Cleanup SDK cruft, start on spec

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015 The KBase Project and its Contributors
+Copyright (c) 2019 The KBase Project and its Contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

README.md

@@ -4,7 +4,7 @@ This is a [KBase](https://kbase.us) module generated by the [KBase Software Deve
 
 You will need to have the SDK installed to use this module. [Learn more about the SDK and how to use it](https://kbase.github.io/kb_sdk_docs/).
 
-You can also learn more about the apps implemented in this module from its [catalog page](https://narrative.kbase.us/#catalog/modules/SampleService) or its [spec file]($module_name.spec).
+You can also learn more about the apps implemented in this module from its [catalog page](https://narrative.kbase.us/#catalog/modules/SampleService) or its [spec file](SampleService.spec).
 
 # Setup and test
 

RELEASE_NOTES.md

@@ -1,6 +1,6 @@
 # SampleService release notes
 =========================================
 
-0.0.0
+0.1.0
 -----
 * Module created by kb-sdk init

SampleService.spec

@@ -1,16 +1,70 @@
 /*
 A KBase module: SampleService
+
+Handles creating, updating, retriving samples and linking data to samples.
 */
 
 module SampleService {
+
+    /* A key in a metadata key/value pair. Less than 1000 unicode characters. */
+    typedef string metadata_key;
+
+    /* A value in a metadata key/value pair. Less than 1000 unicode characters. */
+    typedef string metadata_value;
+
+    /* Units for a quantity, e.g. km, mol/g, ppm, etc.
+        'None' for unitless quantities.
+        Less than 50 unicode characters.
+     */
+    typedef string units;
+
+    /* A SampleNode ID. Must be unique within a Sample, contain only the characters
+      [a-zA-Z0-9_], and be less than 255 characters.
+     */
+    typedef string node_id;
+
+    /* A Sample ID. Must be globally unique. Always assigned by the Sample service. */
+    typedef string sample_id;
+
+    /* The version of a sample. Always > 0. */
+    typedef int version;
+
+    /* Metadata attached to a sample. */
+    typedef mapping<metadata_key, tuple<metadata_value, units>> metadata;
+
+    /* A node in a sample tree.
+        id - the ID of the node. 
+        meta_controlled - metadata restricted by the sample controlled vocabulary and validators.
+        meta_user - unrestricted metadata.
+     */
     typedef structure {
-        string report_name;
-        string report_ref;
-    } ReportResults;
+        node_id id;
+        metadata meta_controlled;
+        metadata meta_user;
+    } SampleNode;
 
-    /*
-        This example function accepts any number of parameters and returns results in a KBaseReport
-    */
-    funcdef run_SampleService(mapping<string,UnspecifiedObject> params) returns (ReportResults output) authentication required;
+    /* A Sample, consisting of a tree of subsamples and replicates.
+        id - the ID of the sample.
+        single_node - the node in a single node tree.
+     */
+    typedef structure {
+        sample_id id;
+        SampleNode single_node;
+    } Sample;
+
+    /* A Sample ID and version.
+        id - the ID of the sample.
+        version - the version of the sample.
+     */
+    typedef structure {
+        sample_id id;
+        version version;
+    } SampleAddress;
 
+    /* Create a new sample or a sample version.
+        If Sample.id is null, a new Sample is created along with a new ID.
+        Otherwise, a new version of Sample.id is created. If Sample.id does not exist, an error
+          is returned.
+     */
+    funcdef create_sample(Sample sample) returns(SampleAddress address) authentication required; 
 };

TODO.md

@@ -0,0 +1,3 @@
+* coverage
+* https://github.com/kbaseIncubator/samples/pull/1/files
+* The ~10 documents that have been written about this

dependencies.json

@@ -1,8 +1,4 @@
 [ {
-  "module_name" : "KBaseReport",
-  "type" : "sdk",
-  "version_tag" : "release"
-}, {
   "module_name" : "Workspace",
   "type" : "core",
   "file_path" : "https://raw.githubusercontent.com/kbase/workspace_deluxe/master/workspace.spec"

kbase.yml

@@ -2,13 +2,13 @@ module-name:
     SampleService
 
 module-description:
-    A KBase module
+    Handles creating, updating, retriving samples and linking data to samples.
 
 service-language:
     python
 
 module-version:
-    0.0.1
+    0.1.0-alpha1
 
 owners:
     [gaprice]

lib/SampleService/SampleServiceImpl.py

@@ -14,6 +14,8 @@ class SampleService:
 
     Module Description:
     A KBase module: SampleService
+
+Handles creating, updating, retriving samples and linking data to samples.
     '''
 
     ######## WARNING FOR GEVENT USERS ####### noqa
@@ -24,7 +26,7 @@ class SampleService:
     ######################################### noqa
     VERSION = "0.0.1"
     GIT_URL = "https://github.com/mrcreosote/sample_service.git"
-    GIT_COMMIT_HASH = "3bac7cdfc9fe72b5a8b807eb80248c32e2b7929b"
+    GIT_COMMIT_HASH = "c63c061ffbc6f2aef594a7fbdcd07badd8bf4c2a"
 
     #BEGIN_CLASS_HEADER
     #END_CLASS_HEADER
@@ -41,32 +43,55 @@ def __init__(self, config):
         pass
 
 
-    def run_SampleService(self, ctx, params):
+    def create_sample(self, ctx, sample):
         """
-        This example function accepts any number of parameters and returns results in a KBaseReport
-        :param params: instance of mapping from String to unspecified object
-        :returns: instance of type "ReportResults" -> structure: parameter
-           "report_name" of String, parameter "report_ref" of String
+        Create a new sample or a sample version.
+        If Sample.id is null, a new Sample is created along with a new ID.
+        Otherwise, a new version of Sample.id is created. If Sample.id does not exist, an error
+          is returned.
+        :param sample: instance of type "Sample" (A Sample, consisting of a
+           tree of subsamples and replicates. id - the ID of the sample.
+           single_node - the node in a single node tree.) -> structure:
+           parameter "id" of type "sample_id" (A Sample ID. Must be globally
+           unique. Always assigned by the Sample service.), parameter
+           "single_node" of type "SampleNode" (A node in a sample tree. id -
+           the ID of the node. meta_controlled - metadata restricted by the
+           sample controlled vocabulary and validators. meta_user -
+           unrestricted metadata.) -> structure: parameter "id" of type
+           "node_id" (A SampleNode ID. Must be unique within a Sample,
+           contain only the characters [a-zA-Z0-9_], and be less than 255
+           characters.), parameter "meta_controlled" of type "metadata"
+           (Metadata attached to a sample.) -> mapping from type
+           "metadata_key" (A key in a metadata key/value pair. Less than 1000
+           unicode characters.) to tuple of size 2: type "metadata_value" (A
+           value in a metadata key/value pair. Less than 1000 unicode
+           characters.), type "units" (Units for a quantity, e.g. km, mol/g,
+           ppm, etc. 'None' for unitless quantities. Less than 50 unicode
+           characters.), parameter "meta_user" of type "metadata" (Metadata
+           attached to a sample.) -> mapping from type "metadata_key" (A key
+           in a metadata key/value pair. Less than 1000 unicode characters.)
+           to tuple of size 2: type "metadata_value" (A value in a metadata
+           key/value pair. Less than 1000 unicode characters.), type "units"
+           (Units for a quantity, e.g. km, mol/g, ppm, etc. 'None' for
+           unitless quantities. Less than 50 unicode characters.)
+        :returns: instance of type "SampleAddress" (A Sample ID and version.
+           id - the ID of the sample. version - the version of the sample.)
+           -> structure: parameter "id" of type "sample_id" (A Sample ID.
+           Must be globally unique. Always assigned by the Sample service.),
+           parameter "version" of type "version" (The version of a sample.
+           Always > 0.)
         """
         # ctx is the context object
-        # return variables are: output
-        #BEGIN run_SampleService
-        report = KBaseReport(self.callback_url)
-        report_info = report.create({'report': {'objects_created':[],
-                                                'text_message': params['parameter_1']},
-                                                'workspace_name': params['workspace_name']})
-        output = {
-            'report_name': report_info['name'],
-            'report_ref': report_info['ref'],
-        }
-        #END run_SampleService
+        # return variables are: address
+        #BEGIN create_sample
+        #END create_sample
 
         # At some point might do deeper type checking...
-        if not isinstance(output, dict):
-            raise ValueError('Method run_SampleService return value ' +
-                             'output is not type dict as required.')
+        if not isinstance(address, dict):
+            raise ValueError('Method create_sample return value ' +
+                             'address is not type dict as required.')
         # return the results
-        return [output]
+        return [address]
     def status(self, ctx):
         #BEGIN_STATUS
         returnVal = {'state': "OK",