diff --git a/lib/fba_tools/authclient.py b/lib/fba_tools/authclient.py
index 9a15713..3bdf984 100644
--- a/lib/fba_tools/authclient.py
+++ b/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)
diff --git a/lib/fba_tools/fba_toolsClient.pm b/lib/fba_tools/fba_toolsClient.pm
index 8eb3392..517654d 100644
--- a/lib/fba_tools/fba_toolsClient.pm
+++ b/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
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
@@ -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
diff --git a/lib/fba_tools/fba_toolsClient.py b/lib/fba_tools/fba_toolsClient.py
index 1dc619e..573d8c7 100644
--- a/lib/fba_tools/fba_toolsClient.py
+++ b/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"
diff --git a/lib/fba_tools/fba_toolsImpl.pm b/lib/fba_tools/fba_toolsImpl.pm
index b28c36c..095be06 100644
--- a/lib/fba_tools/fba_toolsImpl.pm
+++ b/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
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
@@ -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
diff --git a/lib/src/us/kbase/fbatools/ModelObjectSelectionParams.java b/lib/src/us/kbase/fbatools/ModelObjectSelectionParams.java
index 55391c4..1b57e88 100644
--- a/lib/src/us/kbase/fbatools/ModelObjectSelectionParams.java
+++ b/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 additionalProperties = new HashMap();
@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 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)+"]");
}
}
diff --git a/lib/src/us/kbase/fbatools/PredictAuxotrophyParams.java b/lib/src/us/kbase/fbatools/PredictAuxotrophyParams.java
index d848e15..60346cb 100644
--- a/lib/src/us/kbase/fbatools/PredictAuxotrophyParams.java
+++ b/lib/src/us/kbase/fbatools/PredictAuxotrophyParams.java
@@ -2,6 +2,7 @@
package us.kbase.fbatools;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import javax.annotation.Generated;
import com.fasterxml.jackson.annotation.JsonAnyGetter;
@@ -19,96 +20,78 @@
@JsonInclude(JsonInclude.Include.NON_NULL)
@Generated("com.googlecode.jsonschema2pojo")
@JsonPropertyOrder({
- "genome_id",
- "media_output_id",
+ "genome_ids",
"genome_workspace",
"workspace"
})
public class PredictAuxotrophyParams {
- @JsonProperty("genome_id")
- private String genomeId;
- @JsonProperty("media_output_id")
- private String mediaOutputId;
+ @JsonProperty("genome_ids")
+ private List genomeIds;
@JsonProperty("genome_workspace")
- private String genomeWorkspace;
+ private java.lang.String genomeWorkspace;
@JsonProperty("workspace")
- private String workspace;
- private Map additionalProperties = new HashMap();
+ private java.lang.String workspace;
+ private Map additionalProperties = new HashMap();
- @JsonProperty("genome_id")
- public String getGenomeId() {
- return genomeId;
+ @JsonProperty("genome_ids")
+ public List getGenomeIds() {
+ return genomeIds;
}
- @JsonProperty("genome_id")
- public void setGenomeId(String genomeId) {
- this.genomeId = genomeId;
+ @JsonProperty("genome_ids")
+ public void setGenomeIds(List genomeIds) {
+ this.genomeIds = genomeIds;
}
- public PredictAuxotrophyParams withGenomeId(String genomeId) {
- this.genomeId = genomeId;
- return this;
- }
-
- @JsonProperty("media_output_id")
- public String getMediaOutputId() {
- return mediaOutputId;
- }
-
- @JsonProperty("media_output_id")
- public void setMediaOutputId(String mediaOutputId) {
- this.mediaOutputId = mediaOutputId;
- }
-
- public PredictAuxotrophyParams withMediaOutputId(String mediaOutputId) {
- this.mediaOutputId = mediaOutputId;
+ public PredictAuxotrophyParams withGenomeIds(List genomeIds) {
+ this.genomeIds = genomeIds;
return this;
}
@JsonProperty("genome_workspace")
- public String getGenomeWorkspace() {
+ public java.lang.String getGenomeWorkspace() {
return genomeWorkspace;
}
@JsonProperty("genome_workspace")
- public void setGenomeWorkspace(String genomeWorkspace) {
+ public void setGenomeWorkspace(java.lang.String genomeWorkspace) {
this.genomeWorkspace = genomeWorkspace;
}
- public PredictAuxotrophyParams withGenomeWorkspace(String genomeWorkspace) {
+ public PredictAuxotrophyParams withGenomeWorkspace(java.lang.String genomeWorkspace) {
this.genomeWorkspace = genomeWorkspace;
return this;
}
@JsonProperty("workspace")
- public String getWorkspace() {
+ public java.lang.String getWorkspace() {
return workspace;
}
@JsonProperty("workspace")
- public void setWorkspace(String workspace) {
+ public void setWorkspace(java.lang.String workspace) {
this.workspace = workspace;
}
- public PredictAuxotrophyParams withWorkspace(String workspace) {
+ public PredictAuxotrophyParams withWorkspace(java.lang.String workspace) {
this.workspace = workspace;
return this;
}
@JsonAnyGetter
- public Map getAdditionalProperties() {
+ public Map getAdditionalProperties() {
return this.additionalProperties;
}
@JsonAnySetter
- public void setAdditionalProperties(String name, Object value) {
+ public void setAdditionalProperties(java.lang.String name, Object value) {
this.additionalProperties.put(name, value);
}
@Override
- public String toString() {
- return ((((((((((("PredictAuxotrophyParams"+" [genomeId=")+ genomeId)+", mediaOutputId=")+ mediaOutputId)+", genomeWorkspace=")+ genomeWorkspace)+", workspace=")+ workspace)+", additionalProperties=")+ additionalProperties)+"]");
+ public java.lang.String toString() {
+ return ((((((((("PredictAuxotrophyParams"+" [genomeIds=")+ genomeIds)+", genomeWorkspace=")+ genomeWorkspace)+", workspace=")+ workspace)+", additionalProperties=")+ additionalProperties)+"]");
}
}
diff --git a/scripts/prepare_deploy_cfg.py b/scripts/prepare_deploy_cfg.py
index 395343f..e5b2032 100644
--- a/scripts/prepare_deploy_cfg.py
+++ b/scripts/prepare_deploy_cfg.py
@@ -1,6 +1,9 @@
import sys
+import os
+import os.path
from jinja2 import Template
from ConfigParser import ConfigParser
+import StringIO
if __name__ == "__main__":
if len(sys.argv) != 3:
@@ -12,7 +15,29 @@
text = file.read()
t = Template(text)
config = ConfigParser()
- config.read(sys.argv[2])
+ if os.path.isfile(sys.argv[2]):
+ config.read(sys.argv[2])
+ elif "KBASE_ENDPOINT" in os.environ:
+ kbase_endpoint = os.environ.get("KBASE_ENDPOINT")
+ props = "[global]\n" + \
+ "kbase_endpoint = " + kbase_endpoint + "\n" + \
+ "job_service_url = " + kbase_endpoint + "/userandjobstate\n" + \
+ "workspace_url = " + kbase_endpoint + "/ws\n" + \
+ "shock_url = " + kbase_endpoint + "/shock-api\n" + \
+ "handle_url = " + kbase_endpoint + "/handle_service\n" + \
+ "srv_wiz_url = " + kbase_endpoint + "/service_wizard\n" + \
+ "njsw_url = " + kbase_endpoint + "/njs_wrapper\n"
+ if "AUTH_SERVICE_URL" in os.environ:
+ props += "auth_service_url = " + os.environ.get("AUTH_SERVICE_URL") + "\n"
+ props += "auth_service_url_allow_insecure = " + \
+ os.environ.get("AUTH_SERVICE_URL_ALLOW_INSECURE", "false") + "\n"
+ for key in os.environ:
+ if key.startswith('KBASE_SECURE_CONFIG_PARAM_'):
+ param_name = key[len('KBASE_SECURE_CONFIG_PARAM_'):]
+ props += param_name + " = " + os.environ.get(key) + "\n"
+ config.readfp(StringIO.StringIO(props))
+ else:
+ raise ValueError('Neither ' + sys.argv[2] + ' file nor KBASE_ENDPOINT env-variable found')
props = dict(config.items("global"))
output = t.render(props)
with open(sys.argv[1] + ".orig", 'w') as f: