obis: renamed object_id to sample_id - in the future we will also support experiments

.obis/config.json

-{"data_set_type": "DS_TYPE", "object_id": "/SAMPLE/ID", "openbis_url": "http://localhost:8888"}
+{"data_set_type": "DS_TYPE", "sample_id": "/SAMPLE/ID", "openbis_url": "http://localhost:8888"}
\ No newline at end of file

src/python/OBis/obis/dm/.obis/config.json

-{"data_set_id": "20170814175159563859-9212", "data_set_type": "DS_TYPE", "object_id": "/SAMPLE/ID", "openbis_url": "http://localhost:8888"}
+{"data_set_id": "20170814175159563859-9212", "data_set_type": "DS_TYPE", "sample_id": "/SAMPLE/ID", "openbis_url": "http://localhost:8888"}
\ No newline at end of file

src/python/OBis/obis/dm/config.py

@@ -88,7 +88,7 @@ class ConfigEnv(object):
         self.add_param(ConfigParam(name='verify_certificates', private=True, is_json=True))
         self.add_param(ConfigParam(name='external_dms_id', private=True))
         self.add_param(ConfigParam(name='repository_id', private=True))
-        self.add_param(ConfigParam(name='object_id', private=False))
+        self.add_param(ConfigParam(name='sample_id', private=False))
         self.add_param(ConfigParam(name='data_set_id', private=False))
         self.add_param(ConfigParam(name='data_set_type', private=False))
         self.add_param(ConfigParam(name='data_set_properties', private=False, is_json=True))

src/python/OBis/obis/dm/data_mgmt.py

@@ -414,8 +414,8 @@ class OpenbisSync(object):
     def data_set_properties(self):
         return self.config_dict.get('data_set_properties')
 
-    def object_id(self):
-        return self.config_dict.get('object_id')
+    def sample_id(self):
+        return self.config_dict.get('sample_id')
 
     def check_configuration(self):
         missing_config_settings = []
@@ -425,8 +425,8 @@ class OpenbisSync(object):
             missing_config_settings.append('user')
         if self.data_set_type() is None:
             missing_config_settings.append('data_set_type')
-        if self.object_id() is None:
-            missing_config_settings.append('object_id')
+        if self.sample_id() is None:
+            missing_config_settings.append('sample_id')
         if len(missing_config_settings) > 0:
             return CommandResult(returncode=-1,
                                  output="Missing configuration settings for {}.".format(missing_config_settings))
@@ -497,11 +497,11 @@ class OpenbisSync(object):
         if result.failure():
             return result
         commit_id = result.output
-        object_id = self.object_id()
+        sample_id = self.sample_id()
         contents = GitRepoFileInfo(self.git_wrapper).contents()
         try:
             data_set = self.openbis.new_git_data_set(data_set_type, top_level_path, commit_id, repository_id, external_dms.code,
-                                                     object_id, data_set_code=data_set_code, parents=parent_data_set_id,
+                                                     sample_id, data_set_code=data_set_code, parents=parent_data_set_id,
                                                      properties=properties, contents=contents)
             return CommandResult(returncode=0, output=""), data_set
         except ValueError as e:

src/python/OBis/obis/dm/data_mgmt_test.py

@@ -213,7 +213,7 @@ def set_registration_configuration(dm, properties=None):
     resolver.set_value_for_parameter('openbis_url', "http://localhost:8888", 'local')
     resolver.set_value_for_parameter('user', "auser", 'local')
     resolver.set_value_for_parameter('data_set_type', "DS_TYPE", 'local')
-    resolver.set_value_for_parameter('object_id', "/SAMPLE/ID", 'local')
+    resolver.set_value_for_parameter('sample_id', "/SAMPLE/ID", 'local')
     if properties is not None:
         resolver.set_value_for_parameter('data_set_properties', properties, 'local')
 

src/python/OBis/obis/scripts/cli.py

@@ -131,36 +131,36 @@ def set_property(data_mgmt, prop, value, is_global):
         return CommandResult(returncode=0, output="")
 
 
-def init_data_impl(ctx, object_id, folder, name):
+def init_data_impl(ctx, sample_id, folder, name):
     """Shared implementation for the init_data command."""
     click_echo("init_data {}".format(folder))
     data_mgmt = shared_data_mgmt(ctx.obj)
     name = name if name != "" else None
     result = data_mgmt.init_data(folder, name, create=True)
-    if not object_id or result.failure():
+    if not sample_id or result.failure():
         return check_result("init_data", result)
     with dm.cd(folder):
-        return check_result("init_data", set_property(data_mgmt, 'object_id', object_id, False))
+        return check_result("init_data", set_property(data_mgmt, 'sample_id', sample_id, False))
 
 
 @cli.command()
 @click.pass_context
-@click.option('-o', '--object_id', help='Set the id of the owning object.')
+@click.option('-o', '--sample_id', help='Set the id of the owning object.')
 @click.argument('folder', type=click.Path(exists=False, file_okay=False))
 @click.argument('name', default="")
-def init(ctx, object_id, folder, name):
+def init(ctx, sample_id, folder, name):
     """Initialize the folder as a data folder (alias for init_data)."""
-    return init_data_impl(ctx, object_id, folder, name)
+    return init_data_impl(ctx, sample_id, folder, name)
 
 
 @cli.command()
 @click.pass_context
-@click.option('-o', '--object_id', help='Set the id of the owning object.')
+@click.option('-o', '--sample_id', help='Set the id of the owning object.')
 @click.argument('folder', type=click.Path(exists=False, file_okay=False))
 @click.argument('name', default="")
-def init_data(ctx, object_id, folder, name):
+def init_data(ctx, sample_id, folder, name):
     """Initialize the folder as a data folder."""
-    return init_data_impl(ctx, object_id, folder, name)
+    return init_data_impl(ctx, sample_id, folder, name)
 
 
 @cli.command()

src/vagrant/obis/README.md

@@ -64,9 +64,9 @@ Now create a file and put some content into it. E.g.,
 
     vi info.txt
 
-When finished, we need to set the object_id this data set should be associated with. Then we can commit it.
+When finished, we need to set the sample_id this data set should be associated with. Then we can commit it.
 
-    obis config object_id /DEMO/BIGDATA
+    obis config sample_id /DEMO/BIGDATA
     obis commit -m"Initial data commit."
 
 Log into the sprint server https://sprint-openbis.ethz.ch:8446 and go to the sample /DEMO/BIGDATA. You should see the newly registered data set there. You can take a look at it and see file metadata for its contents.