Merge branch 'v0.6.1' into 'master'

Release v0.6.1

See merge request !62

vasp @ 7d850bd7

-Subproject commit dc59aff14e69a6818fbefeb7b1d504348438e26b
+Subproject commit 7d850bd76e878b1429d6974f5daac456099f6e4f

gui/src/components/App.js

@@ -201,8 +201,14 @@ class NavigationUnstyled extends React.Component {
   }
 
   componentDidMount() {
-    fetch(`${guiBase}/meta.json`)
-      .then((response) => response.json())
+    fetch(`${guiBase}/meta.json`, {
+      method: 'GET',
+      cache: 'no-cache',
+      headers: {
+        'Pragma': 'no-cache',
+        'Cache-Control': 'no-cache, no-store'
+      }
+    }).then((response) => response.json())
       .then((meta) => {
         if (meta.version !== packageJson.version) {
           console.log('GUI API version mismatch')

nomad/metainfo/legacy.py

@@ -280,7 +280,12 @@ class LegacyMetainfoEnvironment:
 
         return env
 
-    def generate_metainfo_code(self, package: Package, directory: str):
+    def generate_metainfo_code(
+            self, package: Package, directory: str = None, package_name: str = None):
+
+        if directory is None:
+            directory = '.'
+
         def format_description(description, indent=0, width=90):
             paragraphs = [paragraph.strip() for paragraph in description.split('\n')]
 
@@ -315,8 +320,14 @@ class LegacyMetainfoEnvironment:
             format_type=format_type,
             format_unit=format_unit)
 
-        with open(os.path.join(directory, '%s.py' % package.name), 'wt') as f:
-            f.write(env.get_template('package.j2').render(pkg=package))
+        with open(os.path.join(
+                directory, '%s.py' % package_name
+                if package_name is not None else package.name), 'wt') as f:
+            code = env.get_template('package.j2').render(pkg=package)
+            code = '\n'.join([
+                line.rstrip() if line.strip() != '' else ''
+                for line in code.split('\n')])
+            f.write(code)
 
 
 if __name__ == '__main__':
@@ -326,3 +337,4 @@ if __name__ == '__main__':
         package_names=['%s.nomadmetainfo.json' % pkg for pkg in ['common', 'public', 'vasp']])
 
     legacy_env = env.legacy_info_env()
+    env.generate_metainfo_code(env.env.all_packages['public.nomadmetainfo.json'], package_name='public')

nomad/metainfo/metainfo.py

@@ -1938,6 +1938,7 @@ class Environment(MSection):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.all_definitions_by_name: Dict[str, List[Definition]] = dict()
+        self.all_packages: Dict[str, Package] = dict()
 
     def resolve_definitions(  # type: ignore
             self, name: str, cls: Type[MSectionBound] = Definition) -> List[MSectionBound]:
@@ -1961,6 +1962,7 @@ class Environment(MSection):
     def on_add_sub_section(self, sub_section_def: SubSection, sub_section: MSection):
         if sub_section_def == Environment.packages:
             package = sub_section.m_as(Package)
+            self.all_packages[package.name] = package
             for definition in package.m_all_contents():
                 if isinstance(definition, Definition):
                     definitions = self.all_definitions_by_name.setdefault(definition.name, [])

nomad/parsing/__init__.py

@@ -71,10 +71,11 @@ based on NOMAD-coe's *python-common* module.
     :members:
 """
 
-from typing import Callable, IO, Union
+from typing import Callable, IO, Union, Dict
 import magic
 import gzip
 import bz2
+import lzma
 import os.path
 
 from nomad import files, config
@@ -87,7 +88,8 @@ from nomad.parsing.artificial import TemplateParser, GenerateRandomParser, Chaos
 
 _compressions = {
     b'\x1f\x8b\x08': ('gz', gzip.open),
-    b'\x42\x5a\x68': ('bz2', bz2.open)
+    b'\x42\x5a\x68': ('bz2', bz2.open),
+    b'\xfd\x37\x7a': ('xz', lzma.open)
 }
 
 
@@ -116,7 +118,7 @@ def match_parser(mainfile: str, upload_files: Union[str, files.StagingUploadFile
     with open(mainfile_path, 'rb') as f:
         compression, open_compressed = _compressions.get(f.read(3), (None, open))
 
-    with open_compressed(mainfile_path, 'rb') as cf:
+    with open_compressed(mainfile_path, 'rb') as cf:  # type: ignore
         buffer = cf.read(config.parser_matching_size)
 
     mime_type = magic.from_buffer(buffer, mime=True)
@@ -147,14 +149,14 @@ parsers = [
     LegacyParser(
         name='parsers/vasp', code_name='VASP',
         parser_class_name='vaspparser.VASPRunParserInterface',
-        mainfile_mime_re=r'(application/xml)|(text/.*)',
+        mainfile_mime_re=r'(application/.*)|(text/.*)',
         mainfile_contents_re=(
             r'^\s*<\?xml version="1\.0" encoding="ISO-8859-1"\?>\s*'
             r'?\s*<modeling>'
             r'?\s*<generator>'
             r'?\s*<i name="program" type="string">\s*vasp\s*</i>'
             r'?'),
-        supported_compressions=['gz', 'bz2']
+        supported_compressions=['gz', 'bz2', 'xz']
     ),
     VaspOutcarParser(
         name='parsers/vasp-outcar', code_name='VASP',

ops/deployments/nomad.prod-1.values.yaml

@@ -15,7 +15,7 @@ worker:
   replicas: 1
   routing: "queue"
   processes: 10
-  nomadtype: "prod-worker"
+  nomadNodeType: "prod-worker"
 
 dbname: fairdi_nomad_prod
 

ops/deployments/nomad.prod-2.values.yaml

@@ -15,7 +15,7 @@ worker:
   replicas: 1
   routing: "queue"
   processes: 10
-  nomadtype: "prod-worker"
+  nomadNodeType: "prod-worker"
 
 dbname: fairdi_nomad_prod
 

ops/helm/nomad/templates/gui-deployment.yml

@@ -39,6 +39,16 @@ data:
         rewrite ^{{ .Values.proxy.external.path }}/gui/service-worker.js /nomad/service-worker.js break;
       }
 
+      location {{ .Values.proxy.external.path }}/gui/meta.json {
+        add_header Last-Modified $date_gmt;
+        add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0';
+        if_modified_since off;
+        expires off;
+        etag off;
+        root      /app/;
+        rewrite ^{{ .Values.proxy.external.path }}/gui/meta.json /nomad/meta.json break;
+      }
+
       location {{ .Values.proxy.external.path }}/api/uploads {
         client_max_body_size 35g;
         proxy_request_buffering off;

requirements.txt

@@ -57,7 +57,7 @@ sphinx
 sphinxcontrib.httpdomain
 sphinx_rtd_theme
 gitpython
-mypy
+mypy==0.730
 pylint==2.3.1
 pylint_plugin_utils==0.5
 pylint_mongoengine==0.3.3