Merge branch 'dev'

Author: kmoad

cravat/admin_util.py

@@ -23,6 +23,7 @@
 import signal
 import subprocess
 from urllib.error import HTTPError
+from pathlib import Path
 
 class InstallProgressHandler(object):
     def __init__(self, module_name, module_version):
@@ -1334,12 +1335,23 @@ def load_yml_conf(yml_conf_path):
     return conf
 
 
-def make_example_input(d):
-    fn = "example_input"
-    ifn = os.path.join(constants.packagedir, fn)
-    ofn = os.path.join(d, fn)
-    shutil.copyfile(ifn, ofn)
-    print(fn + " has been created at " + os.path.abspath(d))
+def make_example_input(out_directory, type='cravat'):
+    if type == 'cravat':
+        out_fn = 'example_input'
+    elif type == 'vcf':
+        out_fn = 'example_input.vcf'
+    elif type == 'hgvs':
+        out_fn = 'example_input.hgvs.txt'
+    elif type == 'dbsnp':
+        out_fn = 'example_input.rsid.txt'
+    else:
+        raise ValueError(f'Invalid example input type: {type}')
+    out_path = Path(out_directory)/out_fn
+    in_path = constants.example_input_paths.get(type)
+    if in_path is None:
+        raise ValueError(f'Invalid example input type: {type}')
+    shutil.copyfile(in_path, out_path)
+    return out_path
 
 
 def module_exists_local(module_name):

cravat/constants.py

@@ -5,6 +5,7 @@
 import sys
 import platform
 import yaml
+from pathlib import Path
 
 # Directories
 custom_modules_dir = None
@@ -81,6 +82,14 @@
 if os.path.exists(main_conf_path) == False:
     shutil.copyfile(os.path.join(packagedir, main_conf_fname), main_conf_path)
 
+# Example inputs
+example_input_paths = {
+    'cravat': Path(packagedir)/'websubmit'/'input-examples'/'cravat.hg38.txt',
+    'vcf': Path(packagedir)/'websubmit'/'input-examples'/'vcf.hg38.txt',
+    'hgvs': Path(packagedir)/'websubmit'/'input-examples'/'hgvs.hg38.txt',
+    'dbsnp': Path(packagedir)/'websubmit'/'input-examples'/'dbsnp.hg38.txt',
+}
+
 # Base modules
 base_modules = [
     'cravat-converter',

cravat/cravat_admin.py

@@ -441,8 +441,12 @@ def send_verify_email (args):
 def check_login (args):
     au.check_login(args.username, args.password)
 
-def make_example_input (arg):
-    au.make_example_input(arg.directory)
+def make_example_input (args):
+    if args.type == 'dbsnp' and au.get_local_module_info('dbsnp-converter') is None:
+        print('Must install dbsnp-converter.')
+        exit(1)
+    out_path = au.make_example_input(args.directory, type=args.type)
+    print(out_path)
 
 def new_annotator (args):
     if args.md is not None:
@@ -793,8 +797,15 @@ def show_version (args):
 # test input file
 parser_make_example_input = subparsers.add_parser('make-example-input',
                                                     help='makes a file with example input variants.')
-parser_make_example_input.add_argument('directory', default='',
-                                        help='Directory to make the example input file in')
+parser_make_example_input.add_argument('directory',
+                                       default=os.getcwd(),
+                                       nargs='?',
+                                       help='Directory to make the example input file in')
+parser_make_example_input.add_argument('--type','-t',
+                                       choices=list(constants.example_input_paths.keys()),
+                                       default='cravat',
+                                       required=False,
+                                       help='Type of example input')
 parser_make_example_input.set_defaults(func=make_example_input)
 
 # new-annotator

cravat/cravat_class.py

@@ -345,6 +345,7 @@ def __init__(self, **kwargs):
         self.annotators = {}
         self.append_mode = False
         self.pipeinput = False
+        self.samples = set()
         try:
             self.metricObj = metrics.cravatMetrics()
             self.make_args_namespace(kwargs)
@@ -658,6 +659,7 @@ async def main(self):
                     print("Check {}".format(self.log_path))
                 self.update_status("Error", force=True)
             self.metricObj.set_job_data('success',success)
+            self.metricObj.set_job_data('sampleCount', len(self.samples))
             self.metricObj.do_job_metrics(self)
             self.close_logger()
             if self.args.do_not_change_status != True:
@@ -1273,6 +1275,7 @@ def run_converter(self):
         converter_class = util.load_class(module.script_path, "MasterCravatConverter")
         converter = converter_class(arg_dict)
         self.numinput, self.converter_format = converter.run()
+        self.samples = converter.samples
 
     def run_genemapper(self):
         module = au.get_local_module_info(self.cravat_conf["genemapper"])

cravat/cravat_convert.py

@@ -85,6 +85,7 @@ def __init__(self, *inargs, **inkwargs):
         self.crl_writer = None
         self.primary_converter = None
         self.converters = {}
+        self.samples = set()
         self.possible_formats = []
         self.ready_to_convert = False
         self.chromdict = {
@@ -457,6 +458,8 @@ def run(self):
                                         )
                                     else:
                                         wdict["sample_id"] = samp_prefix
+                                # keep track of samples
+                                self.samples.add(wdict.get("sample_id", ""))
                                 if "ref_base" not in wdict or wdict["ref_base"] == "":
                                     wdict["ref_base"] = self.wgsreader.get_bases(
                                         chrom, int(wdict["pos"])