Opened 9 years ago
Closed 9 years ago
#786 closed task (fixed)
MeLuDI v.1.2.4 bug fixes and improvements
Reported by: | olle | Owned by: | olle |
---|---|---|---|
Priority: | major | Milestone: | MeLuDI v1.2.5 |
Component: | net.sf.basedb.meludi | Keywords: | |
Cc: |
Description
This ticket covers bug fixes and improvements to MeLuDI v.1.2.4.
Change History (17)
comment:1 by , 9 years ago
Status: | new → assigned |
---|
comment:2 by , 9 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).
- MeLuDI v.1.2.2 was introduced in Ticket #767 (MeLuDI v.1.2.1 bug fixes and improvements).
- MeLuDI v.1.2.3 was introduced in Ticket #768 (MeLuDI v.1.2.2 bug fixes and improvements).
- MeLuDI v.1.2.4 was introduced in Ticket #777 (MeLuDI v.1.2.3 bug fixes and improvements).
comment:3 by , 9 years ago
(In [3349]) Refs #786 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 , 9 years ago
Functional specification update:
- A bug was introduced in DNA/RNA extraction wizards in MeLuDI v1.2.2 2015-04-14 in change set 3245 in Ticket #767, when support for user-defined names for optional extra QIAcube items was added. Several convenience methods/functions for determining if an extract source item was a MeLuDI specimen item depended on the name not starting with the default start string for optional extra QIAcube items, but this code was never updated. The new check should be that the name starts with the letters "
ML
", in order to be regarded as a MeLuDI item.
Design Update:
- Javascript files
edit_dnarna_details.js
,edit_dnarna_prep_details.js
,extraction_formcopy.js
,extraction_preparation.js
, andextraction_registration.js
inresources/sampleproc/
updated in function.isSpecimen(item)
to check if item name starts with string "ML
" to exclude extra items. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated in private methodboolean itemIsSpecimen(String itemName)
to check if item name starts with string "ML
" to exclude extra items.
comment:5 by , 9 years ago
(In [3350]) Refs #786. Bug fixed in DNA/RNA extraction wizards on how to differentiate between MeLuDI items and optional extra QIAcube items, when support for user-defined names for optional extra QIAcube items was added. Several convenience methods/functions for determining if an extract source item was a MeLuDI specimen item depended on the name not starting with the default start string for optional extra QIAcube items. The new check should be that the name should start with the letters "ML
", in order to be regarded as a MeLuDI item.
- Javascript files
edit_dnarna_details.js
,edit_dnarna_prep_details.js
,extraction_formcopy.js
,extraction_preparation.js
, andextraction_registration.js
inresources/sampleproc/
updated in function.isSpecimen(item)
to check if item name starts with string "ML
" to exclude extra items. - Java servlet class/file
ExtractionServlet.java
insrc/net/sf/basedb/meludi/servlet/
updated in private methodboolean itemIsSpecimen(String itemName)
to check if item name starts with string "ML
" to exclude extra items.
comment:6 by , 9 years ago
Functional specification update:
- A bug of omission was introduced in code for edit pop-up dialogs in step 3 of DNA/RNA registration/quantification wizard in change set 3324 in Ticket #777, when support for lot numbers for reagents used in quality control was added. Among other data, the javascript file for the edit pop-up dialog obtains a list of reagent values as input, and when changes should be saved, it reads data from dialog input fields. Since the corresponding JSP file never was updated with input fields for the new quality control reagent lot numbers, the javascript will stop before any data has been sent back.
Design update:
- JSP file
edit_dnarna_details.jsp
inresources/sampleproc/
updated in reagent table with fields for new quality control reagent lot numbers.
comment:7 by , 9 years ago
(In [3351]) Refs #786. Bug of omission fixed in code for edit pop-up dialogs in step 3 of DNA/RNA registration/quantification wizard, that was introduced when support for lot numbers for reagents used in quality control was added, but the JSP file never was updated with input fields for the new entries This caused the dialog javascript to stop before any data had been sent back, when trying to save changes.
- JSP file
edit_dnarna_details.jsp
inresources/sampleproc/
updated in reagent table with fields for new quality control reagent lot numbers.
comment:8 by , 9 years ago
Refactoring:
- Javascript files in DNA/RNA extraction wizards should be refactored by putting common functions in separate javascript files, that are accessed via the JSP files. This will simplify future updates of the functionality.
Design update:
- JSP files
edit_dnarna_details.jsp
,edit_dnarna_prep_details.jsp
,extraction_formcopy.jsp
,extraction_preparation.jsp
, andextraction_registration.jsp
inresources/sampleproc/
updated to include new javascript fileextraction_utils.js
inresources/sampleproc/
in list of included scripts. - Javascript files
edit_dnarna_details.js
,edit_dnarna_prep_details.js
,extraction_formcopy.js
,extraction_preparation.js
, andextraction_registration.js
inresources/sampleproc/
updated to access the following functions from new javascript fileextraction_utils.js
inresources/sampleproc/
:
a.getDetailedQiaCubePosition(nitems, i)
b.getQiaCubePosition(nitems, i)
c.getQiacubePosition(intPosition)
d.getIntQiacubePosition(positionStr)
e.isSpecimen(item)
f.isRna(item)
g.isDna(item)
h.findSeparator(data, searchString)
i.setDecimalDotInsideDoubleQuotes(line)
j.getNumber(sValue)
comment:9 by , 9 years ago
(In [3352]) Refs #786. Javascript files in DNA/RNA extraction wizards refactored by putting common functions in separate javascript file, that is accessed via the JSP files. This will simplify future updates of the functionality.
- JSP files
edit_dnarna_details.jsp
,edit_dnarna_prep_details.jsp
,extraction_formcopy.jsp
,extraction_preparation.jsp
, andextraction_registration.jsp
inresources/sampleproc/
updated to include new javascript fileextraction_utils.js
inresources/sampleproc/
in list of included scripts. - Javascript files
edit_dnarna_details.js
,edit_dnarna_prep_details.js
,extraction_formcopy.js
,extraction_preparation.js
, andextraction_registration.js
inresources/sampleproc/
updated to access the following functions from new javascript fileextraction_utils.js
inresources/sampleproc/
:
a.getDetailedQiaCubePosition(nitems, i)
b.getQiaCubePosition(nitems, i)
c.getQiacubePosition(intPosition)
d.getIntQiacubePosition(positionStr)
e.isSpecimen(item)
f.isRna(item)
g.isDna(item)
h.findSeparator(data, searchString)
i.setDecimalDotInsideDoubleQuotes(line)
j.getNumber(sValue)
- New javascript file
extraction_utils.js
inresources/sampleproc/
added.
comment:10 by , 9 years ago
comment:11 by , 9 years ago
Functional specification update:
- A bug was introduced in the javascript refactoring in change set 3352, in that user-defined primary and secondary QIAcube prefixes was not respected, but replaced with default values "
B
" and "C
", respectively.
Design update:
- Javascript file
extraction_utils.js
inresources/sampleproc/
updated:
a. New functiongetQiacubeSortedPrefixes(primaryQiacubePrefix, secondaryQiacubePrefix)
added. It returns a string of letters in alphabetical order, except that the primary and secondary prefixes given as arguments are placed in the first and second position, respectively.
b. FunctiongetDetailedQiaCubePosition(nitems, i)
updated with new argumentqiacubeSortedPrefixes
togetDetailedQiaCubePosition(nitems, i, qiacubeSortedPrefixes)
.
c. FunctiongetQiacubePosition(intPosition)
renamed "getDetailedQiacubePosition
", in order to have all functions returning a QIAcube position as a combination of an instrument prefix and internal position number having "DetailedQiacubePosition
" in the name. Also one new argument,qiacubeSortedPrefixes
, added to givegetDetailedQiacubePosition(intPosition, qiacubeSortedPrefixes)
.
d. FunctiongetIntQiacubePosition(positionStr)
updated with new argumentqiacubeSortedPrefixes
togetIntQiacubePosition(positionStr, qiacubeSortedPrefixes)
. - Javascript files
extraction_formcopy.js
,extraction_preparation.js
, andextraction_registration.js
inresources/sampleproc/
updated:
a. New argumentqiacubeSortedPrefixes
is added in calls to the updated functions in javascript fileextraction_utils.js
. If the string is not previously available, local functiongetQiacubeSortedPrefixes()
is called to provide it.
b. FunctiongetQiacubeSortedPrefixes()
updated to call new functiongetQiacubeSortedPrefixes(primaryQiacubePrefix, secondaryQiacubePrefix)
in javascript fileextraction_utils.js
to get the string to return.
comment:12 by , 9 years ago
(In [3354]) Refs #786. Bug fixed in javascript refactoring leading to user-defined primary and secondary QIAcube prefixes not being respected, but replaced with default values "B
" and "C
", respectively.
- Javascript file
extraction_utils.js
inresources/sampleproc/
updated:
a. New functiongetQiacubeSortedPrefixes(primaryQiacubePrefix, secondaryQiacubePrefix)
added. It returns a string of letters in alphabetical order, except that the primary and secondary prefixes given as arguments are placed in the first and second position, respectively.
b. FunctiongetDetailedQiaCubePosition(nitems, i)
updated with new argumentqiacubeSortedPrefixes
togetDetailedQiaCubePosition(nitems, i, qiacubeSortedPrefixes)
.
c. FunctiongetQiacubePosition(intPosition)
renamed "getDetailedQiacubePosition
", in order to have all functions returning a QIAcube position as a combination of an instrument prefix and internal position number having "DetailedQiacubePosition
" in the name. Also one new argument,qiacubeSortedPrefixes
, added to givegetDetailedQiacubePosition(intPosition, qiacubeSortedPrefixes)
.
d. FunctiongetIntQiacubePosition(positionStr)
updated with new argumentqiacubeSortedPrefixes
togetIntQiacubePosition(positionStr, qiacubeSortedPrefixes)
. - Javascript files
extraction_formcopy.js
,extraction_preparation.js
, andextraction_registration.js
inresources/sampleproc/
updated:
a. New argumentqiacubeSortedPrefixes
is added in calls to the updated functions in javascript fileextraction_utils.js
. If the string is not previously available, local functiongetQiacubeSortedPrefixes()
is called to provide it.
b. FunctiongetQiacubeSortedPrefixes()
updated to call new functiongetQiacubeSortedPrefixes(primaryQiacubePrefix, secondaryQiacubePrefix)
in javascript fileextraction_utils.js
to get the string to return.
comment:13 by , 9 years ago
Functional specification update:
- DNA/RNA extraction wizards should be updated to not allow editing the pre-selected QIAcube positions for individual samples, since these changes are currently not saved, and might therefore introduce a discrepancy between created lab tracking protocols and stored data. The alternative is to store the edited positions, but there has not been found much need for editing these values.
- For the "Lab tracking protocol for Allprep isolation" wizard, the change results in the "Edit" buttons being removed altogether from the table in step 3. For the "DNA/RNA registration/quantification" wizard, the edit buttons are still needed to edit description text and reagent lot numbers for an individual specimen/DNA/RNA. However, the edit buttons should be restricted to MeLuDI extract source items only, and should be removed for extra QIAcube items.
Design update:
- Javascript file
extraction_preparation.js
inresources/sampleproc/
updated in step 3 by removing the "Edit" buttons:
a. FunctioninitializeStep3()
updated by removing the edit button column.
b. FunctioneditDnaRnaDetails(event)
is removed, as it is no longer needed. - JSP file
edit_dnarna_prep_details.jsp
and javascript fileedit_dnarna_prep_details.js
inresources/sampleproc/
are made redundant by the change, but will be kept in the code for now. - JSP file
edit_dnarna_details.jsp
inresources/sampleproc/
updated by removing the QIAcube position section from the form. - Javascript file
edit_dnarna_details.js
inresources/sampleproc/
updated by removing the QIAcube position section:
a. FunctioninitPage()
updated by removing statements related to QIAcube position.
b. FunctioncheckForm()
updated by excluding QIAcube position check.
c. FunctionsaveDetails()
updated by removing statements related to QIAcube position. - Javascript file
extraction_registration.js
inresources/sampleproc/
updated in functioninitializeStep3()
by restricting the "Edit" buttons to MeLuDI extract source items.
comment:14 by , 9 years ago
(In [3365]) Refs #786. DNA/RNA extraction wizards updated to not allow editing the pre-selected QIAcube positions for individual samples, since these changes are currently not saved, and might therefore introduce a discrepancy between created lab tracking protocols and stored data, and there has not been found much need for editing these values. Also, in the DNA/RNA registration/quantification wizard, the edit buttons should be restricted to MeLuDI extract source items only, and should be removed for extra QIAcube items.
- Javascript file
extraction_preparation.js
inresources/sampleproc/
updated in step 3 by removing the "Edit" buttons:
a. FunctioninitializeStep3()
updated by removing the edit button column.
b. FunctioneditDnaRnaDetails(event)
is removed, as it is no longer needed. - JSP file
edit_dnarna_prep_details.jsp
and javascript fileedit_dnarna_prep_details.js
inresources/sampleproc/
are made redundant by the change, but will be kept in the code for now. - JSP file
edit_dnarna_details.jsp
inresources/sampleproc/
updated by removing the QIAcube position section from the form. - Javascript file
edit_dnarna_details.js
inresources/sampleproc/
updated by removing the QIAcube position section:
a. FunctioninitPage()
updated by removing statements related to QIAcube position.
b. FunctioncheckForm()
updated by excluding QIAcube position check.
c. FunctionsaveDetails()
updated by removing statements related to QIAcube position. - Javascript file
extraction_registration.js
inresources/sampleproc/
updated in functioninitializeStep3()
by restricting the "Edit" buttons to MeLuDI extract source items.
comment:15 by , 9 years ago
(In [3370]) Refs #786. Updates due to version number change to "1.2.5
".
- Version number change to "
1.2.5
":
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:17 by , 9 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
Ticket closed as MeLuDI version 1.2.5 has been created.
Ticket accepted.