.277060+00:00
1234567,testdata.json,"json, metadata",Summary metadata in JSON format.,577da9879649acaf17226a6461bd19c8,2016-08-23T16:06:16.415039+00:00
12345678,testdata.txt,"txt, verbose-data",Complete test data in text format.,fa61a92e21a2597900cbde09d8ddbc1a,2016-09-20T10:10:59.863201+00:00
12345678,testdata.json,"json, metadata",Summary test data JSON.,577da9879649acaf17226a6461bd19c8,2016-09-20T10:10:59.859201+00:00
Usage: ohproj-upload [OPTIONS]
Upload files for the project to Open Humans member accounts.
If using a master access token and not specifying member ID:
(1) Files should be organized in subdirectories according to project
member ID, e.g.:
main_directory/01234567/data.json
main_directory/12345678/data.json
main_directory/23456789/data.json
(2) The metadata CSV should have the following format:
1st column: Project member ID
2nd column: filenames
3rd & additional columns: Metadata fields (see below)
If uploading for a specific member:
(1) The local directory should not contain subdirectories.
(2) The metadata CSV should have the following format:
1st column: filenames
2nd & additional columns: Metadata fields (see below)
The default behavior is to overwrite files with matching filenames on Open
Humans, but not otherwise delete files. (Use --safe or --sync to change
this behavior.)
If included, the following metadata columns should be correctly formatted:
'tags': should be comma-separated strings
'md5': should match the file's md5 hexdigest
'creation_date', 'start_date', 'end_date': ISO 8601 dates or datetimes
Other metedata fields (e.g. 'description') can be arbitrary strings.
Options:
-d, --directory TEXT Target directory for downloaded files. [required]
--metadata-csv TEXT CSV file containing file metadata. [required]
-T, --master-token TEXT Project master access token.
-m, --member TEXT Project member ID.
-t, --access-token TEXT OAuth2 user access token.
--safe Do not overwrite files in Open Humans.
--sync Delete files not present in local directories.
--max-size TEXT Maximum file size to download. [default: 128m]
-v, --verbose Report INFO level logging to stdout
--debug Report DEBUG level logging to stdout.
--help Show this message and exit.
For organizing the data files and creating a metadata file, see the example
usage for the ohproj-metadata command line tool.
Uploading that data with a master access token:
$ ohproj-upload -T MASTER_ACCESS_TOKEN --metadata-csv member_data_metadata.csv -d member_data