feat: add simple CSV/TSV widget using panel Tabulator

Materials-Data-Science-and-Informatics · Aug 9, 2023 · 39925f0 · 39925f0
1 parent f38ff20
commit 39925f0
Show file tree

Hide file tree

Showing 11 changed files with 972 additions and 237 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ Here we provide notes that summarize the most important changes in each released
 
 Please consult the changelog to inform yourself about breaking changes and security issues.
 
+## [v0.1.1](https://github.com/Materials-Data-Science-and-Informatics/metador-core/tree/v0.1.1) <small>(2023-??-??)</small> { id="0.1.1" }
+
+* added CSV/TSV widget
+
 ## [v0.1.0](https://github.com/Materials-Data-Science-and-Informatics/metador-core/tree/v0.1.0) <small>(2023-08-08)</small> { id="0.1.0" }
 
 * updated dependencies to unpin versions

diff --git a/CITATION.cff b/CITATION.cff
@@ -3,7 +3,7 @@ type: software
 message: If you use this software, please cite it using these metadata.
 
 title: metador-core
-version: 0.1.0
+version: 0.1.1
 abstract: Core of Metador, the metadata-first research data management framework.
 repository-code: "https://github.com/Materials-Data-Science-and-Informatics/metador-core"
 license: MIT

diff --git a/codemeta.json b/codemeta.json
@@ -14,11 +14,11 @@
     "audience": [
         {
             "@type": "Audience",
-            "audienceType": "Developers"
+            "audienceType": "Science/Research"
         },
         {
             "@type": "Audience",
-            "audienceType": "Science/Research"
+            "audienceType": "Developers"
         }
     ],
     "author": [
@@ -99,7 +99,7 @@
             "identifier": "pandas",
             "name": "pandas",
             "runtimePlatform": "Python 3",
-            "version": "^1.4.1"
+            "version": "^2.0.3"
         },
         {
             "@type": "SoftwareApplication",
@@ -180,5 +180,5 @@
         }
     ],
     "url": "https://github.com/Materials-Data-Science-and-Informatics/metador-core",
-    "version": "0.1.0"
+    "version": "0.1.1"
 }
diff --git a/docs/notebooks/05_Widgets.ipynb b/docs/notebooks/05_Widgets.ipynb
diff --git a/docs/notebooks/files/table.csv b/docs/notebooks/files/table.csv
@@ -0,0 +1,3 @@
+Event,Date,Participants,Duration
+Some event,2023-08-08,3,2.43
+Another event,2023-08-07,5,1.32
diff --git a/docs/notebooks/files/table.tsv b/docs/notebooks/files/table.tsv
@@ -0,0 +1,3 @@
+Event	Date	Participants	Duration
+Some event	2023-08-08	3	2.43
+Another event	2023-08-07	5	1.32
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 # ---- DO NOT EDIT, managed by somesy ----
 name = "metador-core"
-version = "0.1.0"
+version = "0.1.1"
 description = "Core of Metador, the metadata-first research data management framework."
 authors = ["Anton Pirogov <[email protected]>"]
 license = "MIT"
@@ -50,7 +50,7 @@ isodate = "^0.6.1"
 Pint = "^0.21"
 Pillow = "^9.1.1"
 python-magic = "^0.4.25"
-pandas = "^1.4.1"
+pandas = "^2.0.3"
 overrides = "^7.0.0"
 simple-parsing = "^0.0.20"
 phantom-types = "^2.1.0"
@@ -65,6 +65,7 @@ pytest-cov = "^4.1.0"
 hypothesis = "^6.58.0"
 frozendict = "^2.3.4"
 # somesy = {path = "../somesy", develop = true}
+notebook = "^7.0.2"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "^1.4.2"
@@ -115,6 +116,7 @@ mkdocs-jupyter = "^0.24.2"
 'core.file.text.code__0.1.0'  = "metador_core.widget.common:CodeWidget"
 'core.file.text__0.1.0'  = "metador_core.widget.common:TextWidget"
 'core.file.json__0.1.0'  = "metador_core.widget.common:JSONWidget"
+'core.file.csv__0.1.0'  = "metador_core.widget.common:CSVWidget"
 'core.file.pdf__0.1.0'   = "metador_core.widget.common:PDFWidget"
 'core.file.image__0.1.0' = "metador_core.widget.common:ImageWidget"
 'core.file.audio__0.1.0' = "metador_core.widget.common:AudioWidget"

diff --git a/somesy.toml b/somesy.toml
@@ -1,6 +1,6 @@
 [project]
 name = "metador-core"
-version = "0.1.0"
+version = "0.1.1"
 description = "Core of Metador, the metadata-first research data management framework."
 license = "MIT"
 repository = "https://github.com/Materials-Data-Science-and-Informatics/metador-core"

diff --git a/src/metador_core/widget/common.py b/src/metador_core/widget/common.py
@@ -4,8 +4,10 @@
 """
 
 import json
+from io import StringIO
 from typing import List, Set, Type
 
+import pandas as pd
 import panel as pn
 from overrides import overrides
 from panel.viewable import Viewable
@@ -57,6 +59,36 @@ def supports_meta(cls, obj: MetadataSchema) -> bool:
 # pass content:
 
 
+class CSVWidget(FileWidget):
+    class Plugin(FileWidget.Plugin):
+        name = "core.file.csv"
+        version = (0, 1, 0)
+
+    MIME_TYPES = {"text/csv", "text/tab-separated-values"}
+    FILE_EXTS = {".csv", ".tsv"}
+
+    @overrides
+    def show(self) -> Viewable:
+        df = pd.read_csv(
+            StringIO(self.file_data().decode("utf-8")),
+            sep=None,  # auto-infer csv/tsv
+            engine="python",  # mute warning
+            # smart date processing
+            parse_dates=True,
+            dayfirst=True,
+            cache_dates=True,
+        )
+        return pn.widgets.Tabulator(
+            df,
+            disabled=True,
+            layout="fit_data_table",
+            # NOTE: pagination looks buggy, table sometimes won't show up
+            # need to investigate that further, maybe it's a bug
+            # pagination="remote",
+            # page_size=10,
+        )
+
+
 class MarkdownWidget(FileWidget):
     class Plugin(FileWidget.Plugin):
         name = "core.file.text.md"

diff --git a/src/metador_core/widget/jupyter/standalone.py b/src/metador_core/widget/jupyter/standalone.py
@@ -40,7 +40,7 @@ def silence_flask():
 # As this is only used ad-hoc e.g. by a researcher playing in a notebook,
 # this should be not a problem ("serious" servers are implemented elsewhere!).
 
-DEFAULT_PANEL_EXTS = ["ace"]
+DEFAULT_PANEL_EXTS = ["ace", "tabulator"]
 
 host: str = "127.0.0.1"
 port: int = -1