standalone template retriever

setup.cfg

@@ -80,6 +80,11 @@ all =
     %(doc)s
     %(test)s
 
+
+[options.entry_points]
+console_scripts =
+    templateflow_get=templateflow.templateflow_get:main
+
 [flake8]
 max-line-length = 99
 doctests = False

templateflow/templateflow_get.py

@@ -0,0 +1,197 @@
+#!/opt/gensoft/exe/TemplateFlow_pyclient/0.8.0/venv/bin/python3.8
+
+import argparse
+import os
+import sys
+
+#---- as templateflow.api.TF_LAYOUT.root is set at import time based on default or TEMPLATE_FLOW env var
+#     and it is not writable, we have to import template flow with environnement set if we want to be
+#     abble to set cache dir from command line option
+
+import pprint 
+
+TOOL_VERSION = '0.1'
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='TemplateFlow templates retriever.')
+
+    r_group = parser.add_argument_group('retrieve options')
+    r_group.add_argument('-r', '--resolution', 
+                        action='store',
+                        default='unset',
+                        help='Index to an specific spatial resolution of the template, multiple values coma separated may be given')
+
+    r_group.add_argument('-s', '--suffix', 
+                        action='store',
+                        default='unset',
+                        help='BIDS suffix')
+
+    r_group.add_argument('-a', '--atlas', 
+                        action='store',
+                        default='unset',
+                        help='Name of a particular atlas')
+
+    r_group.add_argument('-e', '--extension', 
+                        action='store',
+                        default='unset',
+                        help='file extension')
+
+    r_group.add_argument('-H', '--hemi', 
+                        action='store',
+                        choices=['R', 'L'],
+                        default='unset',
+                        help='select Hemisphere')
+
+    r_group.add_argument('-S', '--space', 
+                        action='store',
+                        default='unset',
+                        help='Space template is mapped to')
+
+    r_group.add_argument('-d', '--density', 
+                        action='store',
+                        default='unset',
+                        help='Surface density')
+
+    r_group.add_argument('-D', '--desc', 
+                        action='store',
+                        default='unset',
+                        help='Description field')
+
+    r_group.add_argument('-c', '--cohort', 
+                        action='store',
+                        default='unset',
+                        help='Template cohort')
+
+    r_group.add_argument('-L', '--label', 
+                        action='store',
+                        default='unset',
+                        help='Template label')
+
+    i_group = parser.add_argument_group('info environement')
+    i_group.add_argument('-l', '--list', 
+		    action='store_true',
+		    default=False,
+		    help='list available local templates')
+
+    i_group.add_argument('-m', '--metadata', 
+		    action='store_true',
+		    default=False,
+		    help='Get full metadata for given template')
+
+    i_group.add_argument('-C', '--citations', 
+		    action='store_true',
+		    default=False,
+		    help='Get template citations')
+
+    i_group.add_argument('-B', '--bibtex-citations', 
+		    action='store_true',
+		    default=False,
+		    help='Get template citation in bibtex-citations')
+
+    m_group = parser.add_argument_group('misc options')
+    m_group.add_argument('-o', '--tf-cache', 
+		    action='store',
+		    default='unset',
+		    help='Directory to save templates in. default `${HOME}/.cache/templateflow`')
+
+    m_group.add_argument('-v', '--version', 
+		    action='store_true',
+		    default=False, 
+		    help='Display version of this tools AND TemplateFlow Client version')
+
+    parser.add_argument('args', nargs='*',metavar=('template [template ...]') )
+    opts = parser.parse_args(sys.argv[1:])
+    args = opts.args
+    return opts, args
+
+
+def version_info():
+    import templateflow
+    prog = os.path.basename(sys.argv[0])
+    print(f'{prog} v{TOOL_VERSION}')
+    print(f'Using TemplateFlow Client version {templateflow.__version__}')
+    sys.exit(0)
+
+def templates_info():
+    import templateflow.api as tf
+    templates=tf.templates()
+    ident_fmt = '\n'.join(templates)
+    print(f"{len(templates)} templates:\n-------------------\n{ident_fmt}")
+    sys.exit(0)
+
+def metadata_info(args):    
+    import templateflow.api as tf
+    pp = pprint.PrettyPrinter(indent=4)
+    for tmpl in args:
+        infos=tf.get_metadata(tmpl)
+        pp.pprint(infos)
+    sys.exit(0) 
+
+def citation_info(args, bibtex=True):
+    import templateflow.api as tf
+#    bibtex_format = True if  opts.bibtex_citations else False
+    pp = pprint.PrettyPrinter(indent=4)
+    for tmpl in args:
+        print(tmpl)
+
+        infos=tf.get_citations(tmpl, bibtex=bibtex)
+        pp.pprint(infos)
+    sys.exit(0) 
+
+def template_retriever(args, options):
+    import templateflow
+    import templateflow.api as tf
+
+    for tmpl in args:
+        try: 
+            tmpl = tf.get(tmpl, raise_empty=True, **options) 
+            print('\n'.join(map(str, tmpl)))
+        except Exception as msg:
+            print(tmpl, msg)
+    sys.exit(0)
+
+
+def main():
+
+    opts, args = parse_args()
+
+    if opts.version:
+        version_info()
+
+    if opts.list:
+        templates_info()
+
+    if opts.metadata:
+        metadata_info(args)
+
+    if opts.citations or opts.bibtex_citations:
+        citation_info(args, opts.bibtex_citations)
+
+    if opts.tf_cache != 'unset':
+        #---- TemplatFlow cache dir was specified, export it
+        print("saving to ---------->", opts.tf_cache)
+        print("saving to ---------->", os.path.abspath(opts.tf_cache))
+        os.environ['TEMPLATEFLOW_HOME'] = os.path.abspath(opts.tf_cache)
+
+    #---- allow multi resolution requirement    
+    if ',' in opts.resolution:
+        opts.resolution = tuple(opts.resolution.split(','))
+
+    #---- clean unset options and be sure to remove non relevant options 
+    #     to not introduce unknown arguments when calling tf.get
+    options={k:v for k,v in vars(opts).items() if v != 'unset' and v != False}
+    non_options = ['list', 'metadata', 'args', 'tf_cache', 'citations', 'bibtex_citation', 'version']
+    for e in non_options:
+        options.pop(e, None)
+
+    #---- argument None is acquired as a string, not python None. convert it
+    for k,v in options.items():
+        if v == 'None': options[k] = None
+
+    template_retriever(args, options)
+
+
+if __name__ == '__main__':
+    main()
+
+