Impl log collection opt

q2_autopepsirf/actions/diffEnrich.py

@@ -4,11 +4,14 @@
     PepsirfInfoSumOfProbesFmt, PepsirfInfoSNPNFormat,
     PepsirfContingencyTSVFormat, ZscoreNanFormat, EnrichedPeptideDirFmt
 )
+from subprocess import run
 
 import csv
 import os
 import pandas as pd
 import qiime2
+from q2_autopepsirf.utils import collect_logs
+
 
 # Name: diffenrich
 # Process: automatically runs through q2-ps-plot modules and q2-pepsirf modules
@@ -38,6 +41,7 @@ def diffEnrich(
         exact_cs_thresh="20",
         exact_zenrich_thresh=None,
         pepsirf_tsv_dir="./",
+        pepsirf_logs_dir="./logs",
         tsv_base_str=None,
         step_z_thresh=5,
         upper_z_thresh=30,
@@ -304,6 +308,8 @@ def diffEnrich(
         pepsirf_binary=pepsirf_binary
     )
 
+    collect_logs(pepsirf_logs_dir)
+
     # return all files created
     return (
         col_sum, diff, diff_ratio, zscore_out, nan_out, sample_names,

q2_autopepsirf/actions/diffEnrich_deconv.py

@@ -5,6 +5,7 @@
 )
 
 import os
+from q2_autopepsirf.utils import collect_logs
 
 def diffEnrich_deconv(
         ctx,
@@ -27,6 +28,7 @@ def diffEnrich_deconv(
         exact_cs_thresh="20",
         exact_zenrich_thresh=None,
         pepsirf_tsv_dir="./",
+        pepsirf_logs_dir="./logs",
         tsv_base_str=None,
         step_z_thresh=5,
         upper_z_thresh=30,
@@ -62,6 +64,7 @@ def diffEnrich_deconv(
         exact_cs_thresh=exact_cs_thresh,
         exact_zenrich_thresh=exact_zenrich_thresh,
         pepsirf_tsv_dir=pepsirf_tsv_dir,
+        pepsirf_logs_dir=pepsirf_logs_dir,
         tsv_base_str=tsv_base_str,
         step_z_thresh=step_z_thresh,
         upper_z_thresh=upper_z_thresh,
@@ -93,6 +96,8 @@ def diffEnrich_deconv(
         deconv_tsv = dir_out.view(PepsirfDeconvBatchDirFmt)
         deconv_tsv.save(os.path.join(pepsirf_tsv_dir, deconv_base), ext=".tsv")    
 
+    collect_logs(pepsirf_logs_dir)
+
     return (
         dir_out, score_per_round, map_dir, col_sum, diff, diff_ratio, 
         zscore_out, nan_out, sample_names, read_counts, rc_boxplot_out,

q2_autopepsirf/actions/diffEnrich_deconv_tsv.py

@@ -27,6 +27,7 @@ def diffEnrich_deconv_tsv(
         exact_cs_thresh="20",
         exact_zenrich_thresh=None,
         pepsirf_tsv_dir="./",
+        pepsirf_logs_dir="./logs",
         tsv_base_str=None,
         step_z_thresh=5,
         upper_z_thresh=30,
@@ -114,6 +115,7 @@ def diffEnrich_deconv_tsv(
         exact_cs_thresh=exact_cs_thresh,
         exact_zenrich_thresh=exact_zenrich_thresh,
         pepsirf_tsv_dir=pepsirf_tsv_dir,
+        pepsirf_logs_dir=pepsirf_logs_dir,
         tsv_base_str=tsv_base_str,
         step_z_thresh=step_z_thresh,
         upper_z_thresh=upper_z_thresh,

q2_autopepsirf/actions/diffEnrich_tsv.py

@@ -38,6 +38,7 @@ def diffEnrich_tsv(
         exact_cs_thresh="20",
         exact_zenrich_thresh=None,
         pepsirf_tsv_dir="./",
+        pepsirf_logs_dir="./logs",
         tsv_base_str=None,
         step_z_thresh=5,
         upper_z_thresh=30,
@@ -104,6 +105,7 @@ def diffEnrich_tsv(
         exact_cs_thresh=exact_cs_thresh,
         exact_zenrich_thresh=exact_zenrich_thresh,
         pepsirf_tsv_dir=pepsirf_tsv_dir,
+        pepsirf_logs_dir=pepsirf_logs_dir,
         tsv_base_str=tsv_base_str,
         step_z_thresh=step_z_thresh,
         upper_z_thresh=upper_z_thresh,

q2_autopepsirf/plugin_setup.py

@@ -60,6 +60,7 @@
     "upper_z_thresh": Int % Range(2, None),
     "lower_z_thresh": Int % Range(1, None),
     "pepsirf_tsv_dir": Str,
+    "pepsirf_logs_dir": Str,
     "tsv_base_str": Str,
     "hdi": Float % Range(0.0, 1.0),
     "infer_pairs_source": Bool,
@@ -96,6 +97,8 @@
         " tsv-base-str for output of tsv verison of qza files. The"
         " source_samples file and png boxplot outputs will always be put"
         " within this directory.",
+    "pepsirf_logs_dir": "Path to a directory which PepSIRF log files will be"
+        " collected.",
     "tsv_base_str": "The base name for the output tsv files excluding ay"
         " extensions, typcally the raw data filename (EX: --p-tsv-base-str"
         " raw_data). Must also provide pepsirf-tsv-dir, if pepsirf-tsv-dir"
@@ -273,4 +276,3 @@
         " that are used to determine enriched peptides and"
         " **ADD DECONV DESCRIPTION**"
 )
-

q2_autopepsirf/utils.py

@@ -0,0 +1,14 @@
+import os
+import glob
+import shutil
+
+
+def collect_logs(path):
+    # collect pepsirf logs into a directory at `path`
+    # check for there is not a directory for logs already
+    if not os.path.isdir(path):
+        os.mkdir(path)
+    # collect log files
+    files = glob.glob("*.log", recursive=True)
+    for file in files:
+        shutil.move(file, path)