diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
index a341dfe1806c4017775f32cb3692f612e73e7e66..bf2f249601cf58c866ea9d2ff68c4b5d7c8217de 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
@@ -16,14 +16,67 @@
# MasterDataRegistrationTransaction Class
from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
-from utils.file_handling import list_xls_byte_arrays, get_all_scripts
from ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id import CustomASServiceCode
from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExecutionOptions
+# "======================== Helper Functions ========================"
+
+import os
+import sys
+from collections import deque
+from java.nio.file import Files, Paths
+from java.io import File
+from java.util import HashMap
+from java.util import ArrayList
+
+TYPES_FOLDER = "%s/master-data/" % [p for p in sys.path if p.find('core-plugins') >= 0][0]
+SCRIPTS = os.path.join(TYPES_FOLDER, 'scripts')
+
+
+def get_all_scripts():
+ scripts = HashMap()
+ for rel_path, script in list_all_files(SCRIPTS):
+ scripts.put(rel_path, script)
+
+ return scripts
+
+
+def list_xls_byte_arrays():
+ xls = ArrayList()
+ for f in os.listdir(TYPES_FOLDER):
+ if f.endswith('.xls') or f.endswith('.xlsx'):
+ excel_file = open(os.path.join(TYPES_FOLDER, f))
+ xls.add(excel_file.read())
+ excel_file.close()
+ return xls
+
+
+def list_all_files(source_root_path):
+ todo = []
+ todo.append(File(source_root_path))
+ while todo:
+ f = todo.pop()
+ if f.isDirectory():
+ new_files = f.listFiles()
+ if new_files is not None:
+ todo.extend(f.listFiles())
+ continue
+ if f.isFile():
+ source_file = f.getAbsolutePath()
+ script_file = open(source_file)
+ script = script_file.read()
+ script_file.close()
+ file_path = source_file.replace(source_root_path, "")
+ if file_path.startswith("/"):
+ file_path = file_path[1:]
+ yield file_path, script
+
+# "======================== Helper Functions ========================"
+
api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
sessionToken = api.loginAsSystem()
props = CustomASServiceExecutionOptions().withParameter('xls', list_xls_byte_arrays()).withParameter('scripts', get_all_scripts())
result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import-api"), props);
-print("========================eln-life-sciences-types xls ingestion result========================")
+print("======================== master-data xls ingestion result ========================")
print(result)
-print("========================eln-life-sciences-types xls ingestion result========================")
+print("======================== master-data xls ingestion result ========================")
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.biology.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.biology.xls
deleted file mode 100644
index 4ddfe69bc619a91bf1ad2e00009233f26130c162..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.biology.xls and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls
new file mode 100644
index 0000000000000000000000000000000000000000..302cd5a097ddd00cb492830cac26afec782af14e
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.default.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/types.default.xls
similarity index 100%
rename from openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/life-sciences-types/types.default.xls
rename to openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/types.default.xls
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls
index e454fa39ead29bec529cb952522b344f959abbfe..c026315689c7557bb4698693eae5596e21a9af70 100644
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls and b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js
index b394b8f4e0073465a325c78638d37385689f1e1d..c7dfec2ec059250df5c8157b3db00fa54fb4e916 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js
@@ -37,19 +37,19 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Chemical",
"TYPE": "CHEMICAL",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Solution/Buffer",
"TYPE": "SOLUTION_BUFFER",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Media",
"TYPE": "MEDIA",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -61,19 +61,19 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Chemical",
"TYPE": "CHEMICAL",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Solution/Buffer",
"TYPE": "SOLUTION_BUFFER",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Media",
"TYPE": "MEDIA",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -85,19 +85,19 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Chemical",
"TYPE": "CHEMICAL",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Solution/Buffer",
"TYPE": "SOLUTION_BUFFER",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Enzyme",
"TYPE": "ENZYME",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
],
},
@@ -109,19 +109,19 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Chemical",
"TYPE": "CHEMICAL",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Solution/Buffer",
"TYPE": "SOLUTION_BUFFER",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Antibody",
"TYPE": "ANTIBODY",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "QUANTITY", "MANDATORY" : false }, {"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.QUANTITY", "MANDATORY" : false }, {"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
],
},
@@ -133,7 +133,7 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -145,13 +145,13 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Bacteria parents",
"TYPE": "BACTERIA",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -163,13 +163,13 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Yeast parents",
"TYPE": "YEAST",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -181,19 +181,19 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Parental cell line",
"TYPE": "CELL_LINE",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Parental fly",
"TYPE": "FLY",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -205,13 +205,13 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Fly parents",
"TYPE": "FLY",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
}