#767 closed task (fixed)
MeLuDI v.1.2.1 bug fixes and improvements
Reported by: | olle | Owned by: | olle |
---|---|---|---|
Priority: | major | Milestone: | MeLuDI v1.2.2 |
Component: | net.sf.basedb.meludi | Keywords: | |
Cc: |
Description
This ticket covers bug fixes and improvements to MeLuDI v.1.2.1.
Change History (25)
comment:1 by , 10 years ago
Status: | new → assigned |
---|
comment:2 by , 10 years ago
Traceability note:
- MeLuDi v.1.0 was introduced in Ticket #690 (MeLuDi - Registration wizard for melanoma-lung cancer projects).
- MeLuDi v.1.1 was introduced in Ticket #718 (MeLuDi v.1.0 bug fixes and improvements).
- MeLuDi v.1.2 was introduced in Ticket #725 (MeLuDi v.1.1 bug fixes and improvements).
- MeLuDi v.1.2.1 was introduced in Ticket #759 (MeLuDi v.1.2 bug fixes and improvements).
comment:3 by , 10 years ago
(In [3242]) Refs #767 Updates due to version number change to "1.3-dev
".
- Version number change to "
1.3-dev
":
a. Outermost Ant XML build filebuild.xml
in/
updated.
b. Extensions XML configuration fileextensions.xml
inMETA-INF/
updated.
c. Javascript filemeludi-2.js
inresources/
updated.
d. Javascript filesamplereportgenerator.js
inresources/reports/
updated.
e. Java class/fileMeludi.java
insrc/net/sf/basedb/meludi/
updated.
comment:4 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in DNA/RNA extraction wizards to allow user-defined names for optional extra QIAcube items. As the names in the first implementation will be stored in a string with comma-separated values, no comma characters are allowed in the names.
Design update:
- Data access object class/file
Annotationtype.java
insrc/net/sf/basedb/meludi/dao/
updated:
a. New annotation typeEXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
of typeType.TEXT
added for bioplates. - Java servlet class/file
InstallServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated in protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
to include annotations of new text annotation typeAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
for bioplate items. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for commands "GetStartPlates
" and "GetUnprocessedStartPlates
" by calling methodloadAnnotations(DbControl dc, String jsonKey, Annotationtype annotationType, ValueConverter converter, Boolean fromListString, Boolean trim)
for a start plate to retrieveAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
annotations as a string list, where Boolean flagsfromListString
andtrim
are set totrue
. The annotation values are returned as a JSON object with key "extraItemNames
".
b. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetSourceItemListFromStartPlate
" to call newAnnotationtype
methodList<?> getAnnotationValues(DbControl dc, Annotatable item, Boolean fromListString, Boolean trim)
for a start plate to retrieveAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
annotations as a string list, where Boolean flagsfromListString
andtrim
are set totrue
. If extra QIAcube items exist, but no name data has been stored, standard names "E01
", "E02
",..., "E10
", etc. are generated. The extra QIAcube item data is returned as a JSON object with key "extraitems
".
c. Protected methodvoid doPost(HttpServletRequest req, HttpServletResponse resp)
updated for command "RegisterStartPlate
" to callAnnotationtype
methodvoid setAnnotationValues(DbControl dc, Annotatable item, List<?> values)
forAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
annotations to store an extra QIAcube item name list for a start plate. - JSP file
extraction_preparation.jsp
inresources/sampleproc/
updated by adding new hidden multiple select tag with id "extraQiacubeItems
", for storage of data for extra QIAcube items. - Javascript file
extraction_preparation.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep1(response)
updated to hide new select tag with id "extraQiacubeItems
".
b. FunctioninitializeStep3()
updated by calling new functioncreateExtraItemsList(numExtraItems)
to create an extra items list with default names. Table cells for the extra item names are updated to text input fields, with callback function set tot new functionitemNameOnChange(event)
.
c. New functioncreateExtraItemsList(numExtraItems)
added. It creates an extra items list with default names, and stores the list in hidden select tag with id "extraQiacubeItems
"
d. FunctiongetExtraItemsList(numExtraItems)
updated togetExtraItemsList()
and fetching the extra items list from hidden select tag with id "extraQiacubeItems
", instead of creating the items with default names.
e. New functionitemNameOnChange(event)
added. It updates the extra items JSON object by setting the names of the extra items to the values in the name input fields for the latter, after which functionupdateDetailsTable()
is called.
f. FunctionupdateDetailsTable()
updated to set values of input fields for extra item names to those of the extra items in the processed JSON object.
g. Functionsubmit()
updated to include data for extra QIAcube items in JSON object with key "extraItems
", when sending an Ajax request toExtractionServlet
with command "RegisterStartPlate
". - Javascript file
extraction_registration.js
inresources/sampleproc/
updated:
a. FunctionsourceItemListLoaded(response)
updated to get values for global JSON arrayextraItemsList
fromresponse.extraitems
.
b. FunctioninitializeStep3()
updated to not call functiongetExtraItemsList(numExtraItems)
to obtain default values for global JSON arrayextraItemsList
, since it now is supplied by theExtractionServlet
response. - Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated:
a. FunctionsourceItemListLoaded(response)
updated to get values for global JSON arrayextraItemsList
fromresponse.extraitems
.
b. FunctioninitializeStep3()
updated to not call functiongetExtraItemsList(numExtraItems)
to obtain default values for global JSON arrayextraItemsList
, since it now is supplied by theExtractionServlet
response.
comment:5 by , 10 years ago
(In [3245]) Refs #767. MeLuDI updated in DNA/RNA extraction wizards to allow user-defined names for optional extra QIAcube items. As the names in the first implementation will be stored in a string with comma-separated values, no comma characters are allowed in the names.
- Data access object class/file
Annotationtype.java
insrc/net/sf/basedb/meludi/dao/
updated:
a. New annotation typeEXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
of typeType.TEXT
added for bioplates. - Java servlet class/file
InstallServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated in protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
to include annotations of new text annotation typeAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
for bioplate items. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for commands "GetStartPlates
" and "GetUnprocessedStartPlates
" by calling methodloadAnnotations(DbControl dc, String jsonKey, Annotationtype annotationType, ValueConverter converter, Boolean fromListString, Boolean trim)
for a start plate to retrieveAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
annotations as a string list, where Boolean flagsfromListString
andtrim
are set totrue
. The annotation values are returned as a JSON object with key "extraItemNames
".
b. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetSourceItemListFromStartPlate
" to call newAnnotationtype
methodList<?> getAnnotationValues(DbControl dc, Annotatable item, Boolean fromListString, Boolean trim)
for a start plate to retrieveAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
annotations as a string list, where Boolean flagsfromListString
andtrim
are set totrue
. If extra QIAcube items exist, but no name data has been stored, standard names "E01
", "E02
",..., "E10
", etc. are generated. The extra QIAcube item data is returned as a JSON object with key "extraitems
".
c. Protected methodvoid doPost(HttpServletRequest req, HttpServletResponse resp)
updated for command "RegisterStartPlate
" to callAnnotationtype
methodvoid setAnnotationValues(DbControl dc, Annotatable item, List<?> values)
forAnnotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING
annotations to store an extra QIAcube item name list for a start plate. - JSP file
extraction_preparation.jsp
inresources/sampleproc/
updated by adding new hidden multiple select tag with id "extraQiacubeItems
", for storage of data for extra QIAcube items. - Javascript file
extraction_preparation.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep1(response)
updated to hide new select tag with id "extraQiacubeItems
".
b. FunctioninitializeStep3()
updated by calling new functioncreateExtraItemsList(numExtraItems)
to create an extra items list with default names. Table cells for the extra item names are updated to text input fields, with callback function set tot new functionitemNameOnChange(event)
.
c. New functioncreateExtraItemsList(numExtraItems)
added. It creates an extra items list with default names, and stores the list in hidden select tag with id "extraQiacubeItems
"
d. FunctiongetExtraItemsList(numExtraItems)
updated togetExtraItemsList()
and fetching the extra items list from hidden select tag with id "extraQiacubeItems
", instead of creating the items with default names.
e. New functionitemNameOnChange(event)
added. It updates the extra items JSON object by setting the names of the extra items to the values in the name input fields for the latter, after which functionupdateDetailsTable()
is called.
f. FunctionupdateDetailsTable()
updated to set values of input fields for extra item names to those of the extra items in the processed JSON object.
g. Functionsubmit()
updated to include data for extra QIAcube items in JSON object with key "extraItems
", when sending an Ajax request toExtractionServlet
with command "RegisterStartPlate
". - Javascript file
extraction_registration.js
inresources/sampleproc/
updated:
a. FunctionsourceItemListLoaded(response)
updated to get values for global JSON arrayextraItemsList
fromresponse.extraitems
.
b. FunctioninitializeStep3()
updated to not call functiongetExtraItemsList(numExtraItems)
to obtain default values for global JSON arrayextraItemsList
, since it now is supplied by theExtractionServlet
response. - Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated:
a. FunctionsourceItemListLoaded(response)
updated to get values for global JSON arrayextraItemsList
fromresponse.extraitems
.
b. FunctioninitializeStep3()
updated to not call functiongetExtraItemsList(numExtraItems)
to obtain default values for global JSON arrayextraItemsList
, since it now is supplied by theExtractionServlet
response.
In addition, a number of commented-out code sections have been removed, in order to increase the readability of the code.
comment:6 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in DNA/RNA extraction wizards to display any operator delivery comment for a specimen in the "
Comment
" column in step 3 of the wizards, and in the "Remark
" column of created Lab tracking sheets/reports.
Design update:
- Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetUnprocessedItems
" to load annotation value forAnnotationtype.OPERATOR_DELIVERY_COMMENT
for a specimen and return it with JSON key "operatorDeliveryComment
". - Javascript file
extraction_preparation.js
inresources/sampleproc/
updated:
a. FunctionupdateDetailsTable()
updated to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizard, and to insert it in the tool tip field. - Javascript file
extraction_registration.js
inresources/sampleproc/
updated:
a. FunctionupdateDetailsTable()
updated to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizard, and to insert it in the tool tip field. - Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated:
a. FunctionupdateDetailsTable()
updated to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizard, and to insert it in the tool tip field. - Javascript file
extraction_protocol.js
inresources/sampleproc/
updated:
a. FunctiontableRowsForItems(accumItemNo, itemJsonArr, itemType, itemTypeVarName)
updated to display any operator delivery comment for a specimen in the "Remark
" column of created Lab tracking sheets/reports.
comment:7 by , 10 years ago
(In [3246]) Refs #767. MeLuDI updated in DNA/RNA extraction wizards to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizards, and in the "Remark
" column of created Lab tracking sheets/reports.
- Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetUnprocessedItems
" to load annotation value forAnnotationtype.OPERATOR_DELIVERY_COMMENT
for a specimen and return it with JSON key "operatorDeliveryComment
". - Javascript file
extraction_preparation.js
inresources/sampleproc/
updated:
a. FunctionupdateDetailsTable()
updated to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizard, and to insert it in the tool tip field. - Javascript file
extraction_registration.js
inresources/sampleproc/
updated:
a. FunctionupdateDetailsTable()
updated to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizard, and to insert it in the tool tip field. - Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated:
a. FunctionupdateDetailsTable()
updated to display any operator delivery comment for a specimen in the "Comment
" column in step 3 of the wizard, and to insert it in the tool tip field. - Javascript file
extraction_protocol.js
inresources/sampleproc/
updated:
a. FunctiontableRowsForItems(accumItemNo, itemJsonArr, itemType, itemTypeVarName)
updated to display any operator delivery comment for a specimen in the "Remark
" column of created Lab tracking sheets/reports.
comment:8 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in case registration by adding a button for selecting all mutation analysis options except "Other analysis" (check boxes, default = none selected):
Design update:
- JSP file
specimentube.jsp
inresources/sampleproc/
updated in step 2 by adding a "Select all" button with id "selectAllMutationAnalysis
" to the left of the mutation analysis check box set. - Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitPage()
updated by adding click handler to new "Select all" button with id "selectAllMutationAnalysis
" with callback functionmutationAnalysisSelectAll()
.
b. New functionmutationAnalysisSelectAll()
added. It sets all mutation analysis check boxes except "Other analysis" to checked. - JSP file
persinfo.jsp
inresources/personal/
updated in step 3 by adding a "Select all" button with id "selectAllMutationAnalysis
" to the left of the mutation analysis check box set. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitPage()
updated by adding click handler to new "Select all" button with id "selectAllMutationAnalysis
" with callback functionmutationAnalysisSelectAll()
.
b. New functionmutationAnalysisSelectAll()
added. It sets all mutation analysis check boxes except "Other analysis" to checked.
comment:9 by , 10 years ago
(In [3249]) Refs #767. MeLuDI updated in case registration by adding a button for selecting all mutation analysis options except "Other analysis" (check boxes, default = none selected):
- JSP file
specimentube.jsp
inresources/sampleproc/
updated in step 2 by adding a "Select all" button with id "selectAllMutationAnalysis
" to the left of the mutation analysis check box set. - Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitPage()
updated by adding click handler to new "Select all" button with id "selectAllMutationAnalysis
" with callback functionmutationAnalysisSelectAll()
.
b. New functionmutationAnalysisSelectAll()
added. It sets all mutation analysis check boxes except "Other analysis" to checked. - JSP file
persinfo.jsp
inresources/personal/
updated in step 3 by adding a "Select all" button with id "selectAllMutationAnalysis
" to the left of the mutation analysis check box set. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitPage()
updated by adding click handler to new "Select all" button with id "selectAllMutationAnalysis
" with callback functionmutationAnalysisSelectAll()
.
b. New functionmutationAnalysisSelectAll()
added. It sets all mutation analysis check boxes except "Other analysis" to checked.
comment:10 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in case registration by adding buttons to insert standard comments in the "Operator delivery comment" field for a specimen tube. The first button to be added is for the comment "
Utkarvad
", which is Swedish for "Carved out
".
Design update:
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addCarvedOutComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text.
b. New functionaddComment()
added. It retrieves the comment field id and comment text from the JSON attribute, and then adds the comment text in the target field, after an optional space, if a previous comment already exists. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addCarvedOutComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text.
b. New functionaddComment()
added. It retrieves the comment field id and comment text from the JSON attribute, and then adds the comment text in the target field, after an optional space, if a previous comment already exists.
comment:11 by , 10 years ago
(In [3250]) Refs #767. MeLuDI updated in case registration by adding buttons to insert standard comments in the "Operator delivery comment" field for a specimen tube. The first button to be added is for the comment "Utkarvad
", which is Swedish for "Carved out
".
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addCarvedOutComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text.
b. New functionaddComment()
added. It retrieves the comment field id and comment text from the JSON attribute, and then adds the comment text in the target field, after an optional space, if a previous comment already exists. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addCarvedOutComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text.
b. New functionaddComment()
added. It retrieves the comment field id and comment text from the JSON attribute, and then adds the comment text in the target field, after an optional space, if a previous comment already exists.
comment:12 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in case registration by adding buttons to insert standard comments in the "Operator delivery comment" field for a specimen tube for the comment "
MNB
", an abbreviation of "Medium needle biopsy
" ("Mellannålsbiopsi
" in Swedish).
Design update:
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addMnbComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addMnbComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text.
comment:13 by , 10 years ago
(In [3251]) Refs #767. MeLuDI updated in case registration by adding buttons to insert standard comments in the "Operator delivery comment" field for a specimen tube for the comment "MNB
", an abbreviation of "Medium needle biopsy
" ("Mellannålsbiopsi
" in Swedish).
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addMnbComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated by adding HTML code for a new button below the "Operator delivery comment" field for each specimen tube. The button id is "addMnbComment
" plus specimen tube index. A click handler is added to each new comment button, with callback function set toaddComment()
and a JSON attribute added with comment text field id and comment text.
comment:14 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in case registration regarding buttons to insert standard comments in the "Operator delivery comment" fields for items. Since the standard comments normally should be added for all items registered for a case, the standard comments buttons for each item should be replaced by a new section with standard comment buttons at the top of the item information section. Clicking a standard comment button should insert the comment in question into the "Operator delivery comment" fields of all items.
Design update:
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated by adding HTML code for a new section with standard comment buttons at the top of the item information section, replacing the comment buttons below the "Operator delivery comment" field for each specimen tube. A click handler is added to each new comment button, with callback function set toaddCommentGeneral()
and a JSON attribute added with number of items, comment text field base id, and comment text.
b. New functionaddCommentGeneral()
added. It retrieves the number of items, the comment field base id, and comment text from the JSON attribute, and then adds the comment text in the target fields of all items, after an optional space, if a previous comment already exists. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated by adding HTML code for a new section with standard comment buttons at the top of the item information section, replacing the comment buttons below the "Operator delivery comment" field for each specimen tube. A click handler is added to each new comment button, with callback function set toaddCommentGeneral()
and a JSON attribute added with number of items, comment text field base id, and comment text.
b. New functionaddCommentGeneral()
added. It retrieves the number of items, the comment field base id, and comment text from the JSON attribute, and then adds the comment text in the target fields of all items, after an optional space, if a previous comment already exists.
comment:15 by , 10 years ago
(In [3252]) Refs #767. MeLuDI updated in case registration regarding buttons to insert standard comments in the "Operator delivery comment" fields for items. Since the standard comments normally should be added for all items registered for a case, the standard comments buttons for each item are replaced by a new section with standard comment buttons at the top of the item information section. Clicking a standard comment button should insert the comment in question into the "Operator delivery comment" fields of all items.
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated by adding HTML code for a new section with standard comment buttons at the top of the item information section, replacing the comment buttons below the "Operator delivery comment" field for each specimen tube. A click handler is added to each new comment button, with callback function set toaddCommentGeneral()
and a JSON attribute added with number of items, comment text field base id, and comment text.
b. New functionaddCommentGeneral()
added. It retrieves the number of items, the comment field base id, and comment text from the JSON attribute, and then adds the comment text in the target fields of all items, after an optional space, if a previous comment already exists. - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated by adding HTML code for a new section with standard comment buttons at the top of the item information section, replacing the comment buttons below the "Operator delivery comment" field for each specimen tube. A click handler is added to each new comment button, with callback function set toaddCommentGeneral()
and a JSON attribute added with number of items, comment text field base id, and comment text.
b. New functionaddCommentGeneral()
added. It retrieves the number of items, the comment field base id, and comment text from the JSON attribute, and then adds the comment text in the target fields of all items, after an optional space, if a previous comment already exists.
comment:16 by , 10 years ago
Functional specification update:
- MeLuDI should be updated to place DNA extracts on a storage plate, both for input DNA in case registration, and for created DNA extracts in DNA/RNA registration/quantification. The DNA extracts should be placed on a storage plate with name having suffix "
_dna
".
Design update:
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated to disable the storage box options only for the first specimen tube.
b. FunctionstoragePositionsLoaded(response)
updated to ignore the storage box position only for the first specimen tube.
c. FunctionfetchStorageBoxSuffix(tubeContentType)
updated to return suffix "_dna
" for tube content type "DNA
" and suffix "_dna_rna
" for tube content type "DNA_RNA
". The latter suffix does not correspond to the name suffix of a type of storage plates, but works as a flag to command "FindStoragePositions
" inSpecimenTubeRegistrationServlet
to find one place on a storage plate with suffix "_dna
", and one on a storage plate with suffix "_rna
".
d. FunctionboxOnKeyUp(event)
updated to also check validity of storage box names with suffix "_dna
". - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated to disable the storage box options only for the first specimen tube.
b. FunctionstoragePositionsLoaded(response)
updated to ignore the storage box position only for the first specimen tube.
c. FunctionfetchStorageBoxSuffix(tubeContentType)
updated to return suffix "_dna
" for tube content type "DNA
" and suffix "_dna_rna
" for tube content type "DNA_RNA
". The latter suffix does not correspond to the name suffix of a type of storage plates, but works as a flag to command "FindStoragePositions
" inSpecimenTubeRegistrationServlet
to find one place on a storage plate with suffix "_dna
", and one on a storage plate with suffix "_rna
".
d. FunctionboxOnKeyUp(event)
updated to also check validity of storage box names with suffix "_dna
". - Java servlet class/file
SpecimenTubeServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "FindStoragePositions
" and attributestorageBoxSuffix
equal to "_dna_rna
" to find one free well on a storage box with suffix "_dna
" and one on a storage box with suffix "_rna
", and then return the data in a JSONArray in that order. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doPost(HttpServletRequest req, HttpServletResponse resp)
updated for command "RegisterDnaRna
" to get a list of free wells for storage plates with names having suffix "_dna
", in addition to those having suffix "_rna
", and to place created DNA extracts on the next wells on the DNA plate(s).
comment:17 by , 10 years ago
(In [3253]) Refs #767. MeLuDI should updated to place DNA extracts on a storage plate, both for input DNA in case registration, and for created DNA extracts in DNA/RNA registration/quantification. The DNA extracts should be placed on a storage plate with name having suffix "_dna
".
- Javascript file
specimentube.js
inresources/sampleproc/
updated:
a. FunctioninitializeStep3()
updated to disable the storage box options only for the first specimen tube.
b. FunctionstoragePositionsLoaded(response)
updated to ignore the storage box position only for the first specimen tube.
c. FunctionfetchStorageBoxSuffix(tubeContentType)
updated to return suffix "_dna
" for tube content type "DNA
" and suffix "_dna_rna
" for tube content type "DNA_RNA
". The latter suffix does not correspond to the name suffix of a type of storage plates, but works as a flag to command "FindStoragePositions
" inSpecimenTubeRegistrationServlet
to find one place on a storage plate with suffix "_dna
", and one on a storage plate with suffix "_rna
".
d. FunctionboxOnKeyUp(event)
updated to also check validity of storage box names with suffix "_dna
". - Javascript file
persinfo.js
inresources/personal/
updated:
a. FunctioninitializeStep4()
updated to disable the storage box options only for the first specimen tube.
b. FunctionstoragePositionsLoaded(response)
updated to ignore the storage box position only for the first specimen tube.
c. FunctionfetchStorageBoxSuffix(tubeContentType)
updated to return suffix "_dna
" for tube content type "DNA
" and suffix "_dna_rna
" for tube content type "DNA_RNA
". The latter suffix does not correspond to the name suffix of a type of storage plates, but works as a flag to command "FindStoragePositions
" inSpecimenTubeRegistrationServlet
to find one place on a storage plate with suffix "_dna
", and one on a storage plate with suffix "_rna
".
d. FunctionboxOnKeyUp(event)
updated to also check validity of storage box names with suffix "_dna
". - Java servlet class/file
SpecimenTubeServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "FindStoragePositions
" and attributestorageBoxSuffix
equal to "_dna_rna
" to find one free well on a storage box with suffix "_dna
" and one on a storage box with suffix "_rna
", and then return the data in a JSONArray in that order. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doPost(HttpServletRequest req, HttpServletResponse resp)
updated for command "RegisterDnaRna
" to get a list of free wells for storage plates with names having suffix "_dna
", in addition to those having suffix "_rna
", and to place created DNA extracts on the next wells on the DNA plate(s).
comment:18 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in the Lab tracking sheet/report copy wizard in step 1 in the start plate selection menu:
a. The start plates should be displayed in descending order of plate names, since it is normally the most recent plate, that is of interest.
b. If the start plate is processed, as indicated by the event date being set, the latter value should be displayed inside square brackets after the start plate name and number of items.
c. Start plates marked as having been destroyed, should no longer be included in the list.
Design update:
- Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated:
a. FunctioninitPage()
updated in Ajax call toExtractionServlet
with command "GetStartPlates
" to add parameter "orderDesc
" set totrue
, in order to get the list sorted in descending plate name order.
b. FunctioninitializeStep1(response)
updated in the start plate selection menu to add an optional event date (obtained through JSON key "extractionDate
") inside square brackets after the start plate name and number of items, plus a spacer string "--
". The first start plate item in the selection menu is marked as selected by default (since the plates are now displayed in descending plate name order, this is normally the newest start plate).
c. New functionasDate(value)
added. It returns an input date string in "yyyymmdd
" format as "yyyy-mm-dd
" format. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetStartPlates
" to call new static public methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation)
updated to call new public static methodList<ReactionPlate> ReactionPlate.findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation, Boolean destroyed, Boolean orderDesc)
withBoolean
argumentdestroyed
set tofalse
andorderDesc
set to value obtained by parameter "orderDesc
" (if the latter isnull
, argumentorderDesc
is set tofalse
). - Java data access object class/file
ReactionPlate.java
insrc/net/sf/basedb/meludi/dao/
updated:
a. Public static methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation)
updated to call new public static methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation, Boolean destroyed, Boolean orderDesc)
withBoolean
argumentsdestroyed
andorderDesc
set tofalse
to obtain the list to return. Note that this is a change in functionality, since the method previously included plates, that had been marked as destroyed.
b. New public static methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation, Boolean destroyed, Boolean orderDesc)
added. If argumentdestroyed
is equal tonull
, both existing and destroyed plates are included, whiledestroyed
equal tofalse
includes only existing plates, anddestroyed
equal totrue
includes only plates marked as destroyed. If argumentorderDesc
istrue
, the plates will be sorted in descending order by plate name, otherwise ascending.
comment:19 by , 10 years ago
(In [3254]) Refs #767. MeLuDI updated in the Lab tracking sheet/report copy wizard in step 1 in the start plate selection menu:
a. The start plates are now displayed in descending order of plate names, since it is normally the most recent plate, that is of interest.
b. If the start plate is processed, as indicated by the event date being set, the latter value is displayed inside square brackets after the start plate name and number of items.
c. Start plates marked as having been destroyed, should no longer be included in the list.
- Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated:
a. FunctioninitPage()
updated in Ajax call toExtractionServlet
with command "GetStartPlates
" to add parameter "orderDesc
" set totrue
, in order to get the list sorted in descending plate name order.
b. FunctioninitializeStep1(response)
updated in the start plate selection menu to add an optional event date (obtained through JSON key "extractionDate
") inside square brackets after the start plate name and number of items, plus a spacer string "--
". The first start plate item in the selection menu is marked as selected by default (since the plates are now displayed in descending plate name order, this is normally the newest start plate).
c. New functionasDate(value)
added. It returns an input date string in "yyyymmdd
" format as "yyyy-mm-dd
". - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetStartPlates
" to call new static public methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation)
updated to call new public static methodList<ReactionPlate> ReactionPlate.findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation, Boolean destroyed, Boolean orderDesc)
withBoolean
argumentdestroyed
set tofalse
andorderDesc
set to value obtained by parameter "orderDesc
" (if the latter isnull
, argumentorderDesc
is set tofalse
). - Java data access object class/file
ReactionPlate.java
insrc/net/sf/basedb/meludi/dao/
updated:
a. Public static methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation)
updated to call new public static methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation, Boolean destroyed, Boolean orderDesc)
withBoolean
argumentsdestroyed
andorderDesc
set tofalse
to obtain the list to return. Note that this is a change in functionality, since the method previously included plates, that had been marked as destroyed.
b. New public static methodList<ReactionPlate> findByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation, Boolean destroyed, Boolean orderDesc)
added. If argumentdestroyed
is equal tonull
, both existing and destroyed plates are included, whiledestroyed
equal tofalse
includes only existing plates, anddestroyed
equal totrue
includes only plates marked as destroyed. If argumentorderDesc
istrue
, the plates will be sorted in descending order by plate name, otherwise ascending.
comment:20 by , 10 years ago
Functional specification update:
- MeLuDI should be updated in the Lab tracking sheet wizards in step 3 for downloading a NanoDrop sample ID file to add option to use a full column with blank controls, which should be the default.
Design update:
- JSP file
extraction_preparation.jsp
inresources/sampleproc/
updated in step 3 by adding a check box with id "blankControlColumn
" and label "Column with blank controls
" to the right of the button for downloading a NanoDrop sample ID file. The check box should be checked by default. - Javascript file
extraction_preparation.js
inresources/sampleproc/
updated in functiondownloadSampleIdFile()
to include parameter "blankControlColumn
" in Ajax request toExtractionServlet
with command "DownloadNanoDropSampleIdFile
". The value of the new parameter is set to the checked status of check box with id "blankControlColumn
". - JSP file
extraction_formcopy.jsp
inresources/sampleproc/
updated in step 3 by adding a check box with id "blankControlColumn
" and label "Column with blank controls
" to the right of the button for downloading a NanoDrop sample ID file. The check box should be checked by default. - Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated in functiondownloadSampleIdFile()
to include parameter "blankControlColumn
" in Ajax request toExtractionServlet
with command "DownloadNanoDropSampleIdFile
". The value of the new parameter is set to the checked status of check box with id "blankControlColumn
". - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "DownloadNanoDropSampleIdFile
" to obtain value of Boolean parameter "blankControlColumn
", and if the latter is notfalse
, add a full column with blank controls at the right of the last column containing a sample. If the value of parameter "blankControlColumn
" isfalse
, a single blank cell will be added after the last cell containing a sample.
b. (Unrelated to the new option for NanoDrop sample ID file.) Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetStartPlates
" to use methodBoolean.valueOf()
to convert the value of parameter "orderDesc
" to a Boolean variable. This hoprfully increases the consistency and readability of the code.
comment:21 by , 10 years ago
(In [3255]) Refs #767. MeLuDI updated in the Lab tracking sheet wizards in step 3 for downloading a NanoDrop sample ID file to add option to use a full column with blank controls, which should be the default.
- JSP file
extraction_preparation.jsp
inresources/sampleproc/
updated in step 3 by adding a check box with id "blankControlColumn
" and label "Column with blank controls
" to the right of the button for downloading a NanoDrop sample ID file. The check box should be checked by default. - Javascript file
extraction_preparation.js
inresources/sampleproc/
updated in functiondownloadSampleIdFile()
to include parameter "blankControlColumn
" in Ajax request toExtractionServlet
with command "DownloadNanoDropSampleIdFile
". The value of the new parameter is set to the checked status of check box with id "blankControlColumn
". - JSP file
extraction_formcopy.jsp
inresources/sampleproc/
updated in step 3 by adding a check box with id "blankControlColumn
" and label "Column with blank controls
" to the right of the button for downloading a NanoDrop sample ID file. The check box should be checked by default. - Javascript file
extraction_formcopy.js
inresources/sampleproc/
updated in functiondownloadSampleIdFile()
to include parameter "blankControlColumn
" in Ajax request toExtractionServlet
with command "DownloadNanoDropSampleIdFile
". The value of the new parameter is set to the checked status of check box with id "blankControlColumn
". - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated:
a. Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "DownloadNanoDropSampleIdFile
" to obtain value of Boolean parameter "blankControlColumn
", and if the latter is notfalse
, add a full column with blank controls at the right of the last column containing a sample. If the value of parameter "blankControlColumn
" isfalse
, a single blank cell will be added after the last cell containing a sample.
b. (Unrelated to the new option for NanoDrop sample ID file.) Protected methodvoid doGet(HttpServletRequest req, HttpServletResponse resp)
updated for command "GetStartPlates
" to use methodBoolean.valueOf()
to convert the value of parameter "orderDesc
" to a Boolean variable. This hoprfully increases the consistency and readability of the code.
comment:22 by , 10 years ago
Functional specification update:
- It was decided to release MeLuDI in its current state as MeLuDI v.1.2.2.
comment:23 by , 10 years ago
(In [3256]) Refs #767. Updates due to version number change to "1.2.2
".
- Version number change to "
1.2.2
":
a. Outermost Ant XML build filebuild.xml
in/
updated.
b. Extensions XML configuration fileextensions.xml
inMETA-INF/
updated.
c. Javascript filemeludi-2.js
inresources/
updated.
d. Javascript filesamplereportgenerator.js
inresources/reports/
updated.
e. Java class/fileMeludi.java
insrc/net/sf/basedb/meludi/
updated.
comment:24 by , 9 years ago
Milestone: | MeLuDI v1.2.2 → MeLuDI v1.3 |
---|---|
Resolution: | → fixed |
Status: | assigned → closed |
Ticket closed as MeLuDI version 1.2.2 has been created.
comment:25 by , 9 years ago
Milestone: | MeLuDI v1.3 → MeLuDI v1.2.2 |
---|
Milestone reset to MeLuDI v1.2.2, which is the milestone related to this ticket.
Ticket accepted.