Merge branch 'v0.8.2' into 'master'

0.8.2 release

See merge request !134

.gitlab-ci.yml

@@ -143,19 +143,20 @@ release:
     - docker pull $TEST_IMAGE
     - docker tag $TEST_IMAGE $LATEST_IMAGE
     - docker push $LATEST_IMAGE
-
   except:
     - /^dev-.*$/
   when: manual
+  only:
+    - branches
 
 release_version:
   stage: release
   script:
     - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN gitlab-registry.mpcdf.mpg.de
-    - docker pull $LATEST_IMAGE
-    - docker tag $LATEST_IMAGE $CI_COMMIT_TAG
-    - docker tag $LATEST_IMAGE $STABLE_IMAGE
+    - docker pull $TEST_IMAGE
+    - docker tag $TEST_IMAGE $LATEST_IMAGE
+    - docker push $LATEST_IMAGE
+    - docker tag $TEST_IMAGE $STABLE_IMAGE
     - docker push $STABLE_IMAGE
-    - docker push $CI_COMMIT_TAG
   only:
     - tags

.gitmodules

-[submodule "dependencies/nomad-meta-info"]
-	path = dependencies/nomad-meta-info
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
-	branch = nomad-fair
 [submodule "dependencies/python_common"]
 	path = dependencies/python_common
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
@@ -12,7 +8,7 @@
 	branch = nomad-fair
 [submodule "dependencies/parsers/exciting"]
 	path = dependencies/parsers/exciting
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting.git
+	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting-fairdi.git
 	branch = nomad-fair
 [submodule "dependencies/parsers/fhi-aims"]
 	path = dependencies/parsers/fhi-aims

Dockerfile

@@ -106,26 +106,23 @@ WORKDIR /app
 # transfer installed packages from dependency stage
 COPY --from=build /usr/local/lib/python3.7/site-packages /usr/local/lib/python3.7/site-packages
 RUN echo "copy 1"
-# copy the meta-info, since it files are loaded via relative paths. TODO that should change.
-COPY --from=build /install/dependencies/nomad-meta-info /app/dependencies/nomad-meta-info
-RUN echo "copy 2"
 # copy the documentation, its files will be served by the API
 COPY --from=build /install/docs/.build /app/docs/.build
-RUN echo "copy 3"
+RUN echo "copy 2"
 # copy the source distribution, its files will be served by the API
 COPY --from=build /install/dist /app/dist
-RUN echo "copy 4"
+RUN echo "copy 3"
 # copy the nomad command
 COPY --from=build /usr/local/bin/nomad /usr/bin/nomad
-RUN echo "copy 5"
+RUN echo "copy 4"
 # copy the gui
 RUN mkdir -p /app/gui
 COPY --from=gui_build /app/build /app/gui/build
-RUN echo "copy 6"
+RUN echo "copy 5"
 # copy the encyclopedia gui production code
 COPY --from=gui_build /encyclopedia /app/dependencies/encyclopedia-gui/client
 RUN rm -rf /app/dependencies/encyclopedia-gui/client/src
-RUN echo "copy 7"
+RUN echo "copy 6"
 
 RUN mkdir -p /app/.volumes/fs
 RUN useradd -ms /bin/bash nomad

README.md

@@ -37,7 +37,7 @@ nomad parse --show-backend <your-file-to-parse>
 
 ### For NOMAD developer
 
-Read the [docs](https://repository.nomad-coe.eu/app/docs). The documentation is also part
+Read the [docs](https://repository.nomad-coe.eu/app/docs/index.html). The documentation is also part
 of the source code. It covers aspects like introduction, architecture, development setup/deployment,
 contributing, and API reference.
 

nomad-dos-fingerprints @ 562ae7d2

-Subproject commit bb633623789ee9850873ba0b16a32c66c8265558
+Subproject commit 562ae7d26fa108c7c31ebe38775c767aba1e642c

nomad-meta-info @ a2df84b2

-Subproject commit a2df84b2dfc2c96344e7261580a40d655c904047

aptfim @ d394f7ae

-Subproject commit 45daba83219defb908044193214acce48baf76e9
+Subproject commit d394f7ae375cd2355127abc67e07b1592f18d4f4

eels @ 6f0e7ec8

-Subproject commit 38ed55429bd8c2289471c5dbc162bcdd80b7bb94
+Subproject commit 6f0e7ec897284382d8ef30b0ee0372f010ce468f

exciting @ 0edade50

-Subproject commit 2849061c5212de8e2845ec0c3ed96b7a7f4e67d9
+Subproject commit 0edade50d6be30bc83dca35d382bb6d462ea6f91

fhi-aims @ d342d8a1

-Subproject commit ca7513c0e23b20d738f65b081b482e74a8d0527d
+Subproject commit d342d8a14dc49d528fe7ca867c3f5891d8b73077

mpes @ aa701e8f

-Subproject commit 124b42b9851329682e11c2f1f3e00056d215bd3b
+Subproject commit aa701e8f2780419e7911972c8e2a16d188008902

vasp @ 1a0c8cb0

-Subproject commit ba060d7c8cb902d16e47ca382ef986662a5f3fa4
+Subproject commit 1a0c8cb0801375a78134c67f7a6d31319a338503

python_common @ cf843eda

-Subproject commit 4c83e96bcbf9080d431b7b22f1ecabd4b64dec27
+Subproject commit cf843eda3e4650bc240eb0d1a1ab5b0cea6dda96

docs/api.rst

-API(s) Documentation
+API Reference
 ====================
 
 This is just a brief summary of all API endpoints of the NOMAD API. For a more compelling documention

docs/api_tutorial.md

@@ -69,10 +69,24 @@ identified an entry (given via a `upload_id`/`calc_id`, see the query output), a
 you want to download it:
 
 ```
-curl "http://repository.nomad-coe.eu/app/api/raw/calc/f0KQE2aiSz2KRE47QtoZtw/6xe9fZ9xoxBYZOq5lTt8JMgPa3gX/*" -o download.zip
+curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/*" -o download.zip
 ```
 
-This basically requests all the files (`*`) that belong to this entry. If you have a query
+With `*` you basically requests all the files under an entry or path..
+If you need a specific file (that you already know) of that calculation:
+
+```
+curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/INFO.OUT"
+```
+
+You can also download a specific file from the upload (given a `upload_id`), if you know
+the path of that file:
+
+```
+curl "http://repository.nomad-coe.eu/app/api/raw/JvdvikbhQp673R4ucwQgiA/exciting_basis_set_error_study/monomers_expanded_k8_rgkmax_080_PBE/72_Hf/INFO.OUT"
+```
+
+If you have a query
 that is more selective, you can also download all results. Here all compounds that only
 consist of Si, O, bulk material simulations of cubic systems (currently ~100 entries):
 

docs/archive.rst

 .. _access-the-archive-label:
 
-Accessing the Archive
-=====================
+Using the NOMAD Archive
+=======================
 
 Of course, you can access the NOMAD Archive directly via the NOMAD API (see the `API tutorial <api_tutorial.html>`_
 and `API reference <api.html>`_). But, it is more effective and convenient to use NOMAD's Python client

docs/client/install.rst

@@ -5,14 +5,16 @@ We release the NOMAD client library as a Python `distutils <https://docs.python.
 You can download and install it the usual way using *pip* (or *conda*).
 
 Install from pypi
+
 .. code-block:: sh
 
     pip install nomad-lab
 
 Download and install latest release from nomad
+
 .. code-block:: sh
 
-    curl https://repository.nomad-coe.eu/v0.8/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
+    curl https://repository.nomad-coe.eu/app/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
     pip install ./nomad-lab.tar.gz
 
 There are different layers of dependencies that you have to install, in order to use

docs/conf.py

@@ -25,8 +25,8 @@ sys.path.insert(0, os.path.abspath('..'))
 
 # -- Project information -----------------------------------------------------
 
-project = 'nomad-FAIRDI'
-copyright = '2018, FAIRDI e.V.'
+project = 'NOMAD Repository and Archive'
+copyright = '2014-2020, FAIRDI e.V.'
 author = 'FAIRDI e.V.'
 
 # The short X.Y version
@@ -200,4 +200,4 @@ def setup(app):
     # }, True)
     # app.add_transform(AutoStructify)
 
-extlinks = {'api': ('https://repository.nomad-coe.eu/v0.8/api/%s', 'NOMAD API ')}
\ No newline at end of file
+extlinks = {'api': ('https://repository.nomad-coe.eu/app/api/%s', 'NOMAD API ')}
\ No newline at end of file

docs/parser_tutorial.md → docs/dev/parser_tutorial.md

-# How to write a parser for nomad@FAIRDI
+# How to write a parser
 
 ## The parser project
 
@@ -313,7 +313,7 @@ is stored in a database for analysis. Do not abuse the logging.
 ## Testing and Debugging
 You a writing a python program. You know what to do.
 
-## Added the parser to nomad@FAIRDI
+## Adding the parser to nomad@FAIRDI
 
 First, you add your parser to the dependencies. Put it into the dependencies folder, then:
 ```
@@ -343,3 +343,71 @@ parser_examples = [
     ('parsers/vaspoutcar', 'tests/data/parsers/vasp_outcar/OUTCAR'),
 ]
 ```
+
+## FAIRDI parsers
+The new fairdi parsers avoid the use of a backend and instead make use of the new metainfo
+sections. The project structure is the same as above with the addition of a `metainfo`
+folder
+
+```
+myparser/myparser/metainfo
+```
+This contains a file containing the definitions and an `__init__.py`. One should refer
+to `nomad.metainfo.example.py` for a guide in writing the metainfo definitions.
+Consequently, the parser class implementation is modified as in the following example.
+
+```python
+import json
+
+from .metainfo import m_env
+from nomad.parsing.parser import MatchingParser
+from nomad.datamodel.metainfo.general_experimental import section_experiment as msection_experiment
+from nomad.datamodel.metainfo.general_experimental import section_data as msection_data
+from nomad.datamodel.metainfo.general_experimental_method import section_method as msection_method
+from nomad.datamodel.metainfo.general_experimental_sample import section_sample as msection_sample
+
+
+class ExampleParser(MatchingParser):
+    def __init__(self):
+        super().__init__(
+            name='parsers/example', code_name='example', code_homepage='https://github.com/example/example',
+            domain='ems', mainfile_mime_re=r'(application/json)|(text/.*)', mainfile_name_re=(r'.*.example')
+        )
+
+    def run(self, filepath, logger=None):
+        self._metainfo_env = m_env
+
+        with open(filepath, 'rt') as f:
+            data = json.load(f)
+
+        section_experiment = msection_experiment()
+
+        # Read general tool environment details
+        section_experiment.experiment_location = data.get('experiment_location')
+        section_experiment.experiment_facility_institution = data.get('experiment_facility_institution')
+
+        # Read data parameters
+        section_data = section_experiment.m_create(msection_data)
+        section_data.data_repository_name = data.get('data_repository_name')
+        section_data.data_preview_url = data.get('data_repository_url')
+
+        # Read parameters related to method
+        section_method = section_experiment.m_create(msection_method)
+        section_method.experiment_method_name = data.get('experiment_method')
+        section_method.probing_method = 'electric pulsing'
+
+        # Read parameters related to sample
+        section_sample = section_experiment.m_create(msection_sample)
+        section_sample.sample_description = data.get('specimen_description')
+        section_sample.sample_microstructure = data.get('specimen_microstructure')
+        section_sample.sample_constituents = data.get('specimen_constitution')
+
+        return section_experiment
+```
+The parser extends the ``MatchingParser`` class which already implements the determination
+of the necessary file for parsing. The main difference to the old framework is the absense
+the opening and closing of sections. One only needs to create a section which can be
+accessed at any point in the code. The ``run`` method should return the root section.
+
+Lastly, one should add an instance of the parser class in the list of parsers at
+``nomad.parsing``.
\ No newline at end of file

docs/dev/setup.md

@@ -77,7 +77,7 @@ conda activate nomad_env
 
 To install libmagick for conda, you can use (other channels might also work):
 ```
-conda -c conda-forge install --name nomad_env libmagic
+conda install -c conda-forge --name nomad_env libmagic
 ```
 
 #### pip

docs/index.rst

-nomad@FAIRDI
-============
+NOMAD Repository and Archive
+============================
 
 This project is a prototype for the continuation of the original NOMAD-coe software
 and infrastructure with a simplyfied architecture and consolidated code base.
@@ -10,12 +10,12 @@ and infrastructure with a simplyfied architecture and consolidated code base.
    introduction.md
    upload.rst
    api_tutorial.md
-   api.rst
-   archive.rst
-   metainfo.rst
    client/client.rst
+   metainfo.rst
+   archive.rst
    ops/ops.rst
    dev/setup.md
    dev/dev_guidelines.rst
-   parser_tutorial.md
+   dev/parser_tutorial.md
+   api.rst
    reference.rst

docs/metainfo.rst

 .. _metainfo-label:
 
-Metainfo
-========
+NOMAD Metainfo
+==============
+
+Introduction
+------------
+
+The NOMAD Metainfo stores descriptive and structured information about materials-science
+data contained in the NOMAD Archive. The Metainfo can be understood as the schema of
+the Archive. The NOMAD Archive data is
+structured to be independent of the electronic-structure theory code or molecular-simulation,
+(or beyond). The NOMAD Metainfo can be browsed as part of the `NOMAD Repository and Archive web application <https://repository.nomad-coe.eu/app/gui/metainfo>`_.
+
+Typically (meta-)data definitions are generated only for a predesigned and specific scientific field,
+application or code. In contrast, the NOMAD Metainfo considers all pertinent information
+in the input and output files of the supported electronic-structure theory, quantum chemistry,
+and molecular-dynamics (force-field) codes. This ensures a complete coverage of all
+material and molecule properties, even though some properties might not be as important as
+others, or are missing in some input/output files of electronic-structure programs.
+
+.. image:: assets/metainfo_example.png
+
+NOMAD Metainfo is kept independent of the actual storage format and is not bound to any
+specific storage method. In our practical implementation, we use a binary form of JSON,
+called `msgpack <https://msgpack.org/>`_ on our servers and provide Archive data as JSON via
+our API. For NOMAD end-users the internal storage format is of little relevance, because
+the archive data is solely served by NOMAD's API.
+
+The NOMAD Metainfo started within the `NOMAD Laboratory <https://nomad-lab.eu>`_. It was discussed at the
+`CECAM workshop Towards a Common Format for Computational Materials Science Data <https://th.fhi-berlin.mpg.de/meetings/FCMSD2016/>`_
+and is open to external contributions and extensions. More information can be found in:
+
+- `Towards a Common Format for Computational Materials Science Data (Psi-K 2016 Highlight) <http://th.fhi-berlin.mpg.de/site/uploads/Publications/Psik_Highlight_131-2016.pdf>`_ provides a description on how to establish code-independent formats in detail and presents the challenges and practical strategies for achieving a common format for the representation of computational material-science data.
+- `The Novel Materials Discovery Laboratory - Data formats and compression, D1.1 <https://www.nomad-coe.eu/uploads/outreach/Public%20Deliverables/NOMAD%20D1.1%20public%20KO20June2016.pdf>`_ outlines possible data formats, concepts, and compression techniques used to build a homogeneous (code-independent) data archive, called the NOMA
+
+
+Metainfo Python Interface
+-------------------------
 
 .. automodule:: nomad.metainfo
 
@@ -34,6 +69,9 @@ Python modules:
     from nomad.datamodel.metainfo.public import section_run
     my_run = section_run()
 
+Many more examples about how to read the NOMAD Metainfo programmatically can be found
+`here <https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/tree/master/examples/access_metainfo.py>`_.
+
 API
 ___
 

docs/reference.rst

-Reference
-=========
+Python Reference
+================
 
 nomad.metainfo
 --------------

docs/upload.rst

-==============
-Uploading Data
-==============
+======================================
+Uploading Data to the NOMAD Repository
+======================================
 
 To contribute your data to the repository, please, login to our `upload page <../uploads>`_ (you need to register first, if you do not have a NOMAD account yet).
 

examples/access_metainfo.py

+# pylint: skip-file
+# type: ignore
+from nomad import metainfo
+from nomad.datamodel.metainfo import public, common
+
+# Access the quantities of a section definition
+for quantity in public.section_method.m_def.quantities:
+    print(quantity.name, quantity.type, quantity.shape, quantity.unit)
+
+
+# Access all the quantities of a section definition, including those added by other packages
+import vaspparser.metainfo.vasp  # noqa
+for quantity in public.section_method.m_def.all_quantities.values():
+    print(quantity.name, quantity.type, quantity.shape, quantity.unit)
+
+
+# Access sub-sections and their definitions
+for sub_section in public.section_run.m_def.sub_sections:
+    print(sub_section.name)  # access the name of the sub section definition
+    print(sub_section.sub_section.name)  # access the name of the section definition that the sub section refers to
+
+
+# Go through all sub sections recursively
+def visit_section(section, indent=0):
+    print(' ' * indent + section.name)
+    for sub_section in section.all_sub_sections.values():
+        visit_section(sub_section.sub_section, indent + 2)
+
+
+visit_section(public.section_run.m_def)
+
+
+# Look at the EntryArchive, e.g. where section_metadata (and everything else) is a subsection
+from nomad.datamodel import EntryArchive  # noqa
+visit_section(EntryArchive.m_def)
+
+
+# To get everything within a metainfo package (i.e. what was former in a .nomadmetainfo.json file) as JSON/dict data:
+import json  # noqa
+import nomad.datamodel.datamodel  # noqa
+
+print(json.dumps(nomad.datamodel.datamodel.m_package.m_to_dict(), indent=2))
+print(json.dumps(public.m_package.m_to_dict(), indent=2))
+
+
+# Using an environment that manages multiple packages and provides utility functions
+# to find definitions by name.
+from nomad.datamodel.metainfo import m_env  # noqa, contains all common, public, general metainfo
+from vaspparser.metainfo import m_env as vasp_m_env  # noqa, contains also the vasp specific definitions
+print(m_env.packages)
+# Resolve definition by name
+print(m_env.resolve_definitions('number_of_atoms', metainfo.Quantity))
+# Traverse all definitions:
+for definition in m_env.m_all_contents():
+    print(definition)
+
+
+# Dimensions are either numbers or rangens (e.g. 3, 1..3, 0..*) or references to
+# shapeless, unitless, integer quantities (usually) of the same section.
+# These quantities are not specifically designated as dimensions, because they represent
+# quantities in their own right and are often used on their own.
+# Dimensions of a specific quantity:
+quantity = public.section_system.atom_labels
+for dim in quantity.shape:
+    if isinstance(dim, str):
+        section = quantity.m_parent
+        print('%s[%s]: %s' % (quantity.name, dim, m_env.resolve_definitions(dim, metainfo.Quantity)))
+
+# All quantities used as dimensions in a package:
+for definition in public.m_package.m_all_contents():
+    if definition.m_def == metainfo.Quantity.m_def:
+        for dim in definition.shape:
+            if isinstance(dim, str) and '..' not in dim:
+                print('%s[%s]: %s' % (quantity.name, dim, m_env.resolve_definitions(dim, metainfo.Quantity)))
+
+
+# Categories are special classes, similar to sections and they Python definition is a
+# subclass of MCategory or MSection:
+print(public.atom_forces_type, issubclass(public.atom_forces_type, metainfo.MCategory))
+print(public.section_system, issubclass(public.section_system, metainfo.MSection))
+# Or the definition of the definition is Category or Section respectively:
+print(public.atom_forces_type, public.atom_forces_type.m_def == metainfo.Category.m_def)
+print(public.section_system, public.section_system.m_def == metainfo.Section.m_def)
+# Get all sections and categories definitions in a package:
+print(public.m_package.category_definitions)
+print(public.m_package.section_definitions)
+# Access the categories of a metainfo definition, e.g. quantity
+print(public.section_single_configuration_calculation.energy_total.categories)
+
+
+print(m_env.resolve_definition('EntryMetadata', metainfo.Section).all_quantities)
+print(m_env.resolve_definition('Bulk', metainfo.Section).all_quantities)
+print(m_env.resolve_definition('OptimadeEntry', metainfo.Section).all_quantities)
\ No newline at end of file

examples/client.py

@@ -2,8 +2,6 @@ from nomad import config
 from nomad.client import ArchiveQuery
 from nomad.metainfo import units
 
-# this will not be necessary, once this is the official NOMAD version
-config.client.url = 'http://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/testing-major/api'
 
 query = ArchiveQuery(
     query={

examples/search.py

@@ -3,7 +3,7 @@ from nomad import config, infrastructure, search
 
 config.elastic.host = 'localhost'
 config.elastic.port = 19202
-config.elastic.index_name = 'fairdi_nomad_prod_v0_7'
+config.elastic.index_name = 'fairdi_nomad_prod_v0_8'
 
 infrastructure.setup_elastic()
 

gui/package.json

 {
   "name": "nomad-fair-gui",
-  "version": "0.8.1",
+  "version": "0.8.2",
   "commit": "e98694e",
   "private": true,
   "dependencies": {

gui/public/env.js

@@ -8,9 +8,9 @@ window.nomadEnv = {
   'matomoUrl': 'https://repository.nomad-coe.eu/fairdi/stat',
   'matomoSiteId': '2',
   'version': {
-    "label": "0.8.1",
-    "isBeta": true,
-    "usesBetaData": true,
+    "label": "0.8.2",
+    "isBeta": false,
+    "usesBetaData": false,
     "officialUrl": "https://repository.nomad-coe.eu/app/gui"
   }
 }

gui/src/components/DataTable.js

@@ -248,7 +248,8 @@ class DataTableUnStyled extends React.Component {
       whiteSpace: 'nowrap',
       maxWidth: 200,
       paddingLeft: theme.spacing(3),
-      paddingRight: theme.spacing(3)
+      paddingRight: theme.spacing(3),
+      height: theme.spacing.unit * 6
     },
     ellipsisFront: {
       direction: 'rtl',
@@ -293,14 +294,14 @@ class DataTableUnStyled extends React.Component {
     super(props)
     this.handleSelectAllClick = this.handleSelectAllClick.bind(this)
     this.handleSelectedColumnsChanged = this.handleSelectedColumnsChanged.bind(this)
+  }
+
+  defaultSelectedColumns() {
     let selectedColumns = this.props.selectedColumns || Object.keys(this.props.columns)
     if (this.props.selectedColumnsKey) {
       selectedColumns = globalSelectedColumns[this.props.selectedColumnsKey] || selectedColumns
     }
-    this.state = {
-      ...this.state,
-      selectedColumns: selectedColumns
-    }
+    return selectedColumns
   }
 
   state = {
@@ -375,7 +376,8 @@ class DataTableUnStyled extends React.Component {
 
   renderDetails(row) {
     const { classes, entryDetails, id, entryActions } = this.props
-    const { selectedColumns, selectedEntry } = this.state
+    const { selectedEntry } = this.state
+    const selectedColumns = this.state.selectedColumns || this.defaultSelectedColumns()
     if (entryDetails) {
       return (
         <tr>
@@ -400,7 +402,8 @@ class DataTableUnStyled extends React.Component {
     const {
       classes, data, total, order, orderBy, id, rows, selectActions, actions,
       entryDetails, entryActions, columns, entityLabels, pagination } = this.props
-    const { selectedColumns, selectedEntry } = this.state
+    const { selectedEntry } = this.state
+    const selectedColumns = this.state.selectedColumns || this.defaultSelectedColumns()
 
     const totalNumber = total || 0
 

gui/src/components/DatasetPage.js

@@ -75,6 +75,7 @@ export default function DatasetPage() {
       query={{dataset_id: [datasetId]}}
       ownerTypes={['all', 'public']}
       initialResultTab="entries"
+      resultListProps={{showAccessColumn: true}}
       availableResultTabs={['entries', 'groups', 'datasets']}
     />
   </div>

gui/src/components/Markdown.js

@@ -217,7 +217,7 @@ function Markdown(props) {
   return (
     <Typography variant="body1"
       className={classes.root}
-      dangerouslySetInnerHTML={{__html: marked(content)}}
+      dangerouslySetInnerHTML={{__html: marked(content || '')}}
     />
   )
 }

gui/src/components/UserdataPage.js

@@ -54,7 +54,7 @@ Once you assigned a DOI to a dataset, no entries can be removed or added to the
 
 function UserdataPage() {
   return <Search
-    ownerTypes={['user', 'staging']}
+    ownerTypes={['user', 'shared', 'staging']}
     initialOwner="user"
     initialRequest={{order_by: 'upload_time', uploads_grouped: true}}
     initialResultTab="uploads"

gui/src/components/entry/RawFiles.js

@@ -63,6 +63,10 @@ class RawFiles extends React.Component {
       whiteSpace: 'nowrap',
       direction: 'rtl',
       textAlign: 'left'
+    },
+    mainfileLabel: {
+      fontSize: '10pt',
+      fontWeight: 'bold'
     }
   })