Skip to content

Commit

Permalink
Merge pull request #27 from emdb-empiar/DAOTHER-9144
Browse files Browse the repository at this point in the history 
Daother 9144
  • Loading branch information
@neliebi
neliebi authored Feb 5, 2024
2 parents fe2485b + 00a0868 commit 34c5f67
Show file tree
Hide file tree
Showing 19 changed files with 97,854 additions and 51 deletions.
28 changes: 22 additions & 6 deletions emdb_schemas/current/doc/emdb_xsd.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4680,7 +4680,7 @@ <h3>Showing:</h3>
<table style="table-layout:fixed;white-space:pre-wrap;white-space:-moz-pre-wrap;white-space:-pre-wrap;white-space: -o-pre-wrap;word-wrap: break-word;_white-space:pre;" class="preWrapContainer">
<tr>
<td width="100%">
<pre><span class="tEl">&lt;emd</span><span class="tT"> </span><span class="tAN">emdb_id=</span><span class="tAV">""</span><span class="tT"> </span><span class="tAN">version=</span><span class="tAV">"3.0.9.1"</span><span class="tEl">&gt;</span><span class="tI">
<pre><span class="tEl">&lt;emd</span><span class="tT"> </span><span class="tAN">emdb_id=</span><span class="tAV">""</span><span class="tT"> </span><span class="tAN">version=</span><span class="tAV">"3.0.9.2"</span><span class="tEl">&gt;</span><span class="tI">
</span><span class="tEl">&lt;admin</span><span class="tT"> </span><span class="tAN">composite_map=</span><span class="tAV">""</span><span class="tEl">&gt;</span><span class="tT" style="white-space:normal">{1,1}</span><span class="tEl">&lt;/admin&gt;</span><span class="tI">
</span><span class="tEl">&lt;crossreferences</span><span class="tEl">&gt;</span><span class="tT" style="white-space:normal">{1,1}</span><span class="tEl">&lt;/crossreferences&gt;</span><span class="tI">
</span><span class="tEl">&lt;sample</span><span class="tEl">&gt;</span><span class="tT" style="white-space:normal">{1,1}</span><span class="tEl">&lt;/sample&gt;</span><span class="tI">
Expand Down Expand Up @@ -4724,7 +4724,7 @@ <h3>Showing:</h3>
<tr>
<td class="firstColumn"><b><a href="emdb_xsd.html#entry_type_version" target="mainFrame" title="No namespace" onclick="updatePageTitle('Schema documentation for emdb.xsd')">version</a></b></td>
<td><b>xs:token</b></td>
<td>3.0.9.1</td>
<td>3.0.9.2</td>
<td>optional</td>
<td>
<div class="annotation"></div>
Expand Down Expand Up @@ -85114,7 +85114,7 @@ <h3>Showing:</h3>
<tr>
<td class="firstColumn"><b><a href="emdb_xsd.html#entry_type_version" target="mainFrame" title="No namespace" onclick="updatePageTitle('Schema documentation for emdb.xsd')">version</a></b></td>
<td><b>xs:token</b></td>
<td>3.0.9.1</td>
<td>3.0.9.2</td>
<td>optional</td>
<td>
<div class="annotation"></div>
Expand Down Expand Up @@ -85157,7 +85157,7 @@ <h3>Showing:</h3>
</span><span class="tEl">&lt;/xs:element&gt;</span><span class="tI">
</span><span class="tEl">&lt;/xs:sequence&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:attribute</span><span class="tAN"> name=</span><span class="tAV">"emdb_id"</span><span class="tAN"> type=</span><span class="tAV">"emdb_id_type"</span><span class="tAN"> use=</span><span class="tAV">"required"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:attribute</span><span class="tAN"> name=</span><span class="tAV">"version"</span><span class="tAN"> type=</span><span class="tAV">"xs:token"</span><span class="tAN"> default=</span><span class="tAV">"3.0.9.1"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:attribute</span><span class="tAN"> name=</span><span class="tAV">"version"</span><span class="tAN"> type=</span><span class="tAV">"xs:token"</span><span class="tAN"> default=</span><span class="tAV">"3.0.9.2"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tC">&lt;!-- &lt;xs:attribute name="composite_structure" type="xs:boolean"/&gt; --&gt;</span><span class="tI">
</span><span class="tEl">&lt;/xs:complexType&gt;</span></pre>
</td>
Expand Down Expand Up @@ -93006,6 +93006,13 @@ <h3>Showing:</h3>
<div class="annotation"></div>
</td>
</tr>
<tr>
<td class="firstColumn">enumeration</td>
<td width="30%"><b>GATAN ALPINE (2.3k x 3.2k)</b></td>
<td>
<div class="annotation"></div>
</td>
</tr>
<tr>
<td class="firstColumn">enumeration</td>
<td width="30%"><b>GATAN K2 (4k x 4k)</b></td>
Expand Down Expand Up @@ -93048,6 +93055,13 @@ <h3>Showing:</h3>
<div class="annotation"></div>
</td>
</tr>
<tr>
<td class="firstColumn">enumeration</td>
<td width="30%"><b>GATAN K3 BIOCONTINUUM (6k x 4k)</b></td>
<td>
<div class="annotation"></div>
</td>
</tr>
<tr>
<td class="firstColumn">enumeration</td>
<td width="30%"><b>GATAN K3 BIOQUANTUM (6k x 4k)</b></td>
Expand Down Expand Up @@ -93306,12 +93320,14 @@ <h3>Showing:</h3>
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"FEI FALCON II (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"FEI FALCON III (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"FEI FALCON IV (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN ALPINE (2.3k x 3.2k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K2 (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K2 BASE (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K2 IS (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K2 QUANTUM (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K2 SUMMIT (4k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K3 (6k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K3 BIOCONTINUUM (6k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN K3 BIOQUANTUM (6k x 4k)"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN MULTISCAN"</span><span class="tEl">/&gt;</span><span class="tI">
</span><span class="tEl">&lt;xs:enumeration</span><span class="tAN"> value=</span><span class="tAV">"GATAN ORIUS SC1000 (4k x 2.7k)"</span><span class="tEl">/&gt;</span><span class="tI">
Expand Down Expand Up @@ -113435,7 +113451,7 @@ <h3>Showing:</h3>
<table class="propertiesTable">
<tr>
<td class="firstColumn" style="white-space: nowrap;">default</td>
<td><b>3.0.9.1</b></td>
<td><b>3.0.9.2</b></td>
</tr>
</table>
</div>
Expand Down Expand Up @@ -113467,7 +113483,7 @@ <h3>Showing:</h3>
<table style="table-layout:fixed;white-space:pre-wrap;white-space:-moz-pre-wrap;white-space:-pre-wrap;white-space: -o-pre-wrap;word-wrap: break-word;_white-space:pre;" class="preWrapContainer">
<tr>
<td width="100%">
<pre><span class="tEl">&lt;xs:attribute</span><span class="tAN"> name=</span><span class="tAV">"version"</span><span class="tAN"> type=</span><span class="tAV">"xs:token"</span><span class="tAN"> default=</span><span class="tAV">"3.0.9.1"</span><span class="tEl">/&gt;</span></pre>
<pre><span class="tEl">&lt;xs:attribute</span><span class="tAN"> name=</span><span class="tAV">"version"</span><span class="tAN"> type=</span><span class="tAV">"xs:token"</span><span class="tAN"> default=</span><span class="tAV">"3.0.9.2"</span><span class="tEl">/&gt;</span></pre>
</td>
</tr>
</table>
Expand Down
Binary file modified emdb_schemas/current/doc/img/emdb_xsd_Complex_Type_entry_type.jpeg
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified emdb_schemas/current/doc/img/emdb_xsd_Element_emd.jpeg
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
18 changes: 10 additions & 8 deletions emdb_schemas/current/emdb.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,24 +2,24 @@
# -*- coding: utf-8 -*-

#
# Generated Wed Dec 6 16:40:58 2023 by generateDS.py version 2.43.3.
# Generated Mon Feb 5 18:29:43 2024 by generateDS.py version 2.43.3.
# Python 3.9.7 (default, Sep 16 2021, 08:50:36) [Clang 10.0.0 ]
#
# Command line options:
# ('--root-element', 'emd')
# ('-f', '')
# ('-o', '/Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_1/emdb.py')
# ('-o', '/Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_2/emdb.py')
# ('--no-warnings', '')
# ('--external-encoding', 'utf-8')
#
# Command line arguments:
# /Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_1/emdb.xsd
# /Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_2/emdb.xsd
#
# Command line:
# /Users/sanja/generateDS/generateDS-2.43.3/generateDS.py --root-element="emd" -f -o "/Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_1/emdb.py" --no-warnings --external-encoding="utf-8" /Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_1/emdb.xsd
# /Users/sanja/generateDS/generateDS-2.43.3/generateDS.py --root-element="emd" -f -o "/Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_2/emdb.py" --no-warnings --external-encoding="utf-8" /Users/sanja/IdeaProjects/emdb_schemas/emdb_schemas/v3/v3_0_9_2/emdb.xsd
#
# Current working directory (os.getcwd()):
# v3_0_9_1
# sanja
#

import sys
Expand Down Expand Up @@ -1034,12 +1034,14 @@ class allowed_film_or_detector_model(str, Enum):
FEIFALCONII_4_KX_4_K='FEI FALCON II (4k x 4k)'
FEIFALCONIII_4_KX_4_K='FEI FALCON III (4k x 4k)'
FEIFALCONIV_4_KX_4_K='FEI FALCON IV (4k x 4k)'
GATANALPINE_2_3_KX_3_2_K='GATAN ALPINE (2.3k x 3.2k)'
GATANK_2_4_KX_4_K='GATAN K2 (4k x 4k)'
GATANK_2BASE_4_KX_4_K='GATAN K2 BASE (4k x 4k)'
GATANK_2IS_4_KX_4_K='GATAN K2 IS (4k x 4k)'
GATANK_2QUANTUM_4_KX_4_K='GATAN K2 QUANTUM (4k x 4k)'
GATANK_2SUMMIT_4_KX_4_K='GATAN K2 SUMMIT (4k x 4k)'
GATANK_3_6_KX_4_K='GATAN K3 (6k x 4k)'
GATANK_3BIOCONTINUUM_6_KX_4_K='GATAN K3 BIOCONTINUUM (6k x 4k)'
GATANK_3BIOQUANTUM_6_KX_4_K='GATAN K3 BIOQUANTUM (6k x 4k)'
GATANMULTISCAN='GATAN MULTISCAN'
GATANORIUSSC_1000_4_KX_2_7_K='GATAN ORIUS SC1000 (4k x 2.7k)'
Expand Down Expand Up @@ -1768,7 +1770,7 @@ class entry_type(GeneratedsSuper):
__hash__ = GeneratedsSuper.__hash__
subclass = None
superclass = None
def __init__(self, emdb_id=None, version='3.0.9.1', admin=None, crossreferences=None, sample=None, structure_determination_list=None, map=None, interpretation=None, validation=None, gds_collector_=None, **kwargs_):
def __init__(self, emdb_id=None, version='3.0.9.2', admin=None, crossreferences=None, sample=None, structure_determination_list=None, map=None, interpretation=None, validation=None, gds_collector_=None, **kwargs_):
self.gds_collector_ = gds_collector_
self.gds_elementtree_node_ = None
self.original_tagname_ = None
Expand Down Expand Up @@ -1894,7 +1896,7 @@ def _exportAttributes(self, outfile, level, already_processed, namespaceprefix_=
if self.emdb_id is not None and 'emdb_id' not in already_processed:
already_processed.add('emdb_id')
outfile.write(' emdb_id=%s' % (self.gds_encode(self.gds_format_string(quote_attrib(self.emdb_id), input_name='emdb_id')), ))
if self.version != "3.0.9.1" and 'version' not in already_processed:
if self.version != "3.0.9.2" and 'version' not in already_processed:
already_processed.add('version')
outfile.write(' version=%s' % (self.gds_encode(self.gds_format_string(quote_attrib(self.version), input_name='version')), ))
def _exportChildren(self, outfile, level, namespaceprefix_='', namespacedef_='', name_='entry_type', fromsubclass_=False, pretty_print=True):
Expand Down Expand Up @@ -33691,7 +33693,7 @@ def validate_allowed_film_or_detector_model(self, value):
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
return False
value = value
enumerations = ['AGFA SCIENTA FILM', 'DECTRIS SINGLA (1k x 1k)', 'DECTRIS ELA (1k x 0.5k)', 'DIRECT ELECTRON APOLLO (4k x 4k)', 'DIRECT ELECTRON DE-10 (5k x 4k)', 'DIRECT ELECTRON DE-12 (4k x 3k)', 'DIRECT ELECTRON DE-16 (4k x 4k)', 'DIRECT ELECTRON DE-20 (5k x 3k)', 'DIRECT ELECTRON DE-64 (8k x 8k)', 'FEI CETA (4k x 4k)', 'FEI EAGLE (2k x 2k)', 'FEI EAGLE (4k x 4k)', 'FEI FALCON I (4k x 4k)', 'FEI FALCON II (4k x 4k)', 'FEI FALCON III (4k x 4k)', 'FEI FALCON IV (4k x 4k)', 'GATAN K2 (4k x 4k)', 'GATAN K2 BASE (4k x 4k)', 'GATAN K2 IS (4k x 4k)', 'GATAN K2 QUANTUM (4k x 4k)', 'GATAN K2 SUMMIT (4k x 4k)', 'GATAN K3 (6k x 4k)', 'GATAN K3 BIOQUANTUM (6k x 4k)', 'GATAN MULTISCAN', 'GATAN ORIUS SC1000 (4k x 2.7k)', 'GATAN ORIUS SC200 (2k x 2k)', 'GATAN ORIUS SC600 (2.7k x 2.7k)', 'GATAN ULTRASCAN 1000 (2k x 2k)', 'GATAN ULTRASCAN 10000 (10k x 10k)', 'GATAN ULTRASCAN 4000 (4k x 4k)', 'GENERIC CCD', 'GENERIC CCD (2k x 2k)', 'GENERIC CCD (4k x 4k)', 'GENERIC FILM', 'GENERIC GATAN', 'GENERIC GATAN (2k x 2k)', 'GENERIC GATAN (4k x 4k)', 'GENERIC IMAGE PLATES', 'GENERIC TVIPS', 'GENERIC TVIPS (2k x 2k)', 'GENERIC TVIPS (4k x 4k)', 'KODAK 4489 FILM', 'KODAK SO-163 FILM', 'OTHER', 'PROSCAN TEM-PIV (2k x 2k)', 'SIA 15C (3k x 3k)', 'TFS FALCON 4i (4k x 4k)', 'TVIPS TEMCAM-F216 (2k x 2k)', 'TVIPS TEMCAM-F224 (2k x 2k)', 'TVIPS TEMCAM-F415 (4k x 4k)', 'TVIPS TEMCAM-F416 (4k x 4k)', 'TVIPS TEMCAM-F816 (8k x 8k)']
enumerations = ['AGFA SCIENTA FILM', 'DECTRIS SINGLA (1k x 1k)', 'DECTRIS ELA (1k x 0.5k)', 'DIRECT ELECTRON APOLLO (4k x 4k)', 'DIRECT ELECTRON DE-10 (5k x 4k)', 'DIRECT ELECTRON DE-12 (4k x 3k)', 'DIRECT ELECTRON DE-16 (4k x 4k)', 'DIRECT ELECTRON DE-20 (5k x 3k)', 'DIRECT ELECTRON DE-64 (8k x 8k)', 'FEI CETA (4k x 4k)', 'FEI EAGLE (2k x 2k)', 'FEI EAGLE (4k x 4k)', 'FEI FALCON I (4k x 4k)', 'FEI FALCON II (4k x 4k)', 'FEI FALCON III (4k x 4k)', 'FEI FALCON IV (4k x 4k)', 'GATAN ALPINE (2.3k x 3.2k)', 'GATAN K2 (4k x 4k)', 'GATAN K2 BASE (4k x 4k)', 'GATAN K2 IS (4k x 4k)', 'GATAN K2 QUANTUM (4k x 4k)', 'GATAN K2 SUMMIT (4k x 4k)', 'GATAN K3 (6k x 4k)', 'GATAN K3 BIOCONTINUUM (6k x 4k)', 'GATAN K3 BIOQUANTUM (6k x 4k)', 'GATAN MULTISCAN', 'GATAN ORIUS SC1000 (4k x 2.7k)', 'GATAN ORIUS SC200 (2k x 2k)', 'GATAN ORIUS SC600 (2.7k x 2.7k)', 'GATAN ULTRASCAN 1000 (2k x 2k)', 'GATAN ULTRASCAN 10000 (10k x 10k)', 'GATAN ULTRASCAN 4000 (4k x 4k)', 'GENERIC CCD', 'GENERIC CCD (2k x 2k)', 'GENERIC CCD (4k x 4k)', 'GENERIC FILM', 'GENERIC GATAN', 'GENERIC GATAN (2k x 2k)', 'GENERIC GATAN (4k x 4k)', 'GENERIC IMAGE PLATES', 'GENERIC TVIPS', 'GENERIC TVIPS (2k x 2k)', 'GENERIC TVIPS (4k x 4k)', 'KODAK 4489 FILM', 'KODAK SO-163 FILM', 'OTHER', 'PROSCAN TEM-PIV (2k x 2k)', 'SIA 15C (3k x 3k)', 'TFS FALCON 4i (4k x 4k)', 'TVIPS TEMCAM-F216 (2k x 2k)', 'TVIPS TEMCAM-F224 (2k x 2k)', 'TVIPS TEMCAM-F415 (4k x 4k)', 'TVIPS TEMCAM-F416 (4k x 4k)', 'TVIPS TEMCAM-F816 (8k x 8k)']
if value not in enumerations:
lineno = self.gds_get_node_lineno_()
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on allowed_film_or_detector_model' % {"value" : encode_str_2_3(value), "lineno": lineno} )
Expand Down
4 changes: 3 additions & 1 deletion emdb_schemas/current/emdb.xsd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
</xs:element>
</xs:sequence>
<xs:attribute name="emdb_id" type="emdb_id_type" use="required"/>
<xs:attribute name="version" type="xs:token" default="3.0.9.1"/>
<xs:attribute name="version" type="xs:token" default="3.0.9.2"/>
<!-- <xs:attribute name="composite_structure" type="xs:boolean"/> -->
</xs:complexType>
<xs:complexType name="admin_type">
Expand Down Expand Up @@ -2683,12 +2683,14 @@
<xs:enumeration value="FEI FALCON II (4k x 4k)"/>
<xs:enumeration value="FEI FALCON III (4k x 4k)"/>
<xs:enumeration value="FEI FALCON IV (4k x 4k)"/>
<xs:enumeration value="GATAN ALPINE (2.3k x 3.2k)"/>
<xs:enumeration value="GATAN K2 (4k x 4k)"/>
<xs:enumeration value="GATAN K2 BASE (4k x 4k)"/>
<xs:enumeration value="GATAN K2 IS (4k x 4k)"/>
<xs:enumeration value="GATAN K2 QUANTUM (4k x 4k)"/>
<xs:enumeration value="GATAN K2 SUMMIT (4k x 4k)"/>
<xs:enumeration value="GATAN K3 (6k x 4k)"/>
<xs:enumeration value="GATAN K3 BIOCONTINUUM (6k x 4k)"/>
<xs:enumeration value="GATAN K3 BIOQUANTUM (6k x 4k)"/>
<xs:enumeration value="GATAN MULTISCAN"/>
<xs:enumeration value="GATAN ORIUS SC1000 (4k x 2.7k)"/>
Expand Down
Loading

0 comments on commit 34c5f67

Please sign in to comment.