From df839272d661c3489f8f96f3cb32d8670d655dd4 Mon Sep 17 00:00:00 2001
From: Kyle Moad <kyle.moad@gmail.com>
Date: Thu, 9 May 2024 13:44:03 -0400
Subject: [PATCH] move base_modules to constants and add hgvs-converter

---
 cravat/constants.py         | 29 ++++++++++++++++++++++++++++-
 cravat/cravat_admin.py      |  4 +---
 cravat/webstore/webstore.py |  7 ++-----
 3 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/cravat/constants.py b/cravat/constants.py
index 9a83e331..68845730 100644
--- a/cravat/constants.py
+++ b/cravat/constants.py
@@ -76,12 +76,39 @@
 # Live conf
 live_conf_fname = "live.yml"
 
-base_modules_key = "base_modules"
 main_conf_fname = "cravat.yml"
 main_conf_path = os.path.join(default_conf_dir, main_conf_fname)
 if os.path.exists(main_conf_path) == False:
     shutil.copyfile(os.path.join(packagedir, main_conf_fname), main_conf_path)
 
+# Base modules
+base_modules = [
+    'cravat-converter',
+    'vcf-converter',
+    'oldcravat-converter',
+    'hgvs-converter',
+    'textreporter',
+    'excelreporter',
+    'tagsampler',
+    'vcfinfo',
+    'hg38',
+    'casecontrol',
+    'wgbase',
+    'wghg19',
+    'wgncrna',
+    'wglollipop',
+    'wgndex',
+    'wgcircossummary',
+    'wgcodingvsnoncodingsummary',
+    'wggosummary',
+    'wgsosamplesummary',
+    'wgsosummary',
+    'wgnote',
+    'wgvcfinfo',
+    'hg38wgs',
+    'varmeta',
+    'wgrankscore',
+]
 
 # metrics
 save_metrics_key = 'save_metrics'
diff --git a/cravat/cravat_admin.py b/cravat/cravat_admin.py
index 10872811..d0ee16d9 100644
--- a/cravat/cravat_admin.py
+++ b/cravat/cravat_admin.py
@@ -408,9 +408,7 @@ def publish_module (args):
     au.publish_module(args.module, args.user, args.password, overwrite=args.overwrite, include_data=args.data)
 
 def install_base (args):
-    sys_conf = au.get_system_conf()
-    base_modules = sys_conf.get(constants.base_modules_key,[])
-    args = SimpleNamespace(modules=base_modules,
+    args = SimpleNamespace(modules=constants.base_modules,
         force_data=args.force_data,
         version=None,
         yes=True,
diff --git a/cravat/webstore/webstore.py b/cravat/webstore/webstore.py
index 869202f7..0a553449 100644
--- a/cravat/webstore/webstore.py
+++ b/cravat/webstore/webstore.py
@@ -250,9 +250,7 @@ async def queue_install (request):
     return web.Response(text = 'queued ' + queries['module'])
 
 async def get_base_modules (request):
-    global system_conf
-    base_modules = system_conf['base_modules']
-    return web.json_response(base_modules)
+    return web.json_response(constants.base_modules)
 
 async def install_base_modules (request):
     global servermode
@@ -261,8 +259,7 @@ async def install_base_modules (request):
         if r == False:
             response = 'failed'
             return web.json_response(response)
-    base_modules = system_conf.get(constants.base_modules_key,[])
-    for module in base_modules:
+    for module in constants.base_modules:
         install_queue.put({'module': module, 'version': None})
     response = 'queued'
     return web.json_response(response)