Merge pull request #69 from kbaseapps/remake

Remake

lib/fba_tools/authclient.py

@@ -57,7 +57,7 @@ class KBaseAuth(object):
     A very basic KBase auth client for the Python server.
     '''
 
-    _LOGIN_URL = 'https://kbase.us/services/authorization/Sessions/Login'
+    _LOGIN_URL = 'https://kbase.us/services/auth/api/legacy/KBase/Sessions/Login'
 
     def __init__(self, auth_url=None):
         '''
@@ -84,7 +84,7 @@ def get_user(self, token):
                 ret.raise_for_status()
             raise ValueError('Error connecting to auth service: {} {}\n{}'
                              .format(ret.status_code, ret.reason,
-                                     err['error_msg']))
+                                     err['error']['message']))
 
         user = ret.json()['user_id']
         self._cache.add_valid_token(token, user)

lib/fba_tools/fba_toolsClient.pm

@@ -1623,12 +1623,10 @@ Identifies reactions in the model that are not mass balanced
 $params is a fba_tools.PredictAuxotrophyParams
 $results is a fba_tools.PredictAuxotrophyResults
 PredictAuxotrophyParams is a reference to a hash where the following keys are defined:
-	genome_id has a value which is a fba_tools.genome_id
-	media_output_id has a value which is a fba_tools.media_id
+	genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 	genome_workspace has a value which is a fba_tools.workspace_name
 	workspace has a value which is a fba_tools.workspace_name
 genome_id is a string
-media_id is a string
 workspace_name is a string
 PredictAuxotrophyResults is a reference to a hash where the following keys are defined:
 	new_report_ref has a value which is a fba_tools.ws_report_id
@@ -1643,12 +1641,10 @@ ws_report_id is a string
 $params is a fba_tools.PredictAuxotrophyParams
 $results is a fba_tools.PredictAuxotrophyResults
 PredictAuxotrophyParams is a reference to a hash where the following keys are defined:
-	genome_id has a value which is a fba_tools.genome_id
-	media_output_id has a value which is a fba_tools.media_id
+	genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 	genome_workspace has a value which is a fba_tools.workspace_name
 	workspace has a value which is a fba_tools.workspace_name
 genome_id is a string
-media_id is a string
 workspace_name is a string
 PredictAuxotrophyResults is a reference to a hash where the following keys are defined:
 	new_report_ref has a value which is a fba_tools.ws_report_id
@@ -2426,7 +2422,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2443,7 +2441,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2524,7 +2524,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2541,7 +2543,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2622,7 +2626,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 ModelTsvFiles is a reference to a hash where the following keys are defined:
 	compounds_file has a value which is a fba_tools.File
 	reactions_file has a value which is a fba_tools.File
@@ -2642,7 +2648,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 ModelTsvFiles is a reference to a hash where the following keys are defined:
 	compounds_file has a value which is a fba_tools.File
 	reactions_file has a value which is a fba_tools.File
@@ -6586,8 +6594,7 @@ new_report_ref has a value which is a fba_tools.ws_report_id
 
 <pre>
 a reference to a hash where the following keys are defined:
-genome_id has a value which is a fba_tools.genome_id
-media_output_id has a value which is a fba_tools.media_id
+genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 genome_workspace has a value which is a fba_tools.workspace_name
 workspace has a value which is a fba_tools.workspace_name
 
@@ -6598,8 +6605,7 @@ workspace has a value which is a fba_tools.workspace_name
 =begin text
 
 a reference to a hash where the following keys are defined:
-genome_id has a value which is a fba_tools.genome_id
-media_output_id has a value which is a fba_tools.media_id
+genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 genome_workspace has a value which is a fba_tools.workspace_name
 workspace has a value which is a fba_tools.workspace_name
 
@@ -7138,6 +7144,7 @@ a reference to a hash where the following keys are defined:
 workspace_name has a value which is a string
 model_name has a value which is a string
 save_to_shock has a value which is a fba_tools.boolean
+fulldb has a value which is a fba_tools.bool
 
 </pre>
 
@@ -7149,6 +7156,7 @@ a reference to a hash where the following keys are defined:
 workspace_name has a value which is a string
 model_name has a value which is a string
 save_to_shock has a value which is a fba_tools.boolean
+fulldb has a value which is a fba_tools.bool
 
 
 =end text

lib/fba_tools/fba_toolsClient.py

@@ -403,12 +403,11 @@ def predict_auxotrophy(self, params, context=None):
         """
         Identifies reactions in the model that are not mass balanced
         :param params: instance of type "PredictAuxotrophyParams" ->
-           structure: parameter "genome_id" of type "genome_id" (A string
-           representing a Genome id.), parameter "media_output_id" of type
-           "media_id" (A string representing a Media id.), parameter
-           "genome_workspace" of type "workspace_name" (A string representing
-           a workspace name.), parameter "workspace" of type "workspace_name"
-           (A string representing a workspace name.)
+           structure: parameter "genome_ids" of list of type "genome_id" (A
+           string representing a Genome id.), parameter "genome_workspace" of
+           type "workspace_name" (A string representing a workspace name.),
+           parameter "workspace" of type "workspace_name" (A string
+           representing a workspace name.)
         :returns: instance of type "PredictAuxotrophyResults" -> structure:
            parameter "new_report_ref" of type "ws_report_id" (The workspace
            ID for a Report object @id ws KBaseReport.Report)
@@ -565,7 +564,8 @@ def model_to_excel_file(self, model, context=None):
         :param model: instance of type "ModelObjectSelectionParams" ->
            structure: parameter "workspace_name" of String, parameter
            "model_name" of String, parameter "save_to_shock" of type
-           "boolean" (A boolean - 0 for false, 1 for true. @range (0, 1))
+           "boolean" (A boolean - 0 for false, 1 for true. @range (0, 1)),
+           parameter "fulldb" of type "bool" (A binary boolean)
         :returns: instance of type "File" -> structure: parameter "path" of
            String, parameter "shock_id" of String
         """
@@ -578,7 +578,8 @@ def model_to_sbml_file(self, model, context=None):
         :param model: instance of type "ModelObjectSelectionParams" ->
            structure: parameter "workspace_name" of String, parameter
            "model_name" of String, parameter "save_to_shock" of type
-           "boolean" (A boolean - 0 for false, 1 for true. @range (0, 1))
+           "boolean" (A boolean - 0 for false, 1 for true. @range (0, 1)),
+           parameter "fulldb" of type "bool" (A binary boolean)
         :returns: instance of type "File" -> structure: parameter "path" of
            String, parameter "shock_id" of String
         """
@@ -591,7 +592,8 @@ def model_to_tsv_file(self, model, context=None):
         :param model: instance of type "ModelObjectSelectionParams" ->
            structure: parameter "workspace_name" of String, parameter
            "model_name" of String, parameter "save_to_shock" of type
-           "boolean" (A boolean - 0 for false, 1 for true. @range (0, 1))
+           "boolean" (A boolean - 0 for false, 1 for true. @range (0, 1)),
+           parameter "fulldb" of type "bool" (A binary boolean)
         :returns: instance of type "ModelTsvFiles" -> structure: parameter
            "compounds_file" of type "File" -> structure: parameter "path" of
            String, parameter "shock_id" of String, parameter "reactions_file"

lib/fba_tools/fba_toolsImpl.pm

@@ -1780,12 +1780,10 @@ sub check_model_mass_balance
 $params is a fba_tools.PredictAuxotrophyParams
 $results is a fba_tools.PredictAuxotrophyResults
 PredictAuxotrophyParams is a reference to a hash where the following keys are defined:
-	genome_id has a value which is a fba_tools.genome_id
-	media_output_id has a value which is a fba_tools.media_id
+	genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 	genome_workspace has a value which is a fba_tools.workspace_name
 	workspace has a value which is a fba_tools.workspace_name
 genome_id is a string
-media_id is a string
 workspace_name is a string
 PredictAuxotrophyResults is a reference to a hash where the following keys are defined:
 	new_report_ref has a value which is a fba_tools.ws_report_id
@@ -1800,12 +1798,10 @@ ws_report_id is a string
 $params is a fba_tools.PredictAuxotrophyParams
 $results is a fba_tools.PredictAuxotrophyResults
 PredictAuxotrophyParams is a reference to a hash where the following keys are defined:
-	genome_id has a value which is a fba_tools.genome_id
-	media_output_id has a value which is a fba_tools.media_id
+	genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 	genome_workspace has a value which is a fba_tools.workspace_name
 	workspace has a value which is a fba_tools.workspace_name
 genome_id is a string
-media_id is a string
 workspace_name is a string
 PredictAuxotrophyResults is a reference to a hash where the following keys are defined:
 	new_report_ref has a value which is a fba_tools.ws_report_id
@@ -2609,7 +2605,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2626,7 +2624,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2701,7 +2701,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2718,7 +2720,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 File is a reference to a hash where the following keys are defined:
 	path has a value which is a string
 	shock_id has a value which is a string
@@ -2789,7 +2793,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 ModelTsvFiles is a reference to a hash where the following keys are defined:
 	compounds_file has a value which is a fba_tools.File
 	reactions_file has a value which is a fba_tools.File
@@ -2809,7 +2815,9 @@ ModelObjectSelectionParams is a reference to a hash where the following keys are
 	workspace_name has a value which is a string
 	model_name has a value which is a string
 	save_to_shock has a value which is a fba_tools.boolean
+	fulldb has a value which is a fba_tools.bool
 boolean is an int
+bool is an int
 ModelTsvFiles is a reference to a hash where the following keys are defined:
 	compounds_file has a value which is a fba_tools.File
 	reactions_file has a value which is a fba_tools.File
@@ -6540,8 +6548,7 @@ new_report_ref has a value which is a fba_tools.ws_report_id
 
 <pre>
 a reference to a hash where the following keys are defined:
-genome_id has a value which is a fba_tools.genome_id
-media_output_id has a value which is a fba_tools.media_id
+genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 genome_workspace has a value which is a fba_tools.workspace_name
 workspace has a value which is a fba_tools.workspace_name
 
@@ -6552,8 +6559,7 @@ workspace has a value which is a fba_tools.workspace_name
 =begin text
 
 a reference to a hash where the following keys are defined:
-genome_id has a value which is a fba_tools.genome_id
-media_output_id has a value which is a fba_tools.media_id
+genome_ids has a value which is a reference to a list where each element is a fba_tools.genome_id
 genome_workspace has a value which is a fba_tools.workspace_name
 workspace has a value which is a fba_tools.workspace_name
 
@@ -7092,6 +7098,7 @@ a reference to a hash where the following keys are defined:
 workspace_name has a value which is a string
 model_name has a value which is a string
 save_to_shock has a value which is a fba_tools.boolean
+fulldb has a value which is a fba_tools.bool
 
 </pre>
 
@@ -7103,6 +7110,7 @@ a reference to a hash where the following keys are defined:
 workspace_name has a value which is a string
 model_name has a value which is a string
 save_to_shock has a value which is a fba_tools.boolean
+fulldb has a value which is a fba_tools.bool
 
 
 =end text

lib/src/us/kbase/fbatools/ModelObjectSelectionParams.java

@@ -21,7 +21,8 @@
 @JsonPropertyOrder({
     "workspace_name",
     "model_name",
-    "save_to_shock"
+    "save_to_shock",
+    "fulldb"
 })
 public class ModelObjectSelectionParams {
 
@@ -31,6 +32,8 @@ public class ModelObjectSelectionParams {
     private String modelName;
     @JsonProperty("save_to_shock")
     private Long saveToShock;
+    @JsonProperty("fulldb")
+    private Long fulldb;
     private Map<String, Object> additionalProperties = new HashMap<String, Object>();
 
     @JsonProperty("workspace_name")
@@ -78,6 +81,21 @@ public ModelObjectSelectionParams withSaveToShock(Long saveToShock) {
         return this;
     }
 
+    @JsonProperty("fulldb")
+    public Long getFulldb() {
+        return fulldb;
+    }
+
+    @JsonProperty("fulldb")
+    public void setFulldb(Long fulldb) {
+        this.fulldb = fulldb;
+    }
+
+    public ModelObjectSelectionParams withFulldb(Long fulldb) {
+        this.fulldb = fulldb;
+        return this;
+    }
+
     @JsonAnyGetter
     public Map<String, Object> getAdditionalProperties() {
         return this.additionalProperties;
@@ -90,7 +108,7 @@ public void setAdditionalProperties(String name, Object value) {
 
     @Override
     public String toString() {
-        return ((((((((("ModelObjectSelectionParams"+" [workspaceName=")+ workspaceName)+", modelName=")+ modelName)+", saveToShock=")+ saveToShock)+", additionalProperties=")+ additionalProperties)+"]");
+        return ((((((((((("ModelObjectSelectionParams"+" [workspaceName=")+ workspaceName)+", modelName=")+ modelName)+", saveToShock=")+ saveToShock)+", fulldb=")+ fulldb)+", additionalProperties=")+ additionalProperties)+"]");
     }
 
 }