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Commit a019565a authored by barillac's avatar barillac
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experimental step + vocabularies + annotations_state added 

SVN: 34215
parent d7532af6
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plasmid/source/core-plugins/weismigration/1/as/definitions.py
+ 21
− 4
View file @ a019565a
......@@ -80,7 +80,7 @@ antibodyDefinition = [
["BOX", "General", "Box", DataType.VARCHAR, None, "", None, None, False],
["EMPTY", "General", "empty?", DataType.VARCHAR, None, "", None, None, False],
["CATALOG_NUM", "General", "Catalog#", DataType.VARCHAR, None, "", None, None, False]
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
......@@ -99,7 +99,7 @@ strainDefinition = [
["REMOVED", "General", "removed", DataType.VARCHAR, None, "", None, None, False],
["UNMARKED_MUTATIONS", "General", "unmarked mutations", DataType.VARCHAR, None, "", None, None, False],
["WHO_ENTERED", "General", "who entered", DataType.VARCHAR, None, "", None, None, False]
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
oligoDefinition = [
......@@ -135,6 +135,7 @@ oligoDefinition = [
["CATEGORY", "General", "category", DataType.CONTROLLEDVOCABULARY, "OLIGO_CATEGORY", "", None, None, False],
["REORDERED", "General", "Reordered", DataType.VARCHAR, None, "", None, None, False],
["NOTES", "Comments", "Notes", DataType.VARCHAR, None, "", None, None, False]
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
plasmidDefinition = [
......@@ -165,6 +166,7 @@ plasmidDefinition = [
["SIZE_PARENT", "General", "Size parent", DataType.REAL, None, "", None, None, False],
["VECTOR", "General", "Vector", DataType.VARCHAR, None, "", None, None, False],
["VECTOR_TYPE", "General", "Vector Type", DataType.VARCHAR, None, "", None, None, False]
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
chemicalDefinition = [
......@@ -181,6 +183,7 @@ chemicalDefinition = [
["USED_BY", "General", "used by", DataType.VARCHAR, None, "", None, None, False],
["LOCATION", "Storage", "Location", DataType.VARCHAR, None, "", None, None, False],
["COMMENTS", "Comments", "Comments", DataType.VARCHAR, None, "", None, None, False],
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
RestrictionEnzymeDefinition = [
......@@ -188,7 +191,21 @@ RestrictionEnzymeDefinition = [
["BLOCK", "Storage", "Block", DataType.VARCHAR, None, "", None, None, False],
["POSITION", "Storage", "Position", DataType.VARCHAR, None, "", None, None, False],
["COMMENT", "Comments", "Comment", DataType.VARCHAR, None, "", None, None, False]
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
ExperimentalStepDefinition= [
["NAME", "General", "Name", DataType.MULTILINE_VARCHAR, None, "Name", None, None],
["OWNER", "General", "Owner", DataType.CONTROLLEDVOCABULARY, "LAB_MEMBERS", "Who produced/owned the sample", None, None],
["EXPERIMENTAL_GOALS", "General", "Experimental Goals", DataType.MULTILINE_VARCHAR, None, "Goal of the experiment", None, None],
["EXPERIMENTAL_RESULTS", "General", "Experimental Results", DataType.MULTILINE_VARCHAR, None, "Brief summary of the results obtained", None, None],
["START_DATE", "General", "Start date", DataType.TIMESTAMP, None, "Date when the experimental step is started", None, None],
["END_DATE", "General", "End date", DataType.TIMESTAMP, None, "Date when the experimental step is completed", None, None],
["EXPERIMENTAL_READOUT", "Readout details", "Experimental readout", DataType.CONTROLLEDVOCABULARY, "EXPERIMENTAL_READOUT", "Experimental readout used in the experiment", None, None],
["MACHINE", "Readout details", "Machine", DataType.CONTROLLEDVOCABULARY, "MACHINE", "Machine used to perform the experiment", None, None],
["FREEFORM_TABLE_STATE", "Readout details", "Freeform Table State", DataType.MULTILINE_VARCHAR, None, "Table describing how the order of samples measured in the experiments", None, None],
["PUBLICATION", "Comments", "Publication", DataType.MULTILINE_VARCHAR, None, "Publication from where the information was first found OR technical sheet given by the manufacturer", None, None],
["NOTES", "Comments", "Notes", DataType.MULTILINE_VARCHAR, None, "Notes", None, None],
["XMLCOMMENTS", "Comments", "Comments List", DataType.XML, None, "Several comments can be added by different users", commentsSampleScriptName, None],
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
+ 18
− 6
View file @ a019565a
......@@ -147,13 +147,25 @@ commentsScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "comments.py",
thymidineScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "thymidine_count.py",
definitions.thymidineScriptName,
"Count number of thymidine in sequence",
gcScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "gc.py",
definitions.gcScriptName,
"Count percentage of G and C in sequence",
"DYNAMIC_PROPERTY",
"SAMPLE");
atScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "at.py",
definitions.atScriptName,
"Count percentage of A and T in sequence",
"DYNAMIC_PROPERTY",
"SAMPLE");
lengthScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py",
definitions.lengthScriptName,
"Count length sequence",
"DYNAMIC_PROPERTY",
"SAMPLE");
##
## Vocabulary Types
##
......@@ -171,11 +183,11 @@ createExperimentTypeWithProperties("METHOD", "FOLDER FOR ORGANIZING METHODS SAMP
##
## Sample Types
##
#createSampleTypeWithProperties("ANTIBODY", "", definitions.antibodyDefinition);
createSampleTypeWithProperties("ANTIBODY", "", definitions.antibodyDefinition);
#addStorageGroups(definitions.numberOfStorageGroups, "ANTIBODY");
# createSampleTypeWithProperties("STRAIN", "", definitions.strainDefinition);
createSampleTypeWithProperties("STRAIN", "", definitions.strainDefinition);
# addStorageGroups(definitions.numberOfStorageGroups, "STRAIN");
# createSampleTypeWithProperties("PLASMID", "", definitions.plasmidDefinition);
createSampleTypeWithProperties("PLASMID", "", definitions.plasmidDefinition);
# addStorageGroups(definitions.numberOfStorageGroups, "PLASMID");
createSampleTypeWithProperties("OLIGO", "", definitions.oligoDefinition);
createSampleTypeWithProperties("CHEMICAL", "", definitions.chemicalDefinition);
......
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