From 9b287ef06c3a3f4bc72bdd52a59fc0b2ae98016a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 8 Jul 2019 16:17:56 +0200
Subject: [PATCH] Push scripts into subpackages.

---
 packages/app/setup.py            |   2 +
 packages/data/setup.py           |   3 +-
 packages/meta/setup.py           |   4 -
 scripts/build_universe_config.py |  35 ---
 scripts/check_galaxy.py          | 416 -------------------------------
 5 files changed, 4 insertions(+), 456 deletions(-)
 delete mode 100644 scripts/build_universe_config.py
 delete mode 100755 scripts/check_galaxy.py

diff --git a/packages/app/setup.py b/packages/app/setup.py
index 1f1b2fa3b07f..61c68cbb3a89 100644
--- a/packages/app/setup.py
+++ b/packages/app/setup.py
@@ -102,6 +102,8 @@ def get_var(var_name):
 ]
 ENTRY_POINTS = '''
         [console_scripts]
+        galaxy-main=galaxy.main:main
+        galaxy-config=galaxy.config.script:main
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
diff --git a/packages/data/setup.py b/packages/data/setup.py
index 12556d60ed4f..28faa87c3d98 100644
--- a/packages/data/setup.py
+++ b/packages/data/setup.py
@@ -47,7 +47,8 @@ def get_var(var_name):
 ]
 ENTRY_POINTS = '''
         [console_scripts]
-        gx-build-objects=galaxy.model.store.build_objects:main
+        galaxy-build-objects=galaxy.model.store.build_objects:main
+        galaxy-manage-db=galaxy.model.orm.scripts:manage_db
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
diff --git a/packages/meta/setup.py b/packages/meta/setup.py
index ba0cd02ba7b6..07e0d7a2d4f5 100644
--- a/packages/meta/setup.py
+++ b/packages/meta/setup.py
@@ -32,10 +32,6 @@ def get_var(var_name):
 PACKAGES = []
 ENTRY_POINTS = '''
         [console_scripts]
-        galaxy-paster=galaxy.util.pastescript.serve:run
-        galaxy-main=galaxy.main:main
-        galaxy-config=galaxy.config.script:main
-        galaxy-manage-db=galaxy.model.orm.scripts:manage_db
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
diff --git a/scripts/build_universe_config.py b/scripts/build_universe_config.py
deleted file mode 100644
index 44c15be7c29c..000000000000
--- a/scripts/build_universe_config.py
+++ /dev/null
@@ -1,35 +0,0 @@
-from os import listdir
-from os.path import join
-from re import match
-from sys import argv
-
-from six.moves.configparser import ConfigParser
-
-
-def merge():
-    """
-    Merges all .ini files in a specified directory into a file (defaults to
-    ./config/galaxy.ini ).
-    """
-    if len(argv) < 2:
-        message = "%s: Must specify directory to merge configuration files from." % argv[0]
-        raise Exception(message)
-    conf_directory = argv[1]
-    conf_files = [f for f in listdir(conf_directory) if match(r'.*\.ini', f)]
-    conf_files.sort()
-
-    parser = ConfigParser()
-    for conf_file in conf_files:
-        parser.read([join(conf_directory, conf_file)])
-    # TODO: Expand enviroment variables here, that would
-    # also make Galaxy much easier to configure.
-
-    destination = "config/galaxy.ini"
-    if len(argv) > 2:
-        destination = argv[2]
-
-    parser.write(open(destination, 'w'))
-
-
-if __name__ == '__main__':
-    merge()
diff --git a/scripts/check_galaxy.py b/scripts/check_galaxy.py
deleted file mode 100755
index 22f96a6bf0cc..000000000000
--- a/scripts/check_galaxy.py
+++ /dev/null
@@ -1,416 +0,0 @@
-#!/usr/bin/env python
-"""
-check_galaxy can be run by hand, although it is meant to run from cron
-via the check_galaxy.sh script in Galaxy's cron/ directory.
-"""
-from __future__ import print_function
-
-import filecmp
-import formatter
-import getopt
-import htmllib
-import os
-import socket
-import sys
-import tempfile
-import time
-
-import twill
-import twill.commands as tc
-
-# options
-if "DEBUG" in os.environ:
-    debug = os.environ["DEBUG"]
-else:
-    debug = False
-scripts_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
-test_data_dir = os.path.join(scripts_dir, os.pardir, "test-data")
-# what tools to run - not so pretty
-tools = {
-    "gops_intersect_1":
-    [
-        {
-            "inputs":
-            (
-                os.path.join(test_data_dir, "1.bed"),
-                os.path.join(test_data_dir, "2.bed")
-            )
-        },
-        {"check_file": os.path.join(test_data_dir, "gops_intersect_out.bed")},
-        {
-            "tool_run_options":
-            {
-                "input1": "1.bed",
-                "input2": "2.bed",
-                "min": "1",
-                "returntype": ""
-            }
-        }
-    ]
-}
-
-
-# handle arg(s)
-def usage():
-    sys.exit("usage: check_galaxy.py <server>")
-
-
-try:
-    opts, args = getopt.getopt(sys.argv[1:], 'n')
-except getopt.GetoptError as e:
-    print(str(e))
-    usage()
-if len(args) < 1:
-    usage()
-server = args[0]
-if server.endswith(".g2.bx.psu.edu"):
-    if debug:
-        print("Checking a PSU Galaxy server, using maint file")
-    maint = "/errordocument/502/%s/maint" % args[0].split('.', 1)[0]
-else:
-    maint = None
-new_history = False
-for o, a in opts:
-    if o == "-n":
-        if debug:
-            print("Specified -n, will create a new history")
-        new_history = True
-    else:
-        usage()
-
-# state information
-var_dir = os.path.join(os.path.expanduser('~'), ".check_galaxy", server)
-if not os.access(var_dir, os.F_OK):
-    os.makedirs(var_dir, 0o700)
-
-# get user/pass
-login_file = os.path.join(var_dir, "login")
-try:
-    f = open(login_file, 'r')
-except Exception:
-    message = """Please create the file:
-%s
-This should contain a username and password to log in to Galaxy with,
-on one line, separated by whitespace, e.g.:
-
-check_galaxy@example.com password
-
-If the user does not exist, check_galaxy will create it for you.""" % login_file
-    sys.exit(message)
-(username, password) = f.readline().split()
-
-# default timeout for twill browser is never
-socket.setdefaulttimeout(300)
-
-# user-agent
-tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.1)")
-tc.config('use_tidy', 0)
-
-
-class Browser(object):
-
-    def __init__(self):
-        self.server = server
-        self.maint = maint
-        self.tool = None
-        self.tool_opts = None
-        self.id = None
-        self.status = None
-        self.check_file = None
-        self.hid = None
-        self.cookie_jar = os.path.join(var_dir, "cookie_jar")
-        dprint("cookie jar path: %s" % self.cookie_jar)
-        if not os.access(self.cookie_jar, os.R_OK):
-            dprint("no cookie jar at above path, creating")
-            tc.save_cookies(self.cookie_jar)
-        tc.load_cookies(self.cookie_jar)
-
-    def get(self, path):
-        tc.go("http://%s%s" % (self.server, path))
-        tc.code(200)
-
-    def reset(self):
-        self.tool = None
-        self.tool_opts = None
-        self.id = None
-        self.status = None
-        self.check_file = None
-        self.delete_datasets()
-        self.get("/root/history")
-        p = didParser()
-        p.feed(tc.browser.get_html())
-        if len(p.dids) > 0:
-            print("Remaining datasets ids:", " ".join(p.dids))
-            raise Exception("History still contains datasets after attempting to delete them")
-        if new_history:
-            self.get("/history/delete_current")
-            tc.save_cookies(self.cookie_jar)
-
-    def check_redir(self, url):
-        try:
-            tc.get_browser()._browser.set_handle_redirect(False)
-            tc.go(url)
-            tc.code(302)
-            tc.get_browser()._browser.set_handle_redirect(True)
-            dprint("%s is returning redirect (302)" % url)
-            return(True)
-        except twill.errors.TwillAssertionError as e:
-            tc.get_browser()._browser.set_handle_redirect(True)
-            dprint("%s is not returning redirect (302): %s" % (url, e))
-            code = tc.browser.get_code()
-            if code == 502:
-                is_maint = self.check_maint()
-                if is_maint:
-                    dprint("Galaxy is down, but a maint file was found, so not sending alert")
-                    sys.exit(0)
-                else:
-                    sys.exit("Galaxy is down (code 502)")
-            return(False)
-
-    # checks for a maint file
-    def check_maint(self):
-        if self.maint is None:
-            # dprint( "Warning: unable to check maint file for %s" % self.server )
-            return(False)
-        try:
-            self.get(self.maint)
-            return(True)
-        except twill.errors.TwillAssertionError:
-            return(False)
-
-    def login(self, user, pw):
-        self.get("/user/login")
-        tc.fv("1", "email", user)
-        tc.fv("1", "password", pw)
-        tc.submit("Login")
-        tc.code(200)
-        if len(tc.get_browser().get_all_forms()) > 0:
-            # uh ohs, fail
-            p = userParser()
-            p.feed(tc.browser.get_html())
-            if p.no_user:
-                dprint("user does not exist, will try creating")
-                self.create_user(user, pw)
-            elif p.bad_pw:
-                raise Exception("Password is incorrect")
-            else:
-                raise Exception("Unknown error logging in")
-        tc.save_cookies(self.cookie_jar)
-
-    def create_user(self, user, pw):
-        self.get("/user/create")
-        tc.fv("1", "email", user)
-        tc.fv("1", "password", pw)
-        tc.fv("1", "confirm", pw)
-        tc.submit("Submit")
-        tc.code(200)
-        if len(tc.get_browser().get_all_forms()) > 0:
-            p = userParser()
-            p.feed(tc.browser.get_html())
-            if p.already_exists:
-                raise Exception('The user you were trying to create already exists')
-
-    def upload(self, file):
-        self.get("/tool_runner/index?tool_id=upload1")
-        tc.fv("1", "file_type", "bed")
-        tc.formfile("1", "file_data", file)
-        tc.submit("runtool_btn")
-        tc.code(200)
-
-    def runtool(self):
-        self.get("/tool_runner/index?tool_id=%s" % self.tool)
-        for k, v in self.tool_opts.items():
-            tc.fv("1", k, v)
-        tc.submit("runtool_btn")
-        tc.code(200)
-
-    def wait(self):
-        sleep_amount = 1
-        count = 0
-        maxiter = 16
-        while count < maxiter:
-            count += 1
-            self.get("/root/history")
-            page = tc.browser.get_html()
-            if page.find('<!-- running: do not change this comment, used by TwillTestCase.wait -->') > -1:
-                time.sleep(sleep_amount)
-                sleep_amount += 1
-            else:
-                break
-        if count == maxiter:
-            raise Exception("Tool never finished")
-
-    def check_status(self):
-        self.get("/root/history")
-        p = historyParser()
-        p.feed(tc.browser.get_html())
-        if p.status != "ok":
-            raise Exception("JOB %s NOT OK: %s" % (p.id, p.status))
-        self.id = p.id
-        self.status = p.status
-        # return((p.id, p.status))
-
-    def diff(self):
-        self.get("/datasets/%s/display/display?to_ext=bed" % self.id)
-        data = tc.browser.get_html()
-        tmp = tempfile.mkstemp()
-        dprint("tmp file: %s" % tmp[1])
-        tmpfh = os.fdopen(tmp[0], 'w')
-        tmpfh.write(data)
-        tmpfh.close()
-        if filecmp.cmp(tmp[1], self.check_file):
-            dprint("Tool output is as expected")
-        else:
-            if not debug:
-                os.remove(tmp[1])
-            raise Exception("Tool output differs from expected")
-        if not debug:
-            os.remove(tmp[1])
-
-    def delete_datasets(self):
-        self.get("/root/history")
-        p = didParser()
-        p.feed(tc.browser.get_html())
-        dids = p.dids
-        for did in dids:
-            self.get("/datasets/%s/delete" % did)
-
-    def check_if_logged_in(self):
-        self.get("/user?cntrller=user")
-        p = loggedinParser()
-        p.feed(tc.browser.get_html())
-        return p.logged_in
-
-
-class userParser(htmllib.HTMLParser):
-    def __init__(self):
-        htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
-        self.in_span = False
-        self.in_div = False
-        self.no_user = False
-        self.bad_pw = False
-        self.already_exists = False
-
-    def start_span(self, attrs):
-        self.in_span = True
-
-    def start_div(self, attrs):
-        self.in_div = True
-
-    def end_span(self):
-        self.in_span = False
-
-    def end_div(self):
-        self.in_div = False
-
-    def handle_data(self, data):
-        if self.in_span or self.in_div:
-            if data == "No such user (please note that login is case sensitive)":
-                self.no_user = True
-            elif data == "Invalid password":
-                self.bad_pw = True
-            elif data == "User with that email already exists":
-                self.already_exists = True
-
-
-class historyParser(htmllib.HTMLParser):
-    def __init__(self):
-        htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
-        self.status = None
-        self.id = None
-
-    def start_div(self, attrs):
-        # find the top history item
-        for i in attrs:
-            if i[0] == "class" and i[1].startswith("historyItemWrapper historyItem historyItem-"):
-                self.status = i[1].rsplit("historyItemWrapper historyItem historyItem-", 1)[1]
-                dprint("status: %s" % self.status)
-            if i[0] == "id" and i[1].startswith("historyItem-"):
-                self.id = i[1].rsplit("historyItem-", 1)[1]
-                dprint("id: %s" % self.id)
-        if self.status is not None:
-            self.reset()
-
-
-class didParser(htmllib.HTMLParser):
-    def __init__(self):
-        htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
-        self.dids = []
-
-    def start_div(self, attrs):
-        for i in attrs:
-            if i[0] == "id" and i[1].startswith("historyItemContainer-"):
-                self.dids.append(i[1].rsplit("historyItemContainer-", 1)[1])
-                dprint("got a dataset id: %s" % self.dids[-1])
-
-
-class loggedinParser(htmllib.HTMLParser):
-    def __init__(self):
-        htmllib.HTMLParser.__init__(self, formatter.NullFormatter())
-        self.in_p = False
-        self.logged_in = False
-
-    def start_p(self, attrs):
-        self.in_p = True
-
-    def end_p(self):
-        self.in_p = False
-
-    def handle_data(self, data):
-        if self.in_p:
-            if data == "You are currently not logged in.":
-                self.logged_in = False
-            elif data.startswith("You are currently logged in as "):
-                self.logged_in = True
-
-
-def dprint(str):
-    if debug:
-        print(str)
-
-
-if __name__ == "__main__":
-    dprint("checking %s" % server)
-
-    b = Browser()
-
-    # login (or not)
-    if b.check_if_logged_in():
-        dprint("we are already logged in (via cookies), hooray!")
-    else:
-        dprint("not logged in... logging in")
-        b.login(username, password)
-
-    for tool, params in tools.items():
-
-        check_file = ""
-
-        # make sure history and state is clean
-        b.reset()
-        b.tool = tool
-
-        # get all the tool run conditions
-        for dict in params:
-            for k, v in dict.items():
-                if k == 'inputs':
-                    for file in v:
-                        b.upload(file)
-                elif k == 'check_file':
-                    b.check_file = v
-                elif k == 'tool_run_options':
-                    b.tool_opts = v
-                else:
-                    raise Exception("Unknown key in tools dict: %s" % k)
-
-        b.runtool()
-        b.wait()
-        b.check_status()
-        b.diff()
-        b.delete_datasets()
-
-        # by this point, everything else has succeeded.  there should be no maint.
-        is_maint = b.check_maint()
-        if is_maint:
-            sys.exit("Galaxy is up and fully functional, but a maint file is in place.")
-
-    sys.exit(0)