Add logging

ivelet · Jul 11, 2024 · 6a929e5 · 6a929e5
1 parent a84185d
commit 6a929e5
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/tools/rna_tools/rnaformer/infer_rnaformer.xml b/tools/rna_tools/rnaformer/infer_rnaformer.xml
@@ -1,4 +1,4 @@
-<tool id="infer_rnaformer" name="@EXECUTABLE" version="@TOOL_VERSION@" profile="22.05">
+<tool id="infer_rnaformer" name="@EXECUTABLE@" version="@TOOL_VERSION@" profile="22.05">
     <description>Predict the secondary structure of an RNA with RNAformer</description>
     <macros>
         <token name="@EXECUTABLE@">RNAformer</token>
@@ -7,7 +7,7 @@
     <expand macro="requirements">
         <requirement type="package" version="1.83">biopython</requirement>
     </expand>
-    <command detect_errors="exit_code"><![CDATA[python '$script_file' > '$output' 
+    <command detect_errors="exit_code"><![CDATA[python '$script_file' > '$output'
 ]]></command>
 <configfiles>
         <configfile name="script_file"><![CDATA[import RNAformer
@@ -24,19 +24,27 @@ from RNAformer.utils.configuration import Config
 
 from Bio import SeqIO
 
+import logging
+import sys
+
+print("Start tool", file=sys.stderr)
+
 config_file_path = '$__tool_directory__/RNAformer_32M_config_intra_family_finetuned.yml'
 model_file_path = '$__tool_directory__/RNAformer_32M_state_dict_intra_family_finetuned.pth'
 if not os.path.exists(model_file_path):
+    print("No model, try downloading", file=sys.stderr)
     download_url = "https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_state_dict_intra_family_finetuned.pth"
     logging.info(f"Model file {model_file_path} not found. Downloading from {download_url}...")
     urllib.request.urlretrieve(download_url, model_file_path)
     logging.info(f"Downloaded model file to {model_file_path}.")
 if not os.path.exists(config_file_path):
+p   rint("No config, try downloading", file=sys.stderr)
     download_url = "https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_config_intra_family_finetuned.yml"
     logging.info(f"Model file {config_file_path} not found. Downloading from {download_url}...")
     urllib.request.urlretrieve(download_url, config_file_path)
     logging.info(f"Downloaded model file to {config_file_path}.")
 
+print("Load model and config", file=sys.stderr)
 config = Config(config_file=config_file_path)
 config.RNAformer.cycling = 6
 model = RiboFormer(config.RNAformer)

diff --git a/tools/rna_tools/rnaformer/macros.xml b/tools/rna_tools/rnaformer/macros.xml
@@ -1,4 +1,5 @@
 <macros>
+    <token name="@EXECUTABLE@">RNAformer</token>
     <token name="@TOOL_VERSION@">1.0.0</token>
     <token name="@profile@">22.05</token>
     <xml name="requirements">