Mercurial > repos > peterjc > effectivet3

changeset 8:60a9b3f760cc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.0.17 Used cached URL, python style updates
author peterjc
date Wed, 01 Feb 2017 09:22:21 -0500
parents 5f85301d50bf
children 512530020360
files tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.xml tools/effectiveT3/tool_dependencies.xml
diffstat 4 files changed, 67 insertions(+), 63 deletions(-) [+]
line wrap: on
line diff
--- a/tools/effectiveT3/README.rst	Mon Sep 21 05:52:29 2015 -0400
+++ b/tools/effectiveT3/README.rst	Wed Feb 01 09:22:21 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy wrapper for EffectiveT3 v1.0.1
 =====================================
 
-This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2011-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -94,6 +94,8 @@
         - Includes new standard classification model v2.0.2 (Sep 2015)
           as the default entry in ``tool-data/effectiveT3.loc``
         - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar``
+v0.0.17 - Update tool dependency definition to use cached URL.
+        - Minor internal changes to Python script for error reporting & style.
 ======= ======================================================================
 
 
--- a/tools/effectiveT3/effectiveT3.py	Mon Sep 21 05:52:29 2015 -0400
+++ b/tools/effectiveT3/effectiveT3.py	Wed Feb 01 09:22:21 2017 -0500
@@ -16,30 +16,26 @@
 import subprocess
 
 # The Galaxy auto-install via tool_dependencies.xml will set this environment variable
-effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
-effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")
+effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
+effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar")
 
 if "-v" in sys.argv or "--version" in sys.argv:
     # TODO - Get version of the JAR file dynamically?
-    print("Wrapper v0.0.16, TTSS_GUI-1.0.1.jar")
+    print("Wrapper v0.0.17, TTSS_GUI-1.0.1.jar")
     sys.exit(0)
 
-def sys_exit(msg, error_level=1):
-   """Print error message to stdout and quit with given error level."""
-   sys.stderr.write("%s\n" % msg)
-   sys.exit(error_level)
-
 if len(sys.argv) != 5:
-   sys_exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
+    sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
 
 model, threshold, fasta_file, tabular_file = sys.argv[1:]
 
 if not os.path.isfile(fasta_file):
-   sys_exit("Input FASTA file not found: %s" % fasta_file)
+    sys.exit("Input FASTA file not found: %s" % fasta_file)
 
 if threshold not in ["selective", "sensitive"] \
-and not threshold.startswith("cutoff="):
-   sys_exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+    and not threshold.startswith("cutoff="):
+    sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+
 
 def clean_tabular(raw_handle, out_handle):
     """Clean up Effective T3 output to make it tabular."""
@@ -48,65 +44,66 @@
     errors = 0
     for line in raw_handle:
         if not line or line.startswith("#") \
-        or line.startswith("Id; Description; Score;"):
+            or line.startswith("Id; Description; Score;"):
             continue
         assert line.count(";") >= 3, repr(line)
         # Normally there will just be three semi-colons, however the
         # original FASTA file's ID or description might have had
         # semi-colons in it as well, hence the following hackery:
         try:
-            id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
+            id_descr, score, effective = line.rstrip("\r\n").rsplit(";", 2)
             # Cope when there was no FASTA description
             if "; " not in id_descr and id_descr.endswith(";"):
                 id = id_descr[:-1]
                 descr = ""
             else:
-                id, descr = id_descr.split("; ",1)
+                id, descr = id_descr.split("; ", 1)
         except ValueError:
-            sys_exit("Problem parsing line:\n%s\n" % line)
+            sys.exit("Problem parsing line:\n%s\n" % line)
         parts = [s.strip() for s in [id, descr, score, effective]]
         out_handle.write("\t".join(parts) + "\n")
         count += 1
         if float(score) < 0:
-           errors += 1
+            errors += 1
         if effective.lower() == "true":
-           positive += 1
+            positive += 1
     return count, positive, errors
 
+
 def run(cmd):
     # Avoid using shell=True when we call subprocess to ensure if the Python
     # script is killed, so too is the child process.
     try:
         child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except Exception, err:
-        sys_exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     # Use .communicate as can get deadlocks with .wait(),
     stdout, stderr = child.communicate()
     return_code = child.returncode
     if return_code or stderr.startswith("Exception in thread"):
-        cmd_str= " ".join(cmd)  # doesn't quote spaces etc
+        cmd_str = " ".join(cmd)  # doesn't quote spaces etc
         if stderr and stdout:
-            sys_exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
+            sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
         else:
-            sys_exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
+            sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
 
 
-if not os.path.isdir(effectiveT3_dir):
-    sys_exit("Effective T3 folder not found: %r" % effectiveT3_dir)
+if not os.path.isdir(effective_t3_dir):
+    sys.exit("Effective T3 folder not found: %r" % effective_t3_dir)
 
-if not os.path.isfile(effectiveT3_jar):
-    sys_exit("Effective T3 JAR file not found: %r" % effectiveT3_jar)
+if not os.path.isfile(effective_t3_jar):
+    sys.exit("Effective T3 JAR file not found: %r" % effective_t3_jar)
 
-if not os.path.isdir(os.path.join(effectiveT3_dir, "module")):
-    sys_exit("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module"))
+if not os.path.isdir(os.path.join(effective_t3_dir, "module")):
+    sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module"))
 
-effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
-if not os.path.isfile(effectiveT3_model):
+effective_t3_model = os.path.join(effective_t3_dir, "module", model)
+if not os.path.isfile(effective_t3_model):
     sys.stderr.write("Contents of %r is %s\n"
-                     % (os.path.join(effectiveT3_dir, "module"),
-                        ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
-    sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
-    sys_exit("Effective T3 model JAR file not found: %r" % effectiveT3_model)
+                     % (os.path.join(effective_t3_dir, "module"),
+                        ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module")))))
+    sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar)
+    sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model)
 
 # We will have write access whereever the output should be,
 temp_file = os.path.abspath(tabular_file + ".tmp")
@@ -115,7 +112,7 @@
 tabular_file = os.path.abspath(tabular_file)
 fasta_file = os.path.abspath(fasta_file)
 
-cmd = ["java", "-jar", effectiveT3_jar,
+cmd = ["java", "-jar", effective_t3_jar,
        "-f", fasta_file,
        "-m", model,
        "-t", threshold,
@@ -124,14 +121,14 @@
 
 try:
     # Must run from directory above the module subfolder:
-    os.chdir(effectiveT3_dir)
-except:
-    sys_exit("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
+    os.chdir(effective_t3_dir)
+except Exception:
+    sys.exit("Could not change to Effective T3 folder: %s" % effective_t3_dir)
 
 run(cmd)
 
 if not os.path.isfile(temp_file):
-   sys_exit("ERROR - No output file from Effective T3")
+    sys.exit("ERROR - No output file from Effective T3")
 
 out_handle = open(tabular_file, "w")
 out_handle.write("#ID\tDescription\tScore\tEffective\n")
@@ -143,11 +140,11 @@
 os.remove(temp_file)
 
 if errors:
-   print("%i sequences, %i positive, %i errors"
-         % (count, positive, errors))
+    print("%i sequences, %i positive, %i errors"
+          % (count, positive, errors))
 else:
-   print("%i/%i sequences positive" % (positive, count))
+    print("%i/%i sequences positive" % (positive, count))
 
-if count and count==errors:
-   # Galaxy will still  allow them to see the output file
-   sys_exit("All your sequences gave an error code")
+if count and count == errors:
+    # Galaxy will still  allow them to see the output file
+    sys.exit("All your sequences gave an error code")
--- a/tools/effectiveT3/effectiveT3.xml	Mon Sep 21 05:52:29 2015 -0400
+++ b/tools/effectiveT3/effectiveT3.xml	Wed Feb 01 09:22:21 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.16">
+<tool id="effectiveT3" name="Effective T3" version="0.0.17">
     <description>Find bacterial effectors in protein sequences</description>
     <requirements>
         <requirement type="package" version="1.0.1">effectiveT3</requirement>
--- a/tools/effectiveT3/tool_dependencies.xml	Mon Sep 21 05:52:29 2015 -0400
+++ b/tools/effectiveT3/tool_dependencies.xml	Wed Feb 01 09:22:21 2017 -0500
@@ -3,29 +3,34 @@
     <package name="effectiveT3" version="1.0.1">
         <install version="1.0">
             <actions>
-                <!-- Set environment variable so Python script knows where to look -->
+                <!-- Main JAR file -->
+                <!-- Original URL http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_GUI-1.0.1.jar -->
+                <action type="download_file" sha256sum="5a811a86a14dffbc5ae91dc45f40791642b8866266ffd2337b97d4c298129cab" target_filename="TTSS_GUI-1.0.1.jar">https://depot.galaxyproject.org/software/TTSS_GUI/TTSS_GUI_1.0.1_src_all.jar</action>
+                <action type="move_file"><source>TTSS_GUI-1.0.1.jar</source><destination>$INSTALL_DIR</destination></action>
+                <!-- Model specific JAR files -->
+                <action type="make_directory">$INSTALL_DIR/module</action>
+                <!-- Original URL http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_ANIMAL-1.0.1.jar -->
+                <action type="download_file" sha256sum="3d9cd8e805387d2dfa855076b3d5f7f97334aa612288075111329fb036c94e34" target_filename="TTSS_ANIMAL-1.0.1.jar">https://depot.galaxyproject.org/software/TTSS_ANIMAL/TTSS_ANIMAL_1.0.1_src_all.jar</action>
+                <action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>        
+                <!-- Original URL http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_PLANT-1.0.1.jar -->
+                <action type="download_file" sha256sum="593f0052ace030c2fa16cf336f3916a21bc2addbaefdfa149b084b1425e42a13" target_filename="TTSS_PLANT-1.0.1.jar">https://depot.galaxyproject.org/software/TTSS_PLANT/TTSS_PLANT_1.0.1_src_all.jar</action>
+                <action type="move_file"><source>TTSS_PLANT-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
+                <!-- Original URL http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-1.0.1.jar -->
+                <action type="download_file" sha256sum="865809e5ead6d8bb038e854ccaebc7c102b72738ff3557553af9b9ac8e529336" target_filename="TTSS_STD-1.0.1.jar">https://depot.galaxyproject.org/software/TTSS_STD/TTSS_STD_1.0.1_src_all.jar</action>
+                <action type="move_file"><source>TTSS_STD-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
+                <!-- Original URL http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-2.0.2.jar -->
+                <action type="download_file" sha256sum="860c6e3680fa1f3c6ac2362605205af4cdd9a1caefee59fdbd37d1453c9bad44" target_filename="TTSS_STD-2.0.2.jar">https://depot.galaxyproject.org/software/TTSS_STD/TTSS_STD_2.0.2_src_all.jar</action>
+                <action type="move_file"><source>TTSS_STD-2.0.2.jar</source><destination>$INSTALL_DIR/module/</destination></action>
+                <!-- Make this accessible -->
                 <action type="set_environment">
                     <environment_variable name="EFFECTIVET3" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
-                <!-- Main JAR file -->
-                <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_GUI-1.0.1.jar</action>
-                <!-- If using action type download_file will need to move the file,
-                <action type="move_file"><source>TTSS_GUI-1.0.1.jar</source><destination>$INSTALL_DIR/</destination></action>
-                -->
-                <!-- Three model JAR files -->
-                <action type="make_directory">$INSTALL_DIR/module</action>
-                <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_ANIMAL-1.0.1.jar</action>
-                <action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>        
-                <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_PLANT-1.0.1.jar</action>
-                <action type="move_file"><source>TTSS_PLANT-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
-                <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-1.0.1.jar</action>
-                <action type="move_file"><source>TTSS_STD-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
-                <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-2.0.2.jar</action>
-                <action type="move_file"><source>TTSS_STD-2.0.2.jar</source><destination>$INSTALL_DIR/module/</destination></action>
             </actions>
         </install>
         <readme>
 Downloads effectiveT3 v1.0.1 and associated models from http://effectors.org/ aka http://effectors.csb.univie.ac.at/
+
+Sets environment variable $EFFECTIVET3 to the directory containing the main JAR file whose subdirectory module/ holds the model JAR files.
         </readme>
     </package>
 </tool_dependency>