--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fill_ctd.py	Wed Sep 09 12:51:25 2020 +0000
@@ -0,0 +1,190 @@
+import collections
+import json
+import operator
+import os
+import re
+import subprocess
+import sys
+from functools import reduce  # forward compatibility for Python 3
+
+from CTDopts.CTDopts import (
+    _Choices,
+    _InFile,
+    _Null,
+    _NumericRange,
+    CTDModel
+)
+
+
+def getFromDict(dataDict, mapList):
+    return reduce(operator.getitem, mapList, dataDict)
+
+
+def setInDict(dataDict, mapList, value):
+    getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
+
+
+def mergeDicts(d, e):
+    """
+    insert values from the dict e into dict d
+    no values of d are overwritten
+    """
+    for k, v in e.items():
+        if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
+            mergeDicts(d[k], e[k])
+        elif k not in d and not isinstance(e[k], collections.abc.Mapping):
+            d[k] = e[k]
+        else:
+            sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
+            sys.exit(1)
+
+
+def _json_object_hook_noenvlookup(d):
+    return _json_object_hook(d, envlookup=False)
+
+
+def _json_object_hook(d, envlookup=True):
+    """
+    wee helper to transform the json written by galaxy
+    while loading
+    - True/False (bool objects) -> "true"/"false" (lowercase string)
+    - data inputs with multiple and optional true give [None] if no file is given -> []
+    - None -> "" (empty string)
+    - replace bash expressions (if envlookup is True):
+      - environment variables (need to consist capital letters and _) by their value
+      - expressions
+    """
+    for k in d.keys():
+        # if type(d[k]) is bool:
+        #     d[k] = str(d[k]).lower()
+        # else
+        if type(d[k]) is list and len(d[k]) == 1 and d[k][0] is None:
+            d[k] = []
+        elif d[k] is None:
+            d[k] = ""
+        elif envlookup and type(d[k]) is str and d[k].startswith("$"):
+            m = re.fullmatch(r"\$([A-Z_]+)", d[k])
+            if m:
+                d[k] = os.environ.get(m.group(1), "")
+                continue
+            m = re.fullmatch(r"\$(\{[A-Z_]+):-(.*)\}", d[k])
+            if m:
+                d[k] = os.environ.get(m.group(1), m.group(2))
+                continue
+
+            try:
+                p = subprocess.run("echo %s" % d[k], shell=True, check=True, stdout=subprocess.PIPE, encoding="utf8")
+                d[k] = p.stdout.strip()
+            except subprocess.CalledProcessError:
+                sys.stderr.write("fill_ctd error: Could not evaluate %s" % d[k])
+                continue
+    return d
+
+
+def qstring2list(qs):
+    """
+    transform a space separated string that is quoted by " into a list
+    """
+    lst = list()
+    qs = qs.split(" ")
+    quoted = False
+    for p in qs:
+        if p == "":
+            continue
+        if p.startswith('"') and p.endswith('"'):
+            lst.append(p[1:-1])
+        elif p.startswith('"'):
+            quoted = True
+            lst.append(p[1:] + " ")
+        elif p.endswith('"'):
+            quoted = False
+            lst[-1] += p[:-1]
+        else:
+            if quoted:
+                lst[-1] += p + " "
+            else:
+                lst.append(p)
+    return lst
+
+
+def fix_underscores(args):
+    if type(args) is dict:
+        for k in list(args.keys()):
+            v = args[k]
+            if type(v) is dict:
+                fix_underscores(args[k])
+            if k.startswith("_"):
+                args[k[1:]] = v
+                del args[k]
+    elif type(args) is list:
+        for i, v in enumerate(args):
+            if type(v) is dict:
+                fix_underscores(args[i])
+
+
+input_ctd = sys.argv[1]
+
+# load user specified parameters from json
+with open(sys.argv[2]) as fh:
+    args = json.load(fh, object_hook=_json_object_hook_noenvlookup)
+
+# load hardcoded parameters from json
+with open(sys.argv[3]) as fh:
+    hc_args = json.load(fh, object_hook=_json_object_hook)
+
+# insert the hc_args into the args
+mergeDicts(args, hc_args)
+
+if "adv_opts_cond" in args:
+    args.update(args["adv_opts_cond"])
+    del args["adv_opts_cond"]
+
+# IDMapper has in and spectra:in params, in is used in out as format_source",
+# which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
+# therefore hardcoded params change the name of spectra:in to spectra:_in
+# which is corrected here again
+# TODO remove once PR is in and adapt profile accordingly
+fix_underscores(args)
+
+model = CTDModel(from_file=input_ctd)
+
+# transform values from json that correspond to
+# - old style booleans (string + restrictions) -> transformed to a str
+# - unrestricted ITEMLIST which are represented as strings
+#   ("=quoted and space separated) in Galaxy -> transform to lists
+# - optional data input parameters that have defaults and for which no
+#   value is given -> overwritte with the default
+for p in model.get_parameters():
+
+    # check if the parameter is in the arguments from the galaxy tool
+    # (from the json file(s)), since advanced parameters are absent
+    # if the conditional is set to basic parameters
+    try:
+        getFromDict(args, p.get_lineage(name_only=True))
+    except KeyError:
+        # few tools use dashes in parameters which are automatically replaced
+        # by underscores by Galaxy. in these cases the dictionary needs to be
+        # updated
+        # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
+        try:
+            lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
+            val = getFromDict(args, lineage)
+        except KeyError:
+            continue
+        else:
+            setInDict(args, lineage, val)
+
+    if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
+        v = getFromDict(args, p.get_lineage(name_only=True))
+        setInDict(args, p.get_lineage(name_only=True), str(v).lower())
+
+    elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange):
+        v = getFromDict(args, p.get_lineage(name_only=True))
+        if type(v) is str:
+            setInDict(args, p.get_lineage(name_only=True), qstring2list(v))
+    elif p.type is _InFile and not (p.default is None or type(p.default) is _Null):
+        v = getFromDict(args, p.get_lineage(name_only=True))
+        if v in [[], ""]:
+            setInDict(args, p.get_lineage(name_only=True), p.default)
+
+model.write_ctd(input_ctd, arg_dict=args)