From 751bac23c02e75d51739ac83c91c2e727b7de1d6 Mon Sep 17 00:00:00 2001
From: Tiago Grego <tgrego@ebi.ac.uk>
Date: Wed, 27 Nov 2024 13:35:02 +0000
Subject: [PATCH] remove setup.py

---
 .../support-mini-x86-32/interproscan.sh       |   5 -
 .../support-mini-x86-32/setup.py              | 102 ------------------
 2 files changed, 107 deletions(-)
 delete mode 100755 core/jms-implementation/support-mini-x86-32/setup.py

diff --git a/core/jms-implementation/support-mini-x86-32/interproscan.sh b/core/jms-implementation/support-mini-x86-32/interproscan.sh
index f3f6691b0..8c5533fc5 100644
--- a/core/jms-implementation/support-mini-x86-32/interproscan.sh
+++ b/core/jms-implementation/support-mini-x86-32/interproscan.sh
@@ -49,11 +49,6 @@ then
     exit 1
 fi
 
-if ! python3 setup.py "$PROPERTIES"
-then
-    exit 1
-fi
-
 "$JAVA" \
  -XX:ParallelGCThreads=8 \
  -Xms2028M -Xmx9216M \
diff --git a/core/jms-implementation/support-mini-x86-32/setup.py b/core/jms-implementation/support-mini-x86-32/setup.py
deleted file mode 100755
index 2006e6fe9..000000000
--- a/core/jms-implementation/support-mini-x86-32/setup.py
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import glob
-import os
-import subprocess as sp
-import sys
-
-
-PROPERTIES="interproscan.properties"
-
-
-def load_properties(file, properties):
-    with open(file, "rt") as fh:
-        for line in map(str.strip, fh):
-            if not line or line[0] == "#":
-                continue
-
-            fields = line.split("=", 1)
-            if len(fields) == 2:
-                key = fields[0].strip()
-                value = fields[1].strip()
-                properties[key] = value
-
-    try:
-        bin_dir = properties["bin.directory"]
-        data_dir = properties["data.directory"]
-    except KeyError:
-        return
-
-    for key, value in properties.items():
-        if "${bin.directory}" in value:
-            value = value.replace("${bin.directory}", bin_dir)
-
-        if "${data.directory}" in value:
-            value = value.replace("${data.directory}", data_dir)
-
-        properties[key] = value
-
-
-def is_ready(hmmfile):
-    for ext in [".h3m", ".h3i", ".h3f", ".h3p"]:
-        if not os.path.isfile(hmmfile + ext):
-            return False
-
-    return True
-
-
-def hmmpress(binary, force, database):
-    if force:
-        cmd = [binary, "-f", database]
-    else:
-        cmd = [binary, database]
-
-    proc = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
-    outs, errs = proc.communicate()
-
-    if proc.returncode != 0:
-        sys.stderr.write(errs.decode())
-        sys.exit(1)
-
-
-def realpath(path):
-    return os.path.realpath(os.path.expanduser(path))
-
-
-def main():
-    parser = argparse.ArgumentParser(description="index HMM databases")
-    parser.add_argument("properties", help="InterProScan properties file")
-    parser.add_argument("-f", "--force", action="store_true",
-                        help="re-index all HMM databases (default: off)")
-    args = parser.parse_args()
-
-    properties = {}
-    load_properties(PROPERTIES, properties)
-
-    if realpath(args.properties) != realpath(PROPERTIES):
-        load_properties(args.properties, properties)
-
-    ignore = {"binary.tmhmm.path", "funfam.hmm.path", "smart.hmm.path"}
-    for key, path in properties.items():
-        if "hmm.path" in key and key not in ignore:
-            bin_key = "binary.hmmer3.path"
-
-            if os.path.isfile(path):
-                hmmfiles = [path]
-            else:
-                hmmfiles = glob.iglob(os.path.join(path, "**", "*.hmm"),
-                                      recursive=True)
-
-            for hmmfile in hmmfiles:
-                if args.force or not is_ready(hmmfile):
-                    try:
-                        bin_path = os.path.join(properties[bin_key], "hmmpress")
-                    except KeyError:
-                        continue
-                    else:
-                        hmmpress(bin_path, args.force, hmmfile)
-
-
-if __name__ == '__main__':
-    main()