From c7e47b1430628fa3c34a81708728d1458d319bf7 Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Fri, 13 Nov 2015 13:00:51 +0000
Subject: [PATCH] scripts for dynamic properties added
SVN: 35054
---
.../weismigration/1/as/definitions.py | 112 ++++++++++--------
.../weismigration/1/as/definitionsVoc.py | 10 +-
.../1/as/initialize-master-data.py | 51 ++++++++
3 files changed, 123 insertions(+), 50 deletions(-)
diff --git a/plasmid/source/core-plugins/weismigration/1/as/definitions.py b/plasmid/source/core-plugins/weismigration/1/as/definitions.py
index 58c8a0a2687..a0c38ceaf78 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/definitions.py
@@ -20,6 +20,15 @@ gcScriptName= "GC"
atScriptName= "AT"
lengthScriptName= "SEQUENCE_LENGTH"
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
@@ -56,77 +65,81 @@ experimentDefinition = [
#Sample Types
#
antibodyDefinition = [
- ["BY", "General", "By", DataType.VARCHAR, None, "", None, 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],
+ ["REF_NUM", "General", "RefNum", DataType.VARCHAR, None, "", antibodyrefnumScriptName, 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],
["SPECIES", "General", "Species", DataType.VARCHAR, None, "", None, None, False],
- ["VENDOR", "General", "Vendor", DataType.VARCHAR, None, "", None, None, False],
- ["WBDIL", "General", "WBDil", DataType.VARCHAR, None, "", None, None, False],
- ["IFDIL", "General", "IFDil", DataType.VARCHAR, None, "", None, None, False],
+ ["TYPE", "General", "Type", DataType.VARCHAR, None, "", None, None, False],
["FORM", "General", "Form", DataType.VARCHAR, None, "", None, None, False],
["PRIMARY", "General", "Primary", DataType.VARCHAR, None, "", None, None, False],
["SECONDARY", "General", "Secondary", DataType.VARCHAR, None, "", None, None, False],
["COUPLED", "General", "Coupled", DataType.VARCHAR, None, "", None, None, False],
- ["BOX", "General", "Box", 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],
- ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None, False]
+ ["VENDOR", "General", "Vendor", 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],
+ ["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 = [
+ ["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],
+ ["DERIVED_FROM", "General", "derived from", DataType.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],
- ["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],
+ ["GENOTYPE_CONFIRMATION", "General", "genotype confirmation", DataType.MULTILINE_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]
+ ["MAT", "Genotype", "MAT", DataType.CONTROLLEDVOCABULARY, "MAT", "", None, None, False],
+
];
oligoDefinition = [
- ["AT", "General", "AT%", DataType.INTEGER, None, "", atScriptName, None, False],
- ["BY", "General", "By", 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],
+ ["REF_NUM", "General", "RefNum", DataType.VARCHAR, None, "", oligorefnumScriptName, None, False],
+ ["SEQUENCE", "General", "Sequence", DataType.VARCHAR, None, "", None, None, False],
["LENGTH", "General", "Length", DataType.INTEGER, None, "", lengthScriptName, None, False],
- ["LIST", "General", "List", 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],
+ ["GROUP", "General", "Group", 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],
- ["REORDERED", "General", "Reordered", DataType.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]
+ ["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 = [
@@ -154,8 +167,9 @@ plasmidDefinition = [
["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],
["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],
- ["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],
["SELECTION_MARKER", "General", "Selection marker", DataType.CONTROLLEDVOCABULARY, "PLASMID_SELECTION_MAKER", "", None, None, False],
["SIZE", "General", "Size", DataType.REAL, None, "", None, None, False],
@@ -167,7 +181,7 @@ plasmidDefinition = [
chemicalDefinition = [
["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],
["DISSOLVED_IN", "General", "dissolved in", DataType.VARCHAR, None, "", None, None, False],
["USED_FOR", "General", "Used for", DataType.VARCHAR, None, "", None, None, False],
diff --git a/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py b/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
index f273c9f7e3c..052dc7c5dd2 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
@@ -246,5 +246,13 @@ vocabularyDefinitions = {
["BENCH-80", "Bench -80�C"],
["BENCH-RT", "Bench RT"],
["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
diff --git a/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py b/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
index fd8bcab9fc1..a521e606758 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
@@ -182,6 +182,57 @@ lengthScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py",
"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
--
GitLab