Should fix biotools maybe

Author: mboudet

github-ci/src/biocontainersci/biotools.py

@@ -5,21 +5,20 @@
 
 import shutil
 import requests
-import sys
 import os
 import logging
-import re
 import git
 import datetime
 from copy import deepcopy
-from yaml import load, dump
+from yaml import dump
 try:
-    from yaml import CLoader as Loader, CDumper as Dumper
+    from yaml import CDumper as Dumper
 except ImportError:
-    from yaml import Loader, Dumper
+    from yaml import Dumper
 
 from biocontainersci.utils import BiocontainersCIException
 
+
 class Biotools:
 
     GIT_REPO = '[email protected]:bio-tools/content.git'
@@ -90,15 +89,15 @@ def create_pr(self, branch):
         }
         github_url = 'https://api.github.com/repos/%s/pulls' % ("bio-tools/content")
         res = requests.post(
-                github_url,
-                json={
-                    'title': "biocontainers-bot metadata import PR",
-                    'head': branch,
-                    "base": "master"
-                },
-                headers=headers
+            github_url,
+            json={
+                'title': "biocontainers-bot metadata import PR",
+                'head': branch,
+                "base": "master"
+            },
+            headers=headers
         )
-        if not res.status_code in [200, 201]:
+        if res.status_code not in [200, 201]:
             logging.error("[biotools] Failed to create pull request: %s", res.text)
             return False
         pr = res.json()
@@ -107,13 +106,13 @@ def create_pr(self, branch):
         github_url = 'https://api.github.com/repos/%s/issues/%d' % ("bio-tools/content", issue)
 
         res = requests.post(
-                github_url,
-                json={
-                    'labels': [self.BOT_LABEL],
-                },
-                headers=headers
+            github_url,
+            json={
+                'labels': [self.BOT_LABEL],
+            },
+            headers=headers
         )
-        if not res.status_code in [200]:
+        if res.status_code not in [200]:
             logging.error("Failed to add issue label: %d" % res.status_code)
 
         logging.info("Tagged issue: %d" % issue)
@@ -173,37 +172,29 @@ def run(self, f, labels, branch=None):
 
             for file_path in files_to_write:
 
-                if os.path.exists(file_path):
-                    with open(file_path) as fp:
-                        softwares = load(fp, Loader=Loader)
-
                 if name not in softwares["softwares"]:
                     softwares["softwares"][name] = data
 
-                exists = False
-                for download in softwares["softwares"][name]["versions"]:
-                    if download["version"] == container_version:
-                        exists = True
-                        break
+                new_download = {
+                    "url": "biocontainers/" + name + ":" + container_version,
+                    "version": container_version,
+                    "type": "Container file",
+                    "labels": deepcopy(clabels)
+                }
+                softwares["softwares"][name]["versions"].append(new_download)
 
-                if not exists:
-                    new_download = {
-                        "url": "biocontainers/" + name + ":" + container_version,
-                        "version": container_version,
-                        "type": "Container file",
-                        "labels": deepcopy(clabels)
-                    }
-                    softwares["softwares"][name]["versions"].append(new_download)
-
-                    with open(file_path, 'w') as fp:
-                        dump(softwares, fp, Dumper=Dumper)
+                with open(file_path, 'w') as fp:
+                    dump(softwares, fp, Dumper=Dumper)
 
+            changed = False
+            changed_files = [item.a_path for item in repo.index.diff(None)]
+            for file_path in files_to_write:
+                if file_path in changed_files:
                     repo.index.add([file_path])
-            if exists:
-                if biotools is not None:
-                    repo.index.commit("Add version for %s:%s" % (biotools, container_version))
-                else:
-                    repo.index.commit("Add version for %s:%s" % (name, container_version))
+                    changed = True
+
+            if changed:
+                repo.index.commit("Add version for %s:%s" % (name, container_version))
                 try:
                     logging.info("[biotools] Push to branch %s" % branch)