Changeset 195 for Xml/Working
- Timestamp:
- 09/10/08 12:03:10 (4 months ago)
- Location:
- Xml/Working
- Files:
-
- 12 modified
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AnalysisModule.xsd (modified) (6 diffs)
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BinaryFile.xsd (modified) (2 diffs)
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CA.xsd (modified) (2 diffs)
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CLI.xsd (modified) (2 diffs)
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DataHistory.xsd (modified) (2 diffs)
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MLI.xsd (modified) (2 diffs)
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SA.xsd (modified) (10 diffs)
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SPW.xsd (modified) (1 diff)
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STD.xsd (modified) (2 diffs)
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completesample-local.xml (modified) (1 diff)
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completesamplenopre.xml (modified) (2 diffs)
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roi-sa-sample.xml (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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Xml/Working/AnalysisModule.xsd
r153 r195 16 16 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 17 17 --> 18 < schema xmlns = "http://www.w3.org/2001/XMLSchema"18 <xsd:schema 19 19 targetNamespace = "http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02" 20 20 xmlns:AML = "http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-02" … … 27 27 version = "1" 28 28 elementFormDefault = "qualified"> 29 < import namespace = "http://www.openmicroscopy.org/Schemas/CLI/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/CLI/2008-02/CLI.xsd"/>30 < import namespace = "http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02/BinaryFile.xsd"/>31 < import namespace = "http://www.openmicroscopy.org/Schemas/MLI/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/MLI/2008-02/MLI.xsd"/>32 < import namespace = "http://www.openmicroscopy.org/Schemas/OME/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/OME/2008-02/ome.xsd"/>33 < import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/xml.xsd"/>34 < element name = "Entry">35 < complexType>36 < attribute name = "Value" use = "required">37 < annotation>38 < documentation>Tied to DB. LOOKUP_TABLE_ENTRIES.VALUE</documentation>39 </ annotation>40 < simpleType>41 < restriction base = "string">42 < maxLength value = "256"/>43 </ restriction>44 </ simpleType>45 </ attribute>46 < attribute name = "Label">47 < annotation>48 < documentation>Tied to DB. LOOKUP_TABLE_ENTRIES.LABEL</documentation>49 </ annotation>50 < simpleType>51 < restriction base = "string">52 < maxLength value = "256"/>53 </ restriction>54 </ simpleType>55 </ attribute>56 </ complexType>57 </ element>58 < element name = "LookupTable">59 < annotation>60 < documentation>Describes valid values for an input. Think enumerations, (a list of valid values).</documentation>61 </ annotation>62 < complexType>63 < sequence>64 < element ref = "AML:Entry" maxOccurs = "unbounded"/>65 < element ref = "OME:Description" minOccurs = "0"/>66 </ sequence>67 < attribute name = "Name" use = "required">68 < annotation>69 < documentation>Tied to DB. LOOKUP_TABLES.NAME</documentation>70 </ annotation>71 < simpleType>72 < restriction base = "string">73 < maxLength value = "64"/>74 </ restriction>75 </ simpleType>76 </ attribute>77 </ complexType>78 </ element>79 < element name = "FormalInput">80 < annotation>81 < documentation>Specifies an input requirement for a module. Image dimensions and image file locations (repository or other format) should not be specified with this. Image dimensions are intrinsic to an image. They do not represent a special requirement. Image file locations and contents are specified by other elements. Specifically, RawImageFile, RawImageFilePath, XYPlaneFile, and XYPlaneFilePath.82 </ documentation>83 </ annotation>84 < complexType>85 < sequence>86 < element ref = "AML:LookupTable" minOccurs = "0"/>87 < element ref = "OME:Description" minOccurs = "0"/>88 </ sequence>89 < attribute name = "UserDefined" default = "false" type = "boolean">90 < annotation>91 < documentation>OME interprets this as a recommendation rather than a requirement.29 <xsd:import namespace = "http://www.openmicroscopy.org/Schemas/CLI/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/CLI/2008-02/CLI.xsd"/> 30 <xsd:import namespace = "http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/BinaryFile/2008-02/BinaryFile.xsd"/> 31 <xsd:import namespace = "http://www.openmicroscopy.org/Schemas/MLI/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/MLI/2008-02/MLI.xsd"/> 32 <xsd:import namespace = "http://www.openmicroscopy.org/Schemas/OME/2008-02" schemaLocation = "http://www.openmicroscopy.org/Schemas/OME/2008-02/ome.xsd"/> 33 <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/xml.xsd"/> 34 <xsd:element name = "Entry"> <!-- top level definition --> 35 <xsd:complexType> 36 <xsd:attribute name = "Value" use = "required"> 37 <xsd:annotation> 38 <xsd:documentation>Tied to DB. LOOKUP_TABLE_ENTRIES.VALUE</xsd:documentation> 39 </xsd:annotation> 40 <xsd:simpleType> 41 <xsd:restriction base = "xsd:string"> 42 <xsd:maxLength value = "256"/> 43 </xsd:restriction> 44 </xsd:simpleType> 45 </xsd:attribute> 46 <xsd:attribute name = "Label" use="optional"> 47 <xsd:annotation> 48 <xsd:documentation>Tied to DB. LOOKUP_TABLE_ENTRIES.LABEL</xsd:documentation> 49 </xsd:annotation> 50 <xsd:simpleType> 51 <xsd:restriction base = "xsd:string"> 52 <xsd:maxLength value = "256"/> 53 </xsd:restriction> 54 </xsd:simpleType> 55 </xsd:attribute> 56 </xsd:complexType> 57 </xsd:element> 58 <xsd:element name = "LookupTable"> <!-- top level definition --> 59 <xsd:annotation> 60 <xsd:documentation>Describes valid values for an input. Think enumerations, (a list of valid values).</xsd:documentation> 61 </xsd:annotation> 62 <xsd:complexType> 63 <xsd:sequence> 64 <xsd:element ref = "AML:Entry" minOccurs="1" maxOccurs = "unbounded"/> 65 <xsd:element ref = "OME:Description" minOccurs = "0" maxOccurs="1"/> 66 </xsd:sequence> 67 <xsd:attribute name = "Name" use = "required"> 68 <xsd:annotation> 69 <xsd:documentation>Tied to DB. LOOKUP_TABLES.NAME</xsd:documentation> 70 </xsd:annotation> 71 <xsd:simpleType> 72 <xsd:restriction base = "xsd:string"> 73 <xsd:maxLength value = "64"/> 74 </xsd:restriction> 75 </xsd:simpleType> 76 </xsd:attribute> 77 </xsd:complexType> 78 </xsd:element> 79 <xsd:element name = "FormalInput"> <!-- top level definition --> 80 <xsd:annotation> 81 <xsd:documentation>Specifies an input requirement for a module. Image dimensions and image file locations (repository or other format) should not be specified with this. Image dimensions are intrinsic to an image. They do not represent a special requirement. Image file locations and contents are specified by other elements. Specifically, RawImageFile, RawImageFilePath, XYPlaneFile, and XYPlaneFilePath. 82 </xsd:documentation> 83 </xsd:annotation> 84 <xsd:complexType> 85 <xsd:sequence> 86 <xsd:element ref = "AML:LookupTable" minOccurs = "0" maxOccurs="1"/> 87 <xsd:element ref = "OME:Description" minOccurs = "0" maxOccurs="1"/> 88 </xsd:sequence> 89 <xsd:attribute name = "UserDefined" default = "false" use="optional" type = "xsd:boolean"> 90 <xsd:annotation> 91 <xsd:documentation>OME interprets this as a recommendation rather than a requirement. 92 92 Tied to DB. Table FORMAL_INPUTS Column USER_DEFINED 93 </ documentation>94 </ annotation>95 </ attribute>96 < attribute name = "Count" default = "+">97 < annotation>98 < documentation>Specifies how many counts of this formal input are expected. Meanings are specified below93 </xsd:documentation> 94 </xsd:annotation> 95 </xsd:attribute> 96 <xsd:attribute name = "Count" default = "+" use="optional"> 97 <xsd:annotation> 98 <xsd:documentation>Specifies how many counts of this formal input are expected. Meanings are specified below 99 99 ! = exactly one 100 100 ? = zero or one 101 101 + = one or more 102 102 * = zero or more 103 </ documentation>104 </ annotation>105 < simpleType>106 < restriction base = "string">107 < enumeration value = "!"/>108 < enumeration value = "?"/>109 < enumeration value = "+"/>110 < enumeration value = "*"/>111 </ restriction>112 </ simpleType>113 </ attribute>114 < attribute name = "Name" use = "required">115 < annotation>116 < documentation>Valid characters are alphanumeric and spaces.</documentation>117 </ annotation>118 < simpleType>119 < restriction base = "string">120 < pattern value = "[A-Za-z0-9\-\^\(\)_ ]+"/>121 </ restriction>122 </ simpleType>123 </ attribute>124 < attribute name = "SemanticTypeName" use = "required" type = "string"/>125 </ complexType>126 </ element>127 < element name = "FormalOutput">128 < annotation>129 < documentation>Specifies an output element of a module.</documentation>130 </ annotation>131 < complexType>132 < sequence>133 < element ref = "OME:Description" minOccurs = "0"/>134 </ sequence>135 < attribute name = "IBelongTo">136 < annotation>137 < documentation>Concerning MakeNewRegion attribute of ExecutionInstructions, if a new region type is made, then there are two possible places a formal output attribute can be stored: It can be stored as an attribute of the RegionIterator, or it can be stored as an attribute of the new Region.103 </xsd:documentation> 104 </xsd:annotation> 105 <xsd:simpleType> 106 <xsd:restriction base = "xsd:string"> 107 <xsd:enumeration value = "!"/> 108 <xsd:enumeration value = "?"/> 109 <xsd:enumeration value = "+"/> 110 <xsd:enumeration value = "*"/> 111 </xsd:restriction> 112 </xsd:simpleType> 113 </xsd:attribute> 114 <xsd:attribute name = "Name" use = "required"> 115 <xsd:annotation> 116 <xsd:documentation>Valid characters are alphanumeric and spaces.</xsd:documentation> 117 </xsd:annotation> 118 <xsd:simpleType> 119 <xsd:restriction base = "xsd:string"> 120 <xsd:pattern value = "[A-Za-z0-9\-\^\(\)_ ]+"/> 121 </xsd:restriction> 122 </xsd:simpleType> 123 </xsd:attribute> 124 <xsd:attribute name = "SemanticTypeName" use = "required" type = "xsd:string"/> 125 </xsd:complexType> 126 </xsd:element> 127 <xsd:element name = "FormalOutput"> <!-- top level definition --> 128 <xsd:annotation> 129 <xsd:documentation>Specifies an output element of a module.</xsd:documentation> 130 </xsd:annotation> 131 <xsd:complexType> 132 <xsd:sequence> 133 <xsd:element ref = "OME:Description" minOccurs = "0" maxOccurs="1"/> 134 </xsd:sequence> 135 <xsd:attribute name = "IBelongTo" use="optional"> 136 <xsd:annotation> 137 <xsd:documentation>Concerning MakeNewRegion attribute of ExecutionInstructions, if a new region type is made, then there are two possible places a formal output attribute can be stored: It can be stored as an attribute of the RegionIterator, or it can be stored as an attribute of the new Region. 138 138 This tag is supposed to specify which. Can be left blank if module does not make new iterator. 139 139 Tied to DB. FORMAL_OUTPUTS.FEATURE_TAG 140 140 Processed before storage to DB 141 </ documentation>142 </ annotation>143 < simpleType>144 < restriction base = "string">145 < enumeration value = "[Region]"/>146 < enumeration value = "[Iterator]"/>147 </ restriction>148 </ simpleType>149 </ attribute>150 < attribute name = "Count" default = "+">151 < annotation>152 < documentation>Specifies how many counts of this formal output will be produced. Meanings are specified below141 </xsd:documentation> 142 </xsd:annotation> 143 <xsd:simpleType> 144 <xsd:restriction base = "xsd:string"> 145 <xsd:enumeration value = "[Region]"/> 146 <xsd:enumeration value = "[Iterator]"/> 147 </xsd:restriction> 148 </xsd:simpleType> 149 </xsd:attribute> 150 <xsd:attribute name = "Count" default = "+" use="optional"> 151 <xsd:annotation> 152 <xsd:documentation>Specifies how many counts of this formal output will be produced. Meanings are specified below 153 153 ! = exactly one 154 154 ? = zero or one 155 155 + = one or more 156 156 * = zero or more 157 </ documentation>158 </ annotation>159 < simpleType>160 < restriction base = "string">161 < enumeration value = "!"/>162 < enumeration value = "?"/>163 < enumeration value = "+"/>164 < enumeration value = "*"/>165 </ restriction>166 </ simpleType>167 </ attribute>168 < attribute name = "Name" use = "required">169 < simpleType>170 < restriction base = "string">171 < pattern value = "[A-Za-z0-9\-\^\(\)_ ]+"/>172 </ restriction>173 </ simpleType>174 </ attribute>175 < attribute name = "SemanticTypeName" type = "string">176 < annotation>177 < documentation>THIS IS REQUIRED for every formal output outside of the importer. The importer doesn't know what it will run into before it executes, so it can't declare the semantic type of its outputs. If you are writing a module, I HIGHLY HIGHLY recommend that you type your formal outputs.</documentation>178 </ annotation>179 </ attribute>180 </ complexType>181 </ element>182 < element name = "Declaration">183 < annotation>184 < documentation>States module requirements.157 </xsd:documentation> 158 </xsd:annotation> 159 <xsd:simpleType> 160 <xsd:restriction base = "xsd:string"> 161 <xsd:enumeration value = "!"/> 162 <xsd:enumeration value = "?"/> 163 <xsd:enumeration value = "+"/> 164 <xsd:enumeration value = "*"/> 165 </xsd:restriction> 166 </xsd:simpleType> 167 </xsd:attribute> 168 <xsd:attribute name = "Name" use = "required"> 169 <xsd:simpleType> 170 <xsd:restriction base = "xsd:string"> 171 <xsd:pattern value = "[A-Za-z0-9\-\^\(\)_ ]+"/> 172 </xsd:restriction> 173 </xsd:simpleType> 174 </xsd:attribute> 175 <xsd:attribute name = "SemanticTypeName" use="optional" type = "xsd:string"> 176 <xsd:annotation> 177 <xsd:documentation>THIS IS REQUIRED for every formal output outside of the importer. The importer doesn't know what it will run into before it executes, so it can't declare the semantic type of its outputs. If you are writing a module, I HIGHLY HIGHLY recommend that you type your formal outputs.</xsd:documentation> 178 </xsd:annotation> 179 </xsd:attribute> 180 </xsd:complexType> 181 </xsd:element> 182 <xsd:element name = "Declaration"> <!-- top level definition --> 183 <xsd:annotation> 184 <xsd:documentation>States module requirements. 185 185 Formal Inputs are optional because input requirements may be specified by guaranteed image attributes. For example, OME_Image_XYZ_stats requires a path to the OME repository file, and Dimensions. 186 186 These are given by <RawImageFilePath>, <sizeX>, <sizeY>, <sizeZ>, <sizeT>, and <sizeW>. 187 </ documentation>188 </ annotation>189 < complexType>190 < sequence>191 < element ref = "AML:FormalInput" minOccurs = "0" maxOccurs = "unbounded"/>192 < element ref = "AML:FormalOutput" minOccurs = "0" maxOccurs = "unbounded"/>193 </ sequence>194 </ complexType>195 </ element>196 < element name = "AnalysisModule">197 < annotation>198 < documentation>Describes an interface to use with a program.</documentation>199 </ annotation>200 < complexType>201 < sequence>202 < element ref = "OME:Description" minOccurs = "0"/>203 < element ref = "AML:Declaration"/>204 < choice minOccurs = "0">205 < element ref = "CLI:ExecutionInstructions"/>206 < element ref = "MLI:ExecutionInstructions"/>207 </ choice>208 </ sequence>209 < attribute name = "isStreamAlgorithm" default = "false" type = "boolean">210 < annotation>211 < documentation>This is a stub for future development. The database location doesn't even exist yet.187 </xsd:documentation> 188 </xsd:annotation> 189 <xsd:complexType> 190 <xsd:sequence> 191 <xsd:element ref = "AML:FormalInput" minOccurs = "0" maxOccurs = "unbounded"/> 192 <xsd:element ref = "AML:FormalOutput" minOccurs = "0" maxOccurs = "unbounded"/> 193 </xsd:sequence> 194 </xsd:complexType> 195 </xsd:element> 196 <xsd:element name = "AnalysisModule"> <!-- top level definition --> 197 <xsd:annotation> 198 <xsd:documentation>Describes an interface to use with a program.</xsd:documentation> 199 </xsd:annotation> 200 <xsd:complexType> 201 <xsd:sequence> 202 <xsd:element ref = "OME:Description" minOccurs = "0" maxOccurs="1"/> 203 <xsd:element ref = "AML:Declaration" minOccurs="1" maxOccurs="1"/> 204 <xsd:choice minOccurs = "0" maxOccurs="1"> 205 <xsd:element ref = "CLI:ExecutionInstructions" minOccurs="1" maxOccurs="1"/> 206 <xsd:element ref = "MLI:ExecutionInstructions" minOccurs="1" maxOccurs="1"/> 207 </xsd:choice> 208 </xsd:sequence> 209 <xsd:attribute name = "isStreamAlgorithm" default = "false" use="optional" type = "xsd:boolean"> 210 <xsd:annotation> 211 <xsd:documentation>This is a stub for future development. The database location doesn't even exist yet. 212 212 If the output of the analysis will be the same when pixel positions are scrambled, the analysis is a stream algorithm. 213 213 Examples of stream algorithms are: … … 218 218 If a module is a stream algorithm, it can function across the x, y, z, and time dimensions. 219 219 Tied to DB. Table PROGRAMS Column IS_STREAM_ALGORITHM 220 </ documentation>221 </ annotation>222 </ attribute>223 < attribute name = "ModuleType" use = "required">224 < annotation>225 < documentation>As more handlers, are added, this part of the schema needs to be changed220 </xsd:documentation> 221 </xsd:annotation> 222 </xsd:attribute> 223 <xsd:attribute name = "ModuleType" use = "required"> 224 <xsd:annotation> 225 <xsd:documentation>As more handlers, are added, this part of the schema needs to be changed 226 226 Tied to DB. Table PROGRAMS Column MODULE_TYPE 227 </ documentation>228 </ annotation>229 < simpleType>230 < restriction base = "string">231 < pattern value = "OME::Analysis::.+"/>232 </ restriction>233 </ simpleType>234 </ attribute>235 < attribute name = "RegionIterator">236 < annotation>237 < documentation>If the module iterates over a region, specify the iterator here. It will reference a region via the TAG column of the REGIONS table.227 </xsd:documentation> 228 </xsd:annotation> 229 <xsd:simpleType> 230 <xsd:restriction base = "xsd:string"> 231 <xsd:pattern value = "OME::Analysis::.+"/> 232 </xsd:restriction> 233 </xsd:simpleType> 234 </xsd:attribute> 235 <xsd:attribute name = "RegionIterator" use="optional"> 236 <xsd:annotation> 237 <xsd:documentation>If the module iterates over a region, specify the iterator here. It will reference a region via the TAG column of the REGIONS table. 238 238 An example of a module that does not iterate over a region is Find Cells. It examines one image at a time, hence it iterates over an image, not a region. It produces zero or more regions (Ãell) per image. These Cell regions belong to an image. 239 239 This module would not get a RegionIterator attribute. … … 241 241 This module would get a RegionIterator attribute of "CELL". 242 242 Tied to DB. Table PROGRAMS Column DEFAULT_ITERATOR 243 </ documentation>244 </ annotation>245 < simpleType>246 < restriction base = "string">247 < maxLength value = "128"/>248 </ restriction>249 </ simpleType>250 </ attribute>251 < attribute name = "NewRegionName">252 < annotation>253 < documentation>If this module makes new regions, then the new Region's name needs to be specified here.243 </xsd:documentation> 244 </xsd:annotation> 245 <xsd:simpleType> 246 <xsd:restriction base = "xsd:string"> 247 <xsd:maxLength value = "128"/> 248 </xsd:restriction> 249 </xsd:simpleType> 250 </xsd:attribute> 251 <xsd:attribute name = "NewRegionName" use="optional"> 252 <xsd:annotation> 253 <xsd:documentation>If this module makes new regions, then the new Region's name needs to be specified here. 254 254 If the module does not make new regions, do not specify a value for this attribute. 255 255 Tied to DB. PROGRAMS.NEW_FEATURE_TAG 256 </ documentation>257 </ annotation>258 < simpleType>259 < restriction base = "string">260 < maxLength value = "128"/>261 </ restriction>262 </ simpleType>263 </ attribute>264 < attribute name = "Category">265 < annotation>266
