kbaseapps · briehl · Jul 26, 2019
diff --git a/kb_SPAdes.spec b/kb_SPAdes.spec
@@ -15,7 +15,7 @@ module kb_SPAdes {
 
     /* A boolean. 0 = false, anything else = true. */
     typedef int bool;
-    
+
     /* The workspace object name of a PairedEndLibrary file, whether of the
        KBaseAssembly or KBaseFile type.
     */
@@ -96,7 +96,7 @@ module kb_SPAdes {
                      (all values must be odd, less than 128 and listed in ascending order)
                      In the absence of these values, K values are automatically selected.
     min_contig_length - integer to filter out contigs with length < min_contig_length
-                     from the HybridSPAdes output. Default value is 0 implying no filter.    
+                     from the HybridSPAdes output. Default value is 0 implying no filter.
     @optional dna_source
     @optional pipeline_options
     @optional kmer_sizes
@@ -126,7 +126,7 @@ module kb_SPAdes {
         string report_name;
         string report_ref;
     } SPAdesOutput;
-    
+
     /* Run SPAdes on paired end libraries */
     funcdef run_SPAdes(SPAdesParams params) returns(SPAdesOutput output)
         authentication required;
@@ -139,16 +139,6 @@ module kb_SPAdes {
     funcdef run_metaSPAdes(SPAdesParams params) returns(SPAdesOutput output)
         authentication required;
 
-    /*
-        params - the params used to run metaSPAdes.
-        use_defaults - (optional, def 0) if 1, just return the default requirements
-        use_heuristic - (optional, def 1) if 1, only use a heuristic based on the reads metadata to perform estimates
-    */
-    typedef structure {
-        SPAdesParams params;
-        int use_defaults;
-    } MetaSPAdesEstimatorParams;
-
     /*
         cpus - the number of CPUs required for the run
         memory - the minimal amount of memory in MB required for the run
@@ -159,8 +149,8 @@ module kb_SPAdes {
         int memory;
         int walltime;
     } MetaSPAdesEstimate;
-    
-    funcdef estimate_metaSPAdes_requirements(MetaSPAdesEstimatorParams params) returns 
+
+    funcdef estimate_metaSPAdes_requirements(SPAdesParams params) returns
         (MetaSPAdesEstimate results) authentication required;
 };
 
diff --git a/lib/kb_SPAdes/kb_SPAdesClient.pm b/lib/kb_SPAdes/kb_SPAdesClient.pm
@@ -469,11 +469,8 @@ Run SPAdes on paired end libraries for metagenomes
 =begin html
 
 <pre>
-$params is a kb_SPAdes.MetaSPAdesEstimatorParams
+$params is a kb_SPAdes.SPAdesParams
 $results is a kb_SPAdes.MetaSPAdesEstimate
-MetaSPAdesEstimatorParams is a reference to a hash where the following keys are defined:
-	params has a value which is a kb_SPAdes.SPAdesParams
-	use_defaults has a value which is an int
 SPAdesParams is a reference to a hash where the following keys are defined:
 	workspace_name has a value which is a string
 	output_contigset_name has a value which is a string
@@ -495,11 +492,8 @@ MetaSPAdesEstimate is a reference to a hash where the following keys are defined
 
 =begin text
 
-$params is a kb_SPAdes.MetaSPAdesEstimatorParams
+$params is a kb_SPAdes.SPAdesParams
 $results is a kb_SPAdes.MetaSPAdesEstimate
-MetaSPAdesEstimatorParams is a reference to a hash where the following keys are defined:
-	params has a value which is a kb_SPAdes.SPAdesParams
-	use_defaults has a value which is an int
 SPAdesParams is a reference to a hash where the following keys are defined:
 	workspace_name has a value which is a string
 	output_contigset_name has a value which is a string
@@ -924,7 +918,7 @@ kmer_sizes - (optional) K-mer sizes, Default values: 21, 33, 55, 77, 99, 127
                  (all values must be odd, less than 128 and listed in ascending order)
                  In the absence of these values, K values are automatically selected.
 min_contig_length - integer to filter out contigs with length < min_contig_length
-                 from the HybridSPAdes output. Default value is 0 implying no filter.    
+                 from the HybridSPAdes output. Default value is 0 implying no filter.
 @optional dna_source
 @optional pipeline_options
 @optional kmer_sizes
@@ -1011,45 +1005,6 @@ report_ref has a value which is a string
 
 
 
-=head2 MetaSPAdesEstimatorParams
-
-=over 4
-
-
-
-=item Description
-
-params - the params used to run metaSPAdes.
-use_defaults - (optional, def 0) if 1, just return the default requirements
-use_heuristic - (optional, def 1) if 1, only use a heuristic based on the reads metadata to perform estimates
-
-
-=item Definition
-
-=begin html
-
-<pre>
-a reference to a hash where the following keys are defined:
-params has a value which is a kb_SPAdes.SPAdesParams
-use_defaults has a value which is an int
-
-</pre>
-
-=end html
-
-=begin text
-
-a reference to a hash where the following keys are defined:
-params has a value which is a kb_SPAdes.SPAdesParams
-use_defaults has a value which is an int
-
-
-=end text
-
-=back
-
-
-
 =head2 MetaSPAdesEstimate
 
 =over 4

diff --git a/lib/kb_SPAdes/kb_SPAdesClient.py b/lib/kb_SPAdes/kb_SPAdesClient.py
@@ -167,15 +167,10 @@ def run_metaSPAdes(self, params, context=None):
 
     def estimate_metaSPAdes_requirements(self, params, context=None):
         """
-        :param params: instance of type "MetaSPAdesEstimatorParams" (params -
-           the params used to run metaSPAdes. use_defaults - (optional, def
-           0) if 1, just return the default requirements use_heuristic -
-           (optional, def 1) if 1, only use a heuristic based on the reads
-           metadata to perform estimates) -> structure: parameter "params" of
-           type "SPAdesParams" (Input parameters for running SPAdes.
-           workspace_name - the name of the workspace from which to take
-           input and store output. output_contigset_name - the name of the
-           output contigset read_libraries - a list of Illumina
+        :param params: instance of type "SPAdesParams" (Input parameters for
+           running SPAdes. workspace_name - the name of the workspace from
+           which to take input and store output. output_contigset_name - the
+           name of the output contigset read_libraries - a list of Illumina
            PairedEndLibrary files in FASTQ or BAM format. dna_source -
            (optional) the source of the DNA used for sequencing
            'single_cell': DNA amplified from a single cell via MDA anything
@@ -195,7 +190,7 @@ def estimate_metaSPAdes_requirements(self, params, context=None):
            "dna_source" of String, parameter "min_contig_length" of Long,
            parameter "kmer_sizes" of list of Long, parameter
            "skip_error_correction" of type "bool" (A boolean. 0 = false,
-           anything else = true.), parameter "use_defaults" of Long
+           anything else = true.)
         :returns: instance of type "MetaSPAdesEstimate" (cpus - the number of
            CPUs required for the run memory - the minimal amount of memory in
            MB required for the run walltime - an estimate for walltime in

diff --git a/lib/kb_SPAdes/kb_SPAdesImpl.py b/lib/kb_SPAdes/kb_SPAdesImpl.py
@@ -55,9 +55,9 @@ class kb_SPAdes:
     # state. A method could easily clobber the state set by another while
     # the latter method is running.
     ######################################### noqa
-    VERSION = "1.2.3"
+    VERSION = "1.3.0"
     GIT_URL = "https://github.com/briehl/kb_SPAdes"
-    GIT_COMMIT_HASH = "17687df25126cf201693f5686224b4777de36f0b"
+    GIT_COMMIT_HASH = "6f13deac910c9796ce8fc0d39075880f74c1ff4e"
 
     #BEGIN_CLASS_HEADER
     # Class variables and functions can be defined in this block
@@ -821,15 +821,10 @@ def run_metaSPAdes(self, ctx, params):
 
     def estimate_metaSPAdes_requirements(self, ctx, params):
         """
-        :param params: instance of type "MetaSPAdesEstimatorParams" (params -
-           the params used to run metaSPAdes. use_defaults - (optional, def
-           0) if 1, just return the default requirements use_heuristic -
-           (optional, def 1) if 1, only use a heuristic based on the reads
-           metadata to perform estimates) -> structure: parameter "params" of
-           type "SPAdesParams" (Input parameters for running SPAdes.
-           workspace_name - the name of the workspace from which to take
-           input and store output. output_contigset_name - the name of the
-           output contigset read_libraries - a list of Illumina
+        :param params: instance of type "SPAdesParams" (Input parameters for
+           running SPAdes. workspace_name - the name of the workspace from
+           which to take input and store output. output_contigset_name - the
+           name of the output contigset read_libraries - a list of Illumina
            PairedEndLibrary files in FASTQ or BAM format. dna_source -
            (optional) the source of the DNA used for sequencing
            'single_cell': DNA amplified from a single cell via MDA anything
@@ -849,7 +844,7 @@ def estimate_metaSPAdes_requirements(self, ctx, params):
            "dna_source" of String, parameter "min_contig_length" of Long,
            parameter "kmer_sizes" of list of Long, parameter
            "skip_error_correction" of type "bool" (A boolean. 0 = false,
-           anything else = true.), parameter "use_defaults" of Long
+           anything else = true.)
         :returns: instance of type "MetaSPAdesEstimate" (cpus - the number of
            CPUs required for the run memory - the minimal amount of memory in
            MB required for the run walltime - an estimate for walltime in
@@ -860,7 +855,7 @@ def estimate_metaSPAdes_requirements(self, ctx, params):
         # return variables are: results
         #BEGIN estimate_metaSPAdes_requirements
         ws = Workspace(self.workspaceURL, token=ctx["token"])
-        results = estimate_metaSPAdes_reqs(params["params"], ws, use_defaults=params.get("use_defaults", 0)==1)
+        results = estimate_metaSPAdes_reqs(params, ws)
         #END estimate_metaSPAdes_requirements
 
         # At some point might do deeper type checking...

diff --git a/lib/kb_SPAdes/utils/estimator.py b/lib/kb_SPAdes/utils/estimator.py
@@ -1,4 +1,4 @@
-def estimate_metaSPAdes_reqs(params, ws, use_defaults=False):
+def estimate_metaSPAdes_reqs(params, ws):
     """
     Generates an estimate of how much computational power is needed to run metaSPAdes.
     params: dict with keys (only relevant ones given):
@@ -18,19 +18,13 @@ def estimate_metaSPAdes_reqs(params, ws, use_defaults=False):
         raise ValueError("workspace_name is required to estimate metaSPAdes requirements!")
     if len(params.get("read_libraries", [])) == 0:
         raise ValueError("At least one read library is required to estimate metaSPAdes requirements!")
-    if use_defaults:
-        return {
-            "cpus": 16,
-            "memory": 4096,
-            "walltime": 300
-        }
 
     ws_name = params.get("workspace_name")
     reads_refs = []
     for lib_name in params["read_libraries"]:
         reads_refs.append({"ref": lib_name if "/" in lib_name else ws_name + "/" + lib_name})
     reads_infos = ws.get_object_info3({
-        "objects": reads_refs, 
+        "objects": reads_refs,
         "includeMetadata": 1
     })
 
@@ -55,12 +49,12 @@ def estimate_metaSPAdes_reqs(params, ws, use_defaults=False):
     # now we have an approximation of how many kmers there are. we can use
     # that to guesstimate how much memory we need
 
-    predicted_mem = (total_kmers * 2.962e-08 + 16.3) * 1.1 * 1024 
+    predicted_mem = (total_kmers * 2.962e-08 + 16.3) * 1.1 * 1024
 
     est = {
         "cpus": 16,
         "memory": max(int(predicted_mem), 4096),
         "walltime": max(total_kmers/100000, 300)
     }
 
-    return est
+    return est
diff --git a/lib/src/us/kbase/kbspades/HybridSPAdesParams.java b/lib/src/us/kbase/kbspades/HybridSPAdesParams.java
@@ -34,7 +34,7 @@
  *                  (all values must be odd, less than 128 and listed in ascending order)
  *                  In the absence of these values, K values are automatically selected.
  * min_contig_length - integer to filter out contigs with length < min_contig_length
- *                  from the HybridSPAdes output. Default value is 0 implying no filter.    
+ *                  from the HybridSPAdes output. Default value is 0 implying no filter.
  * @optional dna_source
  * @optional pipeline_options
  * @optional kmer_sizes

diff --git a/lib/src/us/kbase/kbspades/KbSPAdesClient.java b/lib/src/us/kbase/kbspades/KbSPAdesClient.java
@@ -227,12 +227,12 @@ public SPAdesOutput runMetaSPAdes(SPAdesParams params, RpcContext... jsonRpcCont
      * <p>Original spec-file function name: estimate_metaSPAdes_requirements</p>
      * <pre>
      * </pre>
-     * @param   params   instance of type {@link us.kbase.kbspades.MetaSPAdesEstimatorParams MetaSPAdesEstimatorParams}
+     * @param   params   instance of type {@link us.kbase.kbspades.SPAdesParams SPAdesParams}
      * @return   parameter "results" of type {@link us.kbase.kbspades.MetaSPAdesEstimate MetaSPAdesEstimate}
      * @throws IOException if an IO exception occurs
      * @throws JsonClientException if a JSON RPC exception occurs
      */
-    public MetaSPAdesEstimate estimateMetaSPAdesRequirements(MetaSPAdesEstimatorParams params, RpcContext... jsonRpcContext) throws IOException, JsonClientException {
+    public MetaSPAdesEstimate estimateMetaSPAdesRequirements(SPAdesParams params, RpcContext... jsonRpcContext) throws IOException, JsonClientException {
         List<Object> args = new ArrayList<Object>();
         args.add(params);
         TypeReference<List<MetaSPAdesEstimate>> retType = new TypeReference<List<MetaSPAdesEstimate>>() {};