fixed some locations, remove Ho2Sn2O7, update to follow tiled dev

BMM-standards.html

@@ -1159,7 +1159,7 @@ <h2 id="Chromium">
                   <td></td>
                   <td>ErCrO<sub>3</sub></td>
                   <td>Erbium Chromate</td>
-                  <td>Er</td>
+                  <td>Lanthanide standards wheel</td>
                   <td></td>
                   <td></td>
                </tr>
@@ -2636,7 +2636,7 @@ <h2 id="Ruthenium">
                   <td></td>
                   <td>PtRu</td>
                   <td>Platinum ruthenium</td>
-                  <td></td>
+                  <td>5d metals wheel</td>
                   <td></td>
                   <td></td>
                </tr>
@@ -3175,7 +3175,7 @@ <h2 id="Samarium">
                   <td></td>
                   <td>Sm<sub>2</sub>O<sub>3</sub></td>
                   <td>Monoclinic Samarium oxide</td>
-                  <td></td>
+                  <td>Lanthanide standards wheel</td>
                   <td></td>
                   <td>L<sub>3</sub> : <a href="Data/Sm/Sm-L3-Sm2O3-m.xdi">Sm-L3-Sm2O3-m.xdi</a><br>L<sub>1</sub> : <a href="Data/Sm/Sm-L1-Sm2O3-m.xdi">Sm-L1-Sm2O3-m.xdi</a></td>
                </tr>
@@ -3406,7 +3406,7 @@ <h2 id="Dysprosium">
                   <td></td>
                   <td>DyScO<sub>3</sub></td>
                   <td>Dysprosium scandate</td>
-                  <td></td>
+                  <td>Lanthanide standards wheel</td>
                   <td></td>
                   <td>L<sub>3</sub> : <a href="Data/Dy/Dy-L3-DyScO3.xdi">Dy-L3-DyScO3.xdi</a><br>L<sub>1</sub> : <a href="Data/Dy/Dy-L1-DyScO3.xdi">Dy-L1-DyScO3.xdi</a></td>
                </tr>
@@ -3462,15 +3462,6 @@ <h2 id="Holmium">
                   <td>L<sub>3</sub> : <a href="Data/Ho/Ho-L3-HolmiumOxide.xdi">Ho-L3-HolmiumOxide.xdi</a><br>L<sub>1</sub> : <a href="Data/Ho/Ho-L1-HolmiumOxide.xdi">Ho-L1-HolmiumOxide.xdi</a></td>
                </tr>
 
-               <tr class=present>
-                  <td></td>
-                  <td>Ho<sub>2</sub>Sn<sub>2</sub>O<sub>7</sub></td>
-                  <td>Holmium stannate</td>
-                  <td></td>
-                  <td></td>
-                  <td></td>
-               </tr>
-
                <tr class=present>
                   <td></td>
                   <td>Ho<sub>2</sub>TiO<sub>5</sub></td>
@@ -3507,7 +3498,7 @@ <h2 id="Erbium">
                <tr class=present>
                   <td>&#10004;</td>
                   <td>Er<sub>2</sub>O<sub>3</sub></td>
-                  <td>Erbium oxide</td>
+                  <td>Erbium trioxide</td>
                   <td>reference wheel</td>
                   <td></td>
                   <td>L<sub>3</sub> : <a href="Data/Er/Er-L3-ErbiumOxide.xdi">Er-L3-ErbiumOxide.xdi</a><br>L<sub>1</sub> : <a href="Data/Er/Er-L1-ErbiumOxide.xdi">Er-L1-ErbiumOxide.xdi</a></td>
@@ -3517,7 +3508,7 @@ <h2 id="Erbium">
                   <td></td>
                   <td>ErCrO<sub>3</sub></td>
                   <td>Erbium chromate</td>
-                  <td>Cr</td>
+                  <td>Lanthanide standards wheel</td>
                   <td></td>
                   <td></td>
                </tr>
@@ -3558,7 +3549,7 @@ <h2 id="Thulium">
                <tr class=present>
                   <td>&#10004;</td>
                   <td>Tm<sub>2</sub>O<sub>3</sub></td>
-                  <td>Thullium oxide</td>
+                  <td>Thullium trioxide</td>
                   <td>reference wheel</td>
                   <td></td>
                   <td>L<sub>3</sub> : <a href="Data/Tm/Tm-L3-ThuliumOxide.xdi">Tm-L3-ThuliumOxide.xdi</a><br>L<sub>1</sub> : <a href="Data/Tm/Tm-L1-ThuliumOxide.xdi">Tm-L1-ThuliumOxide.xdi</a></td>
@@ -3600,7 +3591,7 @@ <h2 id="Ytterbium">
                <tr class=present>
                   <td>&#10004;</td>
                   <td>Yb<sub>2</sub>O<sub>3</sub></td>
-                  <td>Ytterbium oxide</td>
+                  <td>Ytterbium trioxide</td>
                   <td>reference wheel</td>
                   <td></td>
                   <td>L<sub>3</sub> : <a href="Data/Yb/Yb-L3-YtterbiumOxide.xdi">Yb-L3-YtterbiumOxide.xdi</a><br>L<sub>1</sub> : <a href="Data/Yb/Yb-L1-YtterbiumOxide.xdi">Yb-L1-YtterbiumOxide.xdi</a></td>
@@ -3642,7 +3633,7 @@ <h2 id="Lutetium">
                <tr class=present>
                   <td>&#10004;</td>
                   <td>Lu<sub>2</sub>O<sub>3</sub></td>
-                  <td>Lutetium oxide</td>
+                  <td>Lutetium trioxide</td>
                   <td>reference wheel</td>
                   <td></td>
                   <td>L<sub>3</sub> : <a href="Data/Lu/Lu-L3-LutetiumOxide.xdi">Lu-L3-LutetiumOxide.xdi</a><br>L<sub>1</sub> : <a href="Data/Lu/Lu-L1-LutetiumOxide.xdi">Lu-L1-LutetiumOxide.xdi</a></td>

standards.json

@@ -200,7 +200,7 @@
         {
             "material": "ErCrO3",
             "name": "Erbium Chromate",
-            "location": "Er",
+            "location": "Lanthanide standards wheel",
             "refwheel": false
         }
     ],
@@ -1057,7 +1057,7 @@
         {
             "material": "PtRu",
             "name": "Platinum ruthenium",
-            "location": "Ru",
+            "location": "5d metals wheel",
             "refwheel": false,
             "datafile": false
         },
@@ -1338,7 +1338,7 @@
         {
             "material": "Sm2O3",
             "name": "monoclinic Samarium oxide",
-            "location": "Sm",
+            "location": "Lanthanide standards wheel",
             "refwheel": false,
             "lanthanidewheel": false,
             "datafile": "Sm-L3-Sm2O3-m.xdi",
@@ -1471,7 +1471,7 @@
         {
             "material": "DyScO3",
             "name": "Dysprosium scandate",
-            "location": "Dy",
+            "location": "Lanthanide standards wheel",
             "refwheel": false,
             "datafile": "Dy-L3-DyScO3.xdi",
             "datafile2": "Dy-L1-DyScO3.xdi"
@@ -1502,13 +1502,6 @@
             "datafile": "Ho-L3-HolmiumOxide.xdi",
             "datafile2": "Ho-L1-HolmiumOxide.xdi"
         },
-        {
-            "material": "Ho2Sn2O7",
-            "name": "Holmium stannate",
-            "location": "Ho",
-            "refwheel": false,
-            "datafile": false
-        },
         {
             "material": "Ho2TiO5",
             "name": "stuffed pyrochlore holmium titanate",
@@ -1521,7 +1514,7 @@
     "Er": [
         {
             "material": "Er2O3",
-            "name": "Erbium oxide",
+            "name": "Erbium trioxide",
             "refwheel": true,
             "location": "Er",
             "datafile": "Er-L3-ErbiumOxide.xdi",
@@ -1530,7 +1523,7 @@
         {
             "material": "ErCrO3",
             "name": "Erbium chromate",
-            "location": "Cr",
+            "location": "Lanthanide standards wheel",
             "refwheel": false,
             "datafile": false
         },
@@ -1546,7 +1539,7 @@
     "Tm": [
         {
             "material": "Tm2O3",
-            "name": "Thullium oxide",
+            "name": "Thullium trioxide",
             "refwheel": true,
             "location": "Tm",
             "datafile": "Tm-L3-ThuliumOxide.xdi",
@@ -1564,7 +1557,7 @@
     "Yb": [
         {
             "material": "Yb2O3",
-            "name": "Ytterbium oxide",
+            "name": "Ytterbium trioxide",
             "refwheel": true,
             "location": "Yb",
             "datafile2": "Yb-L1-YtterbiumOxide.xdi",
@@ -1580,7 +1573,7 @@
     "Lu": [
         {
             "material": "Lu2O3",
-            "name": "lutetium oxide",
+            "name": "lutetium trioxide",
             "refwheel": true,
             "location": "Lu",
             "datafile": "Lu-L3-LutetiumOxide.xdi",

tiled/config.yml

@@ -1,12 +1,18 @@
 authentication:
   allow_anonymous_access: true
+  single_user_api_key: secret
 trees:
-  - tree: files
+  - tree: catalog
     path: /bmm/standards
     args:
-      directory: /home/bruce/git/bmm-standards/Data
-      readers_by_mimetype:
-        text/x-xdi: xdi:XDIDataFrameAdapter.from_file
-      mimetypes_by_file_ext:
-        .xdi: text/x-xdi
-
+      uri: catalog.db
+      adapters_by_mimetype:
+        text/x-xdi: xdi:read_xdi
+      # Tiled will not serve anything that is outside the directory (directories)
+      # listed here. It is a security feature to protect against something like
+      # /etc/passwd getting registered and served.
+      readable_storage:
+        - /home/bruce/git/bmm-standards/Data     
+      writable_storage: /home/bruce/git/bmm-standards/Processed
+allow_origins:
+  - https://vega.github.io

tiled/xdi.py

@@ -7,16 +7,17 @@
 import collections
 import io
 import re
+import pathlib
 
 import dask
 import pandas as pd
 
 from tiled.adapters.dataframe import DataFrameAdapter
 
 
-def read_xdi(file):
+def read_xdi(file, metadata=None, specs=None, meta=None, divisions=None, access_policy=None):
     "Read XDI-formatted file given a filepath or a readable buffer."
-    if isinstance(file, str):
+    if isinstance(file, (str,pathlib.Path)):
         # Treat file as filepath.
         with open(file, "r") as file_:
             return _read_xdi(file_)
@@ -30,6 +31,9 @@ def _read_xdi(f):
     metadata = {}
     fields = collections.defaultdict(dict)
 
+    #if isinstance(f, pathlib.PosixPath):
+    #    line = f.read_text().split('\n')[0]
+    #else:
     line = f.readline()
     m = re.match(r"#\s*XDI/(\S*)\s*(\S*)?", line)
     if not m:
@@ -86,18 +90,7 @@ def _read_xdi(f):
 
     df = pd.read_table(f, delim_whitespace=True, names=col_labels)
 
-    return df, metadata
-
-
-class XDIDataFrameAdapter(DataFrameAdapter):
-    specs = ["xdi"]
-
-    @classmethod
-    def from_file(cls, file):
-        df, metadata = read_xdi(file)
-        return cls.from_dask_dataframe(
-            dask.dataframe.from_pandas(df, npartitions=1), metadata=metadata
-        )
+    return DataFrameAdapter.from_pandas(df, npartitions=1, metadata=metadata, specs=["xdi"])
 
 
 def write_xdi(df, metadata):