moving collecting of Git repo metadata to utils and io so that wc_kb …

…can be used without Git and from any directory

tests/test_core.py

@@ -565,7 +565,7 @@ def test_ComplexSpeciesType(self):
         species2 = core.Species(species_type=prot2, compartment=comp1)
         species_coeff1 = core.SpeciesCoefficient(species=species1, coefficient=2)
         species_coeff2 = core.SpeciesCoefficient(species=species2, coefficient=3)
-        reaction1 = core.Reaction(participants=[species_coeff1,species_coeff2])
+        reaction1 = core.Reaction(participants=[species_coeff1, species_coeff2])
         complex1.formation_reaction = reaction1
 
         self.assertEqual(complex1.get_subunits(), [prot1, prot1, prot2, prot2, prot2])
@@ -579,5 +579,6 @@ def test_ComplexSpeciesType(self):
         # test get_empirical_formula
         self.assertEqual(complex1.get_empirical_formula(), chem.EmpiricalFormula('C273H408N76O82S2'))
 
+
 class ReactionParticipantAttributeTestCase(unittest.TestCase):
     def test_ReactionParticipantAttribute(self): pass

tests/test_io.py

@@ -54,14 +54,14 @@ def test_write_read(self):
         seq_path = os.path.join(self.dir, 'seq.fna')
 
         writer = io.Writer()
-        writer.run(self.kb, core_path, seq_path)
+        writer.run(self.kb, core_path, seq_path, set_repo_metadata_from_path=False)
 
         reader = io.Reader()
         kb = reader.run(core_path, seq_path)
 
         core_path = os.path.join(self.dir, 'core2.xlsx')
         seq_path = os.path.join(self.dir, 'seq2.fna')
-        writer.run(kb, core_path, seq_path)
+        writer.run(kb, core_path, seq_path, set_repo_metadata_from_path=False)
 
         self.assertTrue(self.kb.is_equal(kb))
 
@@ -79,14 +79,14 @@ def test_write_without_cell_relationships(self):
 
         writer = io.Writer()
         with self.assertRaisesRegexp(ValueError, 'must be set to the instance of `Cell`'):
-            writer.run(self.kb, core_path, seq_path)
+            writer.run(self.kb, core_path, seq_path, set_repo_metadata_from_path=False)
 
     def test_write_read_sloppy(self):
         core_path = os.path.join(self.dir, 'core.xlsx')
         seq_path = os.path.join(self.dir, 'seq.fna')
 
         writer = io.Writer()
-        writer.run(self.kb, core_path, seq_path)
+        writer.run(self.kb, core_path, seq_path, set_repo_metadata_from_path=False)
 
         wb = wc_utils.workbook.io.read(core_path)
         row = wb['Knowledge base'].pop(0)
@@ -166,7 +166,7 @@ def test_convert(self):
         path_seq_2 = os.path.join(self.dir, 'seq_2.fna')
         path_seq_3 = os.path.join(self.dir, 'seq_3.fna')
 
-        io.Writer().run(self.kb, path_core_1, path_seq_1)
+        io.Writer().run(self.kb, path_core_1, path_seq_1, set_repo_metadata_from_path=False)
 
         io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
         kb = io.Reader().run(path_core_2, path_seq_2)
@@ -184,7 +184,7 @@ def test_convert_sloppy(self):
         path_seq_2 = os.path.join(self.dir, 'seq_2.fna')
         path_seq_3 = os.path.join(self.dir, 'seq_3.fna')
 
-        io.Writer().run(self.kb, path_core_1, path_seq_1)
+        io.Writer().run(self.kb, path_core_1, path_seq_1, set_repo_metadata_from_path=False)
 
         wb = wc_utils.workbook.io.read(path_core_1)
         row = wb['Knowledge base'].pop(0)
@@ -204,7 +204,7 @@ def test_convert_sloppy(self):
     def test_create_template(self):
         path_core = os.path.join(self.dir, 'core.xlsx')
         path_seq = os.path.join(self.dir, 'seq.fna')
-        io.create_template(path_core, path_seq)
+        io.create_template(path_core, path_seq, set_repo_metadata_from_path=False)
         kb = io.Reader().run(path_core, path_seq)
 
     def test_validate_implicit_relationships(self):

tests/test_main.py

@@ -37,7 +37,7 @@ def test_validate(self):
         self.assertEqual(Validator().run(kb, get_related=True), None)
         filename_core = path.join(self.tempdir, 'core.xlsx')
         filename_seq = path.join(self.tempdir, 'seq.fna')
-        io.Writer().run(kb, filename_core, filename_seq)
+        io.Writer().run(kb, filename_core, filename_seq, set_repo_metadata_from_path=False)
 
         with CaptureOutput() as capturer:
             with __main__.App(argv=['validate', filename_core, filename_seq]) as app:
@@ -53,7 +53,7 @@ def test_validate_exception(self):
         self.assertNotEqual(Validator().run(kb, get_related=True), None)
         filename_core = path.join(self.tempdir, 'core.xlsx')
         filename_seq = path.join(self.tempdir, 'seq.fna')
-        io.Writer().run(kb, filename_core, filename_seq)
+        io.Writer().run(kb, filename_core, filename_seq, set_repo_metadata_from_path=False)
 
         with self.assertRaisesRegexp(ValueError, '^Knowledge base is invalid: '):
             with __main__.App(argv=['validate', filename_core, filename_seq]) as app:
@@ -63,17 +63,17 @@ def test_difference(self):
         kb1 = wc_kb.KnowledgeBase(id='kb', name='KB', version='0.0.1a', wc_kb_version='0.0.0')
         filename_core_1 = path.join(self.tempdir, 'core1.xlsx')
         filename_seq_1 = path.join(self.tempdir, 'seq1.fna')
-        io.Writer().run(kb1, filename_core_1, filename_seq_1)
+        io.Writer().run(kb1, filename_core_1, filename_seq_1, set_repo_metadata_from_path=False)
 
         kb2 = wc_kb.KnowledgeBase(id='kb', name='KB', version='0.0.1a', wc_kb_version='0.0.0')
         filename_core_2 = path.join(self.tempdir, 'core2.xlsx')
         filename_seq_2 = path.join(self.tempdir, 'seq2.fna')
-        io.Writer().run(kb2, filename_core_2, filename_seq_2)
+        io.Writer().run(kb2, filename_core_2, filename_seq_2, set_repo_metadata_from_path=False)
 
         kb3 = wc_kb.KnowledgeBase(id='kb', name='KB', version='0.0.1a', wc_kb_version='0.0.1')
         filename_core_3 = path.join(self.tempdir, 'core3.xlsx')
         filename_seq_3 = path.join(self.tempdir, 'seq3.fna')
-        io.Writer().run(kb3, filename_core_3, filename_seq_3)
+        io.Writer().run(kb3, filename_core_3, filename_seq_3, set_repo_metadata_from_path=False)
 
         with CaptureOutput() as capturer:
             with __main__.App(argv=['difference',
@@ -117,7 +117,7 @@ def test_normalize(self):
         filename_seq_2 = path.join(self.tempdir, 'seq-2.fna')
 
         kb = wc_kb.KnowledgeBase(id='kb', name='KB', version='0.0.1a', wc_kb_version='0.0.0')
-        io.Writer().run(kb, filename_core_1, filename_seq_1)
+        io.Writer().run(kb, filename_core_1, filename_seq_1, set_repo_metadata_from_path=False)
 
         # with same dest
         with __main__.App(argv=['normalize', filename_core_1, filename_seq_1]) as app:
@@ -141,7 +141,7 @@ def test_convert(self):
         filename_out_seq = path.join(self.tempdir, 'out.seq.fna')
 
         kb = wc_kb.KnowledgeBase(id='kb', name='KB', version='0.0.1a', wc_kb_version='0.0.0')
-        io.Writer().run(kb, filename_in_core, filename_in_seq)
+        io.Writer().run(kb, filename_in_core, filename_in_seq, set_repo_metadata_from_path=False)
 
         with __main__.App(argv=['convert',
                                 filename_in_core, filename_in_seq,
@@ -155,21 +155,21 @@ def test_create_template(self):
         filename_core = path.join(self.tempdir, 'core.xlsx')
         filename_seq = path.join(self.tempdir, 'seq.fna')
 
-        with __main__.App(argv=['create-template', filename_core, filename_seq]) as app:
+        with __main__.App(argv=['create-template', filename_core, filename_seq, '--ignore-repo-metadata']) as app:
             app.run()
 
         self.assertTrue(path.isfile(filename_core))
         self.assertTrue(path.isfile(filename_seq))
 
-    def test_update_wc_kb_version(self):
+    def test_update_version_metadata(self):
         filename_core = path.join(self.tempdir, 'core.xlsx')
         filename_seq = path.join(self.tempdir, 'seq.fna')
 
         kb = wc_kb.KnowledgeBase(id='kb', name='KB', version='0.0.1a', wc_kb_version='0.0.0')
         self.assertNotEqual(kb.wc_kb_version, wc_kb.__version__)
-        io.Writer().run(kb, filename_core, filename_seq)
+        io.Writer().run(kb, filename_core, filename_seq, set_repo_metadata_from_path=False)
 
-        with __main__.App(argv=['update-wc-kb-version', filename_core, filename_seq]) as app:
+        with __main__.App(argv=['update-version-metadata', filename_core, filename_seq, '--ignore-repo-metadata']) as app:
             app.run()
 
         kb = io.Reader().run(filename_core, filename_seq)

tests/test_util.py

@@ -8,6 +8,8 @@
 
 from wc_kb import core
 from wc_kb import util
+import shutil
+import tempfile
 import unittest
 
 
@@ -20,3 +22,26 @@ def test_get_models(self):
 
         self.assertIn(core.KnowledgeBase, util.get_models(inline=False))
         self.assertIn(core.Cell, util.get_models(inline=False))
+
+    def test_set_git_repo_metadata_from_path(self):
+        kb = core.KnowledgeBase()
+        self.assertEqual(kb.url, '')
+
+        util.set_git_repo_metadata_from_path(kb, path='.')
+        self.assertIn(kb.url, [
+            'https://github.com/KarrLab/wc_kb.git',
+            'ssh://git@github.com/KarrLab/wc_kb.git',
+            'git@github.com:KarrLab/wc_kb.git',
+        ])
+
+    def test_set_git_repo_metadata_from_path_error(self):
+        tempdir = tempfile.mkdtemp()
+
+        kb = core.KnowledgeBase()
+        self.assertEqual(kb.url, '')
+
+        with self.assertRaisesRegexp(ValueError, 'is not a Git repository'):
+            util.set_git_repo_metadata_from_path(kb, path=tempdir)
+        self.assertEqual(kb.url, '')
+
+        shutil.rmtree(tempdir)

wc_kb/__main__.py

@@ -121,9 +121,9 @@ def default(self):
         args = self.app.pargs
         kb = io.Reader().run(args.source_core, args.source_seq, strict=args.strict)
         if args.dest_core or args.dest_seq:
-            io.Writer().run(kb, args.dest_core, args.dest_seq)
+            io.Writer().run(kb, args.dest_core, args.dest_seq, set_repo_metadata_from_path=False)
         else:
-            io.Writer().run(kb, args.source_core, args.source_seq)
+            io.Writer().run(kb, args.source_core, args.source_seq, set_repo_metadata_from_path=False)
 
 
 class ConvertController(CementBaseController):
@@ -159,27 +159,33 @@ class Meta:
         stacked_on = 'base'
         stacked_type = 'nested'
         arguments = [
-            (['path_core'], dict(type=str, help='Path to save a template of the core of a knowledge base')),
-            (['path_seq'], dict(type=str, help='Path to save a template of the genome sequence of a knowledge base')),
+            (['path_core'], dict(metavar='path-core', type=str, help='Path to save a template of the core of a knowledge base')),
+            (['path_seq'], dict(metavar='path-seq', type=str, help='Path to save a template of the genome sequence of a knowledge base')),
+            (['--ignore-repo-metadata'], dict(dest='set_repo_metadata_from_path', default=True, action='store_false',
+                                              help=('If set, do not set the Git repository metadata for the knowledge base from '
+                                                    'the parent directory of `path-core`'))),
         ]
 
     @expose(hide=True)
     def default(self):
         args = self.app.pargs
-        io.create_template(args.path_core, args.path_seq)
+        io.create_template(args.path_core, args.path_seq, set_repo_metadata_from_path=args.set_repo_metadata_from_path)
 
 
-class UpdateWcKbVersionController(CementBaseController):
-    """ Update wc_kb_version of a knowledge base """
+class UpdateVersionMetadataController(CementBaseController):
+    """ Update version metadata of a knowledge base (URL, branch, revision, wc_kb version) """
 
     class Meta:
-        label = 'update-wc-kb-version'
-        description = 'Update wc_kb_version of a knowledge base'
+        label = 'update-version-metadata'
+        description = 'Update version metadata of a knowledge base (URL, branch, revision, wc_kb version)'
         stacked_on = 'base'
         stacked_type = 'nested'
         arguments = [
             (['path_core'], dict(type=str, help='Path to the core of the knowledge base')),
             (['path_seq'], dict(type=str, help='Path to the FASTA-formatted genome sequence of a knowledge base')),
+            (['--ignore-repo-metadata'], dict(dest='set_repo_metadata_from_path', default=True, action='store_false',
+                                              help=('If set, do not set the Git repository metadata for the knowledge base from '
+                                                    'the parent directory of `path-core`'))),
             (['--sloppy'], dict(dest='strict', default=True, action='store_false',
                                 help='If set, do not validate the format of the knowledge base file(s)')),
         ]
@@ -189,7 +195,7 @@ def default(self):
         args = self.app.pargs
         kb = io.Reader().run(args.path_core, args.path_seq, strict=args.strict)
         kb.wc_kb_version = wc_kb.__version__
-        io.Writer().run(kb, args.path_core, args.path_seq)
+        io.Writer().run(kb, args.path_core, args.path_seq, set_repo_metadata_from_path=args.set_repo_metadata_from_path)
 
 
 class App(CementApp):
@@ -204,7 +210,7 @@ class Meta:
             NormalizeController,
             ConvertController,
             CreateTemplateController,
-            UpdateWcKbVersionController,
+            UpdateVersionMetadataController,
         ]
 
 

wc_kb/core.py

@@ -8,7 +8,6 @@
 """
 
 from wc_utils.util import chem
-import wc_utils.util.git as git
 import abc
 import Bio.Seq
 import Bio.SeqUtils
@@ -125,10 +124,6 @@ class Meta(obj_model.core.Model.Meta):
         tabular_orientation = obj_model.core.TabularOrientation.column
 
     def __init__(self, **kwargs):
-        md = git.get_repo_metadata()
-        self.url = md.url
-        self.branch = md.branch
-        self.revision = md.revision
         super(KnowledgeBase, self).__init__(**kwargs)
 
 

wc_kb/io.py

@@ -13,6 +13,7 @@
 """
 
 from . import core
+from . import util
 from wc_utils.util.string import indent_forest
 import Bio.SeqIO
 import Bio.SeqRecord
@@ -41,13 +42,15 @@ class Writer(object):
         core.Reaction,
     )
 
-    def run(self, knowledge_base, core_path, seq_path):
+    def run(self, knowledge_base, core_path, seq_path, set_repo_metadata_from_path=True):
         """ Write knowledge base to file(s)
 
         Args:
             knowledge_base (:obj:`core.KnowledgeBase`): knowledge base
             core_path (:obj:`str`): path to save core knowledge base
             seq_path (:obj:`str`): path to save genome sequence
+            set_repo_metadata_from_path (:obj:`bool`, optional): if :obj:`True`, set the Git repository metadata (URL, 
+                branch, revision) for the knowledge base from the parent directory of :obj:`core_path`
 
         Raises:
             :obj:`ValueError`: if any of the relationships with knowledge bases and cells are not set
@@ -66,6 +69,10 @@ def run(self, knowledge_base, core_path, seq_path):
                     if val is None or val != cell:
                         raise ValueError('{}.{} must be set to the instance of `Cell`'.format(obj.__class__.__name__, attr.name))
 
+        # set Git repository metadata from the parent directories of :obj:`core_path`
+        if set_repo_metadata_from_path:
+            util.set_git_repo_metadata_from_path(knowledge_base, core_path)
+
         # gather DNA sequences
         dna_seqs = []
         if cell:
@@ -135,8 +142,8 @@ def run(self, core_path, seq_path, strict=True):
 
         Args:
             core_path (:obj:`str`): path to core knowledge base
-            seq_path (:obj:`str`): path to genome sequence
-            strict (:obj:`str`, optional): if :obj:`True`, validate that the the model file(s) strictly follow the
+            seq_path (:obj:`str`): path to genome sequence            
+            strict (:obj:`bool`, optional): if :obj:`True`, validate that the the model file(s) strictly follow the
                 :obj:`obj_model` serialization format:
 
                 * The worksheets are in the expected order
@@ -241,7 +248,7 @@ def convert(source_core, source_seq, dest_core, dest_seq, strict=True):
         source_seq (:obj:`str`): path to the genome sequence of the source knowledge base
         dest_core (:obj:`str`): path to save the converted core of the knowledge base
         dest_seq (:obj:`str`): path to save the converted genome sequence of the knowledge base
-        strict (:obj:`str`, optional): if :obj:`True`, validate that the the model file(s) strictly follow the
+        strict (:obj:`bool`, optional): if :obj:`True`, validate that the the model file(s) strictly follow the
                 :obj:`obj_model` serialization format:
 
                 * The worksheets are in the expected order
@@ -252,15 +259,17 @@ def convert(source_core, source_seq, dest_core, dest_seq, strict=True):
                 * There are no extra columns
     """
     kb = Reader().run(source_core, source_seq, strict=strict)
-    Writer().run(kb, dest_core, dest_seq)
+    Writer().run(kb, dest_core, dest_seq, set_repo_metadata_from_path=False)
 
 
-def create_template(core_path, seq_path):
+def create_template(core_path, seq_path, set_repo_metadata_from_path=True):
     """ Create file with knowledge base template, including row and column headings
 
     Args:
         core_path (:obj:`str`): path to save temploate of core knowledge base
         seq_path (:obj:`str`): path to save genome sequence
+        set_repo_metadata_from_path (:obj:`bool`, optional): if :obj:`True`, set the Git repository metadata (URL, 
+            branch, revision) for the knowledge base from the parent directory of :obj:`core_path`
     """
     kb = core.KnowledgeBase(id='template', name='Template', version=wc_kb.__version__)
-    Writer().run(kb, core_path, seq_path)
+    Writer().run(kb, core_path, seq_path, set_repo_metadata_from_path=set_repo_metadata_from_path)

wc_kb/util.py

@@ -7,8 +7,10 @@
 """
 
 from . import core
+from wc_utils.util import git
 import obj_model.core
 
+
 def get_models(inline=True):
     """ Get list of models
 
@@ -20,3 +22,16 @@ def get_models(inline=True):
     """
 
     return obj_model.core.get_models(module=core, inline=inline)
+
+
+def set_git_repo_metadata_from_path(kb, path='.'):
+    """ Use Git to set the Git repository URL, branch, and revision metadata for a knowledge base
+
+    Args:
+        kb (:obj:`core.KnowledgeBase`): knowledge base
+        path (:obj:`str`, optional): path to the Git repository for the knowledge base
+    """
+    md = git.get_repo_metadata(dirname=path)
+    kb.url = md.url
+    kb.branch = md.branch
+    kb.revision = md.revision