Add task to checkout configuration from repository

Change-Id: If77203d5162e64b00cdb79eec918944501746852

setup.py

@@ -18,6 +18,7 @@
     "bluepyopt",
     "bluepymm",
     "diameter_synthesis",
+    "gitpython",
     "h5py",
     "joblib",
     "luigi",

synthesis_workflow/tasks/utils.py

@@ -0,0 +1,62 @@
+"""Utils luigi tasks."""
+import shutil
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+import luigi
+from git import Repo
+
+from .config import SynthesisConfig
+from .luigi_tools import copy_params
+from .luigi_tools import ParamLink
+from .luigi_tools import WorkflowTask
+
+
+class GitClone(WorkflowTask):
+    """Task to clone a git repository"""
+
+    url = luigi.Parameter()
+    dest = luigi.Parameter()
+
+    def run(self):
+        """"""
+        Repo.clone_from(self.url, self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(self.dest)
+
+
+@copy_params(
+    tmd_parameters_path=ParamLink(SynthesisConfig),
+    tmd_distributions_path=ParamLink(SynthesisConfig),
+)
+class GetOfficialConfiguration(WorkflowTask):
+    """Task to get official parameters from the git repository"""
+
+    url = luigi.Parameter()
+    specie = luigi.ChoiceParameter(choices=["rat", "mouse", "human"])
+    version = luigi.OptionalParameter(default=None)
+
+    def run(self):
+        """"""
+        with TemporaryDirectory() as tmpdir:
+            dest = Path(tmpdir) / "tmp_repo"
+            # Note: can not be called with yield here because of the TemporaryDirectory
+            GitClone(url=self.url, dest=dest).run()
+            if self.version is not None:
+                r = Repo(dest)
+                r.git.checkout(self.version)
+            shutil.copy(
+                dest / "entities" / "bionames" / self.specie / "tmd_parameters.json",
+                self.tmd_parameters_path,
+            )
+            shutil.copy(
+                dest / "entities" / "bionames" / self.specie / "tmd_distributions.json",
+                self.tmd_distributions_path,
+            )
+
+    def output(self):
+        return {
+            "tmd_parameters": luigi.LocalTarget(self.tmd_parameters_path),
+            "tmd_distributions": luigi.LocalTarget(self.tmd_distributions_path),
+        }