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Commit c7e47b14 authored by barillac's avatar barillac
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scripts for dynamic properties added 

SVN: 35054
parent 12dfbd1a
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plasmid/source/core-plugins/weismigration/1/as/definitions.py
+ 63
− 49
View file @ c7e47b14
...@@ -20,6 +20,15 @@ gcScriptName= "GC" ...@@ -20,6 +20,15 @@ gcScriptName= "GC"
atScriptName= "AT" atScriptName= "AT"
lengthScriptName= "SEQUENCE_LENGTH" lengthScriptName= "SEQUENCE_LENGTH"
annotationsScriptName="ANNOTATIONS" annotationsScriptName="ANNOTATIONS"
antibodyrefnumScriptName="ANTIBODY_REFNUM"
chemicalrefnumScriptName="CHEMICAL_REFNUM"
oligonameScriptName="OLIGO_NAME"
oligorefnumScriptName="OLIGO_REFNUM"
plasmidnameScriptName="PLASMID_NAME"
plasmidrefnumScriptName="PLASMID_REFNUM"
strainnameScriptName="STRAIN_NAME"
strainglycerolScriptName="STRAIN_GLYCEROL_STOCK_NUM"
# #
# Storage # Storage
...@@ -56,77 +65,81 @@ experimentDefinition = [ ...@@ -56,77 +65,81 @@ experimentDefinition = [
#Sample Types #Sample Types
# #
antibodyDefinition = [ antibodyDefinition = [
["BY", "General", "By", DataType.VARCHAR, None, "", None, None, False], ["REF_NUM", "General", "RefNum", DataType.VARCHAR, None, "", antibodyrefnumScriptName, None, False],
["NOTES", "General", "Notes", DataType.MULTILINE_VARCHAR, None, "", None, None, False],
["RECEIVE_DATE", "General", "ReceiveDate", DataType.TIMESTAMP, None, "", None, None, False],
["REF_NUM", "General", "RefNum", DataType.VARCHAR, None, "", None, None, False],
["REQUEST_DATE", "General", "RequestDate", DataType.TIMESTAMP, None, "", None, None, False],
["TYPE", "General", "Type", DataType.VARCHAR, None, "", None, None, False],
["ANTIGEN", "General", "Antigen", DataType.VARCHAR, None, "", None, None, False],
["NAME", "General", "Name", DataType.VARCHAR, None, "", None, None, False], ["NAME", "General", "Name", DataType.VARCHAR, None, "", None, None, False],
["STORAGE_LOCATION", "General", "StorageLocation", DataType.VARCHAR, None, "", None, None, False], ["ANTIGEN", "General", "Antigen", DataType.VARCHAR, None, "", None, None, False],
["MONO_POLY", "General", "MonoPoly", DataType.VARCHAR, None, "", None, None, False], ["MONO_POLY", "General", "MonoPoly", DataType.VARCHAR, None, "", None, None, False],
["SPECIES", "General", "Species", DataType.VARCHAR, None, "", None, None, False], ["SPECIES", "General", "Species", DataType.VARCHAR, None, "", None, None, False],
["VENDOR", "General", "Vendor", DataType.VARCHAR, None, "", None, None, False], ["TYPE", "General", "Type", DataType.VARCHAR, None, "", None, None, False],
["WBDIL", "General", "WBDil", DataType.VARCHAR, None, "", None, None, False],
["IFDIL", "General", "IFDil", DataType.VARCHAR, None, "", None, None, False],
["FORM", "General", "Form", DataType.VARCHAR, None, "", None, None, False], ["FORM", "General", "Form", DataType.VARCHAR, None, "", None, None, False],
["PRIMARY", "General", "Primary", DataType.VARCHAR, None, "", None, None, False], ["PRIMARY", "General", "Primary", DataType.VARCHAR, None, "", None, None, False],
["SECONDARY", "General", "Secondary", DataType.VARCHAR, None, "", None, None, False], ["SECONDARY", "General", "Secondary", DataType.VARCHAR, None, "", None, None, False],
["COUPLED", "General", "Coupled", DataType.VARCHAR, None, "", None, None, False], ["COUPLED", "General", "Coupled", DataType.VARCHAR, None, "", None, None, False],
["BOX", "General", "Box", DataType.VARCHAR, None, "", None, None, False], ["VENDOR", "General", "Vendor", DataType.VARCHAR, None, "", None, None, False],
["EMPTY", "General", "emtpy?", DataType.VARCHAR, None, "", None, None, False], ["CATALOG_NUM", "General", "Catalog#", DataType.VARCHAR, None, "", None, None, False],
["CATALOG_NUM", "General", "Catalog#", DataType.VARCHAR, None, "", None, None, False], ["BY", "General", "By", DataType.VARCHAR, None, "", None, None, False],
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False] ["REQUEST_DATE", "General", "RequestDate", DataType.TIMESTAMP, None, "", None, None, False],
["RECEIVE_DATE", "General", "ReceiveDate", DataType.TIMESTAMP, None, "", None, None, False],
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False]
["NOTES", "Comments", "Notes", DataType.MULTILINE_VARCHAR, None, "", None, None, False],
["WBDIL", "Comments", "WBDil", DataType.VARCHAR, None, "", None, None, False],
["IFDIL", "Comments", "IFDil", DataType.VARCHAR, None, "", None, None, False],
["STORAGE_LOCATION", "Storage", "StorageLocation", DataType.VARCHAR, None, "", None, None, False],
["BOX", "Storage", "Box", DataType.VARCHAR, None, "", None, None, False],
["EMPTY", "Storage", "emtpy?", DataType.VARCHAR, None, "", None, None, False],
]; ];
strainDefinition = [ strainDefinition = [
["NAME", "General", "KWY number", DataType.VARCHAR, None, "", None, None, False],
["NAME_STRAIN", "General", "Strain name", DataType.VARCHAR, None, "", strainnameScriptName, None, False],
["BASE_STRAIN", "General", "base strain", DataType.VARCHAR, None, "", None, None, False], ["BASE_STRAIN", "General", "base strain", DataType.VARCHAR, None, "", None, None, False],
["DERIVED_FROM", "General", "derived from", DataType.VARCHAR, None, "", None, None, False],
["COMMENTS", "General", "comments", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["COMMENTS", "General", "comments", DataType.MULTILINE_VARCHAR, None, "", None, None, False],
["DATE_ENTERED", "General", "date entered", DataType.TIMESTAMP, None, "", None, None, False], ["GENOTYPE_CONFIRMATION", "General", "genotype confirmation", DataType.MULTILINE_VARCHAR, None, "", None, None, False],
["DERIVED_FROM", "General", "derived from", DataType.VARCHAR, None, "", None, None, False],
["FROZEN_STOCK", "General", "frozen stock", DataType.VARCHAR, None, "", None, None, False],
["GENOTYPE_CONFIRMATION", "General", "genotype confirmation", DataType.VARCHAR, None, "", None, None, False],
["GLYCEROL_STOCK_NUMBER", "General", "glycerol stock number", DataType.INTEGER, None, "", None, None, False],
["NAME", "General", "KWY number", DataType.VARCHAR, None, "", None, None, False],
["MAT", "General", "MAT", DataType.VARCHAR, None, "", None, None, False],
["REMOVED", "General", "removed", DataType.VARCHAR, None, "", None, None, False],
["WHO_ENTERED", "General", "who entered", DataType.VARCHAR, None, "", None, None, False], ["WHO_ENTERED", "General", "who entered", DataType.VARCHAR, None, "", None, None, False],
["REMOVED", "General", "removed", DataType.VARCHAR, None, "", None, None, False],
["FROZEN_STOCK", "General", "frozen stock", DataType.VARCHAR, None, "", None, None, False],
["DATE_ENTERED", "General", "date entered", DataType.TIMESTAMP, None, "", None, None, False],
["GLYCEROL_STOCK_NUMBER", "General", "Glycerol stock number", DataType.INTEGER, None, "", strainglycerolScriptName, None, False],
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False] ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False]
["MAT", "Genotype", "MAT", DataType.CONTROLLEDVOCABULARY, "MAT", "", None, None, False],
]; ];
oligoDefinition = [ oligoDefinition = [
["AT", "General", "AT%", DataType.INTEGER, None, "", atScriptName, None, False], ["REF_NUM", "General", "RefNum", DataType.VARCHAR, None, "", oligorefnumScriptName, None, False],
["BY", "General", "By", DataType.VARCHAR, None, "", None, None, False], ["SEQUENCE", "General", "Sequence", DataType.VARCHAR, None, "", None, None, False],
["FROM_NUC", "General", "fromNuc", DataType.INTEGER, None, "", None, None, False],
["GC", "General", "GC%", DataType.INTEGER, None, "", gcScriptName, None, False],
["GROUP", "General", "Group", DataType.VARCHAR, None, "", None, None, False],
["LABELS", "General", "Labels", DataType.VARCHAR, None, "", None, None, False],
["LENGTH", "General", "Length", DataType.INTEGER, None, "", lengthScriptName, None, False], ["LENGTH", "General", "Length", DataType.INTEGER, None, "", lengthScriptName, None, False],
["LIST", "General", "List", DataType.VARCHAR, None, "", None, None, False], ["GROUP", "General", "Group", DataType.VARCHAR, None, "", None, None, False],
["LOCATION", "General", "Location", DataType.VARCHAR, None, "", None, None, False],
["MMEXTCOEFF", "General", "mMExtCoeff", DataType.REAL, None, "", None, None, False],
["MOLWEIGHT", "General", "MolWeight", DataType.REAL, None, "", None, None, False],
["OD", "General", "OD", DataType.REAL, None, "", None, None, False],
["PMOL_UL", "General", "pMol_ul", DataType.REAL, None, "", None, None, False],
["RECEIVE_DATE", "General", "ReceiveDate", DataType.TIMESTAMP, None, "", None, None, False],
["REF_NUM", "General", "RefNum", DataType.VARCHAR, None, "", None, None, False],
["REQUEST_DATE", "General", "RequestDate", DataType.TIMESTAMP, None, "", None, None, False],
["SENSE", "General", "Sense", DataType.VARCHAR, None, "", None, None, False], ["SENSE", "General", "Sense", DataType.VARCHAR, None, "", None, None, False],
["SEQUENCE", "General", "Sequence", DataType.VARCHAR, None, "", None, None, False],
["STANDARD_TM", "General", "StandardTm", DataType.REAL, None, "", None, None, False],
["SYS_NAME", "General", "SysName", DataType.REAL, None, "", None, None, False],
["TONUC", "General", "toNuc", DataType.INTEGER, None, "", None, None, False],
["TYPE", "General", "Type", DataType.CONTROLLEDVOCABULARY, "OLIGO_TYPE", "", None, None, False],
["NAME", "General", "UC Number", DataType.VARCHAR, None, "", None, None, False],
["UG_UL", "General", "ug_ul", DataType.REAL, None, "", None, None, False],
["VOLUME", "General", "Volume", DataType.REAL, None, "", None, None, False],
["CATEGORY", "General", "category", DataType.CONTROLLEDVOCABULARY, "OLIGO_CATEGORY", "", None, None, False], ["CATEGORY", "General", "category", DataType.CONTROLLEDVOCABULARY, "OLIGO_CATEGORY", "", None, None, False],
["REORDERED", "General", "Reordered", DataType.VARCHAR, None, "", None, None, False],
["NOTES", "Comments", "Notes", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["NOTES", "Comments", "Notes", DataType.MULTILINE_VARCHAR, None, "", None, None, False],
["REORDERED", "General", "Reordered", DataType.VARCHAR, None, "", None, None, False],
["LABELS", "General", "Labels", DataType.VARCHAR, None, "", None, None, False],
["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False] ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False]
["XMLCOMMENTS", "Comments", "Comments List", DataType.XML, None, "Several comments can be added by different users", commentsScriptName, None, False],
["NAME", "Storage", "UC Number", DataType.VARCHAR, None, "", None, None, False],
["OLIGO_NAME", "Information", "Oligo name", DataType.VARCHAR, None, "", oligonameScriptName, None, False],
["SYS_NAME", "Information", "SysName", DataType.REAL, None, "", None, None, False],
["TYPE", "Information", "Type", DataType.CONTROLLEDVOCABULARY, "OLIGO_TYPE", "", None, None, False],
["STANDARD_TM", "Information", "StandardTm", DataType.REAL, None, "", None, None, False],
["AT", "Information", "AT%", DataType.INTEGER, None, "", atScriptName, None, False],
["GC", "Information", "GC%", DataType.INTEGER, None, "", gcScriptName, None, False],
["MMEXTCOEFF", "Information", "mMExtCoeff", DataType.REAL, None, "", None, None, False],
["MOLWEIGHT", "Information", "MolWeight", DataType.REAL, None, "", None, None, False],
["OD", "Information", "OD", DataType.REAL, None, "", None, None, False],
["REQUEST_DATE", "Information", "RequestDate", DataType.TIMESTAMP, None, "", None, None, False],
["RECEIVE_DATE", "Information", "ReceiveDate", DataType.TIMESTAMP, None, "", None, None, False],
["FROM_NUC", "Information", "fromNuc", DataType.INTEGER, None, "", None, None, False],
["TONUC", "Information", "toNuc", DataType.INTEGER, None, "", None, None, False],
["LIST", "Information", "List", DataType.VARCHAR, None, "", None, None, False],
["LOCATION", "Information", "Location", DataType.VARCHAR, None, "", None, None, False],
["PMOL_UL", "Information", "pMol_ul", DataType.REAL, None, "", None, None, False],
["UG_UL", "Information", "ug_ul", DataType.REAL, None, "", None, None, False],
["VOLUME", "Information", "Volume", DataType.REAL, None, "", None, None, False],
["BY", "General", "By", DataType.VARCHAR, None, "", None, None, False],
]; ];
plasmidDefinition = [ plasmidDefinition = [
...@@ -154,8 +167,9 @@ plasmidDefinition = [ ...@@ -154,8 +167,9 @@ plasmidDefinition = [
["PCR_3_OLIGO", "General", "PCR 3' oligo", DataType.VARCHAR, None, "", None, None, False], ["PCR_3_OLIGO", "General", "PCR 3' oligo", DataType.VARCHAR, None, "", None, None, False],
["PCR_5_OLIGO", "General", "PCR 5' oligo", DataType.VARCHAR, None, "", None, None, False], ["PCR_5_OLIGO", "General", "PCR 5' oligo", DataType.VARCHAR, None, "", None, None, False],
["NAME", "General", "pKW Number", DataType.VARCHAR, None, "", None, None, False], ["NAME", "General", "pKW Number", DataType.VARCHAR, None, "", None, None, False],
["PL_NAME", "General", "pKW Number Calculated", DataType.VARCHAR, None, "", plasmidnameScriptName, None, False],
["PLASMID_NAME", "General", "Plasmid name", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_NAME", "General", "Plasmid name", DataType.VARCHAR, None, "", None, None, False],
["REF_NUM", "General", "Ref. N.", DataType.INTEGER, None, "", None, None, False], ["REF_NUM", "General", "Ref. N.", DataType.INTEGER, None, "", plasmidrefnumScriptName, None, False],
["REFERENCE", "General", "Reference", DataType.VARCHAR, None, "", None, None, False], ["REFERENCE", "General", "Reference", DataType.VARCHAR, None, "", None, None, False],
["SELECTION_MARKER", "General", "Selection marker", DataType.CONTROLLEDVOCABULARY, "PLASMID_SELECTION_MAKER", "", None, None, False], ["SELECTION_MARKER", "General", "Selection marker", DataType.CONTROLLEDVOCABULARY, "PLASMID_SELECTION_MAKER", "", None, None, False],
["SIZE", "General", "Size", DataType.REAL, None, "", None, None, False], ["SIZE", "General", "Size", DataType.REAL, None, "", None, None, False],
...@@ -167,7 +181,7 @@ plasmidDefinition = [ ...@@ -167,7 +181,7 @@ plasmidDefinition = [
chemicalDefinition = [ chemicalDefinition = [
["NAME", "General", "Chemical", DataType.VARCHAR, None, "", None, None, False], ["NAME", "General", "Chemical", DataType.VARCHAR, None, "", None, None, False],
["ID", "General", "#", DataType.VARCHAR, None, "", None, None, False], ["ID", "General", "#", DataType.VARCHAR, None, "", chemicalrefnumScriptName, None, False],
["COMPANY", "General", "Company", DataType.CONTROLLEDVOCABULARY, "COMPANY", "", None, None, False], ["COMPANY", "General", "Company", DataType.CONTROLLEDVOCABULARY, "COMPANY", "", None, None, False],
["DISSOLVED_IN", "General", "dissolved in", DataType.VARCHAR, None, "", None, None, False], ["DISSOLVED_IN", "General", "dissolved in", DataType.VARCHAR, None, "", None, None, False],
["USED_FOR", "General", "Used for", DataType.VARCHAR, None, "", None, None, False], ["USED_FOR", "General", "Used for", DataType.VARCHAR, None, "", None, None, False],
......
plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
+ 9
− 1
View file @ c7e47b14
...@@ -246,5 +246,13 @@ vocabularyDefinitions = { ...@@ -246,5 +246,13 @@ vocabularyDefinitions = {
["BENCH-80", "Bench -80�C"], ["BENCH-80", "Bench -80�C"],
["BENCH-RT", "Bench RT"], ["BENCH-RT", "Bench RT"],
["BENCH", "Bench"] ["BENCH", "Bench"]
] ],
"MAT" : [
["ALPHA", "a"],
["A", "A"],
["A_ALPHA", "a/A"],
["A_A", "A/A"],
["ALPHA_ALPHA", "a/a"]
]
} }
\ No newline at end of file
plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
+ 51
− 0
View file @ c7e47b14
...@@ -182,6 +182,57 @@ lengthScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py", ...@@ -182,6 +182,57 @@ lengthScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py",
"SAMPLE"); "SAMPLE");
antibodyrefnumScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "antibody_refnum.py",
definitions.antibodyrefnumScriptName,
"Antibody ref num from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
chemicalrefnumScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "chemical_refnum.py",
definitions.chemicalrefnumScriptName,
"Chemical ref num from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
oligonameScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "oligo_name.py",
definitions.oligonameScriptName,
"Oligo name from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
oligorefnumScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "oligo_refnum.py",
definitions.oligorefnumScriptName,
"Oligo ref num from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
plasmidnameScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "plasmid_name.py",
definitions.plasmidnameScriptName,
"Plasmid name from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
plasmidrefnumScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "plasmid_refnum.py",
definitions.plasmidrefnumScriptName,
"Plasmid ref num from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
strainnameScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "strain_name.py",
definitions.strainnameScriptName,
"Strain name from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
strainglycerolScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "strain_glycerol_stock_number.py",
definitions.strainglycerolScriptName,
"Strain glycerol stock number from code",
"DYNAMIC_PROPERTY",
"SAMPLE");
## ##
## Vocabulary Types ## Vocabulary Types
......
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