MeLuDI v.1.2.3 bug fixes and improvements

[olle]

This ticket covers bug fixes and improvements to MeLuDI v.1.2.3.

[olle]

Ticket accepted.

[olle]

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).

[olle]

(In [3298]) Refs #777 Updates due to version number change to "1.3-dev".

1. Version number change to "1.3-dev":
   a. Outermost Ant XML build file build.xml in / updated.
   b. Extensions XML configuration file extensions.xml in META-INF/ updated.
   c. Javascript file meludi-2.js in resources/ updated.
   d. Javascript file samplereportgenerator.js in resources/reports/ updated.
   e. Java class/file Meludi.java in src/net/sf/basedb/meludi/ updated.

[olle]

Functional specification update:

• MeLuDI should be updated in DNA/RNA extraction wizards to display description text for specimens and DNA/RNA extracts as tool tips for the "Comment" column in step 3 of the wizards, and in the "Remark" column of created Lab tracking sheets/reports. The description text should also be inserted in the appropriate input field of the edit pop-up dialog for the item.

Design update:

1. Javascript file extraction_registration.js in resources/sampleproc/ updated:
   a. Function exreg.updateDetailsTable() updated to set initial values of JSON objects item.comment, item.rna.comment, and item.dna.comment to the appropriate description text, before the former are parsed for what to display in the table comment field. This will automatically make the description text appear in the desired fields.
2. Javascript file extraction_formcopy.js in resources/sampleproc/ updated:
   a. Function exreg.updateDetailsTable() updated to set initial values of JSON objects item.comment, item.rna.comment, and item.dna.comment to the appropriate description text, before the former are parsed for what to display in the table comment field. Code for the latter parsing updated to be more similar to that used in javascript file extraction_registration.js.

[olle]

(In [3311]) Refs #777. MeLuDI updated in DNA/RNA extraction wizards to display description text for specimens and DNA/RNA extracts as tool tips for the "Comment" column in step 3 of the wizards, and in the "Remark" column of created Lab tracking sheets/reports. The description text should also be inserted in the appropriate input field of the edit pop-up dialog for the item.

1. Javascript file extraction_registration.js in resources/sampleproc/ updated:
   a. Function exreg.updateDetailsTable() updated to set initial values of JSON objects item.comment, item.rna.comment, and item.dna.comment to the appropriate description text, before the former are parsed for what to display in the table comment field. This will automatically make the description text appear in the desired fields.
2. Javascript file extraction_formcopy.js in resources/sampleproc/ updated:
   a. Function exreg.updateDetailsTable() updated to set initial values of JSON objects item.comment, item.rna.comment, and item.dna.comment to the appropriate description text, before the former are parsed for what to display in the table comment field. Code for the latter parsing updated to be more similar to that used in javascript file extraction_registration.js.

[olle]

Functional specification update:

• MeLuDI should be updated in the DNA/RNA registration/quantification wizard to display existing concentration and deltaCt values for input DNA/RNA extracts in the table in step 3 of the wizard, and in the table of created Lab tracking report.

Design update:

1. Javascript file extraction_registration.js in resources/sampleproc/ updated:
   a. Function exreg.updateDetailsTable() updated for input DNA/RNA extracts to set initial values of JSON objects item.rna.ndConc, item.dna.qubitConc, and item.dna.deltaCt to the values of item.ndConc, item.qubitConc, and item.deltaCt, respectively, before the former are parsed for what to display in the table fields. This will also make the DNA/RNA quantity values to be calculated from the updated concentration values and the extract volumes.

[olle]

(In [3312]) Refs #777. MeLuDI updated in the DNA/RNA registration/quantification wizard to display existing concentration and deltaCt values for input DNA/RNA extracts in the table in step 3 of the wizard, and in the table of created Lab tracking report.

1. Javascript file extraction_registration.js in resources/sampleproc/ updated:
   a. Function exreg.updateDetailsTable() updated for input DNA/RNA extracts to set initial values of JSON objects item.rna.ndConc, item.dna.qubitConc, and item.dna.deltaCt to the values of item.ndConc, item.qubitConc, and item.deltaCt, respectively, before the former are parsed for what to display in the table fields. This will also make the DNA/RNA quantity values to be calculated from the updated concentration values and the extract volumes.

[olle]

(In [3313]) Refs #777. Javascript file edit_dnarna_details.js in resources/sampleproc/ updated by removal of commented-out code, in order to make the code more readable.

[olle]

Functional specification update:

• MeLuDI should be updated to store all input information, when a case with input DNA/RNA are registered. Previously information that was stored in specimen annotations was lost.

Design update:

New extract annotations should be created for this information:

Data	Type	Extract annotation type (new)
Arrival date	Date	"ArrivalDateExtract"
Sampling date	Date	"SamplingDateExtract"
Specimen type	String	"SpecimenTypeExtract"
Viable tumour cells percentage (%)	Int	"ViableTumourCellsPercentExtract"
Operator delivery comment	String	"OperatorDeliveryCommentExtract"

1. Data access object class/file Annotationtype.java in src/net/sf/basedb/meludi/dao/ updated by adding new extract annotation types
   a. ARRIVAL_DATE_EXTRACT (Type.DATE)
   b. SAMPLING_DATE_EXTRACT (Type.DATE)
   c. SPECIMEN_TYPE_EXTRACT (Type.STRING)
   d. VIABLE_TUMOUR_CELLS_PERCENT_EXTRACT (Type.INT)
   e. OPERATOR_DELIVERY_COMMENT_EXTRACT (Type.STRING)
2. Java servlet class/file InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) to include the new extract annotation types.
3. Java servlet class/file SpecimenTubeServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private method void setAnnotations(DbControl dc, Annotatable item, JSONObject jsonCase, int nofSections, String operatorComment) to set values for the new extract annotations to input values.
4. Java servlet class/file PersonalRegistrationServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private method void setAnnotations(DbControl dc, Annotatable item, JSONObject jsonCase, int nofSections, String operatorComment) to set values for the new extract annotations to input values.
5. Java servlet class/file CaseSummaryServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Private method void loadRnaInfo(DbControl dc, Rna rna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Rna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   b. private method void loadDnaInfo(DbControl dc, Dna dna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Dna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   c. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated in calls of methods loadRnaInfo(...) and loadDnaInfo(...) to include a SnapshotManager object argument.
   d. New private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) added. It corresponds to old private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s), but takes an extract as input, instead of a sample.
   e. Private methods String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) and String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) updated to call new private method String fetchSpecimenType(String rawSpecimenType) to obtain the string to return.
   f. New private method String fetchSpecimenType(String rawSpecimenType) added. It returns a more readable string of a specimen type, and contains code, that previously belonged to private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s).
6. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. private method void loadSpecimenInfo(DbControl dc, SpecimenTube sp) updated with new argument SnapshotManager manager, and to copy value for the "SpecimenType" sample annotation to the SpecimenTube data access object using JSON key "specimenType". The value for the "SpecimenType" annotation is passed through new private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) before being copied, in order to get a more readable string.
   b. Private method void loadRnaInfo(DbControl dc, Rna rna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Rna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   c. private method void loadDnaInfo(DbControl dc, Dna dna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Dna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   d. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated for command "GetUnprocessedItems" to load values of annotation "OperatorDeliveryCommentExtract" for RNA and DNA extracts. Also updated in calls of methods loadRnaInfo(...) and loadDnaInfo(...) to include a SnapshotManager object argument.
   e. New private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) added. It obtains the value of sample annotation "SpecimenType", and calls new private method String fetchSpecimenType(String rawSpecimenType) to obtain the string to return.
   f. New private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) added. It obtains the value of extract annotation "SpecimenTypeExtract", and calls new private method String fetchSpecimenType(String rawSpecimenType) to obtain the string to return.
   g. New private method String fetchSpecimenType(String rawSpecimenType) added. It returns a more readable string of a specimen type.
7. JSP file case_summary.jsp in resources/reports/ updated to include rows for the new extract annotations in the DNA and RNA tables, except arrival date, since that is not shown for specimens.
8. Javascript file case_summary.js in resources/reports/ updated in function caseInfoLoaded(response) to add values for the new extract annotations in the DNA and RNA tables, except arrival date, since that is not shown for specimens.

[olle]

(In [3318]) Refs #777. MeLuDI updated to store all input information, when a case with input DNA/RNA are registered. Previously information that was stored in specimen annotations was lost.

New extract annotations created for this information:

Data	Type	Extract annotation type (new)
Arrival date	Date	"ArrivalDateExtract"
Sampling date	Date	"SamplingDateExtract"
Specimen type	String	"SpecimenTypeExtract"
Viable tumour cells percentage (%)	Int	"ViableTumourCellsPercentExtract"
Operator delivery comment	String	"OperatorDeliveryCommentExtract"

1. Data access object class/file Annotationtype.java in src/net/sf/basedb/meludi/dao/ updated by adding new extract annotation types
   a. ARRIVAL_DATE_EXTRACT (Type.DATE)
   b. SAMPLING_DATE_EXTRACT (Type.DATE)
   c. SPECIMEN_TYPE_EXTRACT (Type.STRING)
   d. VIABLE_TUMOUR_CELLS_PERCENT_EXTRACT (Type.INT)
   e. OPERATOR_DELIVERY_COMMENT_EXTRACT (Type.STRING)
2. Java servlet class/file InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) to include the new extract annotation types.
3. Java servlet class/file SpecimenTubeServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private method void setAnnotations(DbControl dc, Annotatable item, JSONObject jsonCase, int nofSections, String operatorComment) to set values for the new extract annotations to input values.
4. Java servlet class/file PersonalRegistrationServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private method void setAnnotations(DbControl dc, Annotatable item, JSONObject jsonCase, int nofSections, String operatorComment) to set values for the new extract annotations to input values.
5. Java servlet class/file CaseSummaryServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Private method void loadRnaInfo(DbControl dc, Rna rna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Rna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   b. private method void loadDnaInfo(DbControl dc, Dna dna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Dna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   c. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated in calls of methods loadRnaInfo(...) and loadDnaInfo(...) to include a SnapshotManager object argument.
   d. New private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) added. It corresponds to old private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s), but takes an extract as input, instead of a sample.
   e. Private methods String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) and String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) updated to call new private method String fetchSpecimenType(String rawSpecimenType) to obtain the string to return.
   f. New private method String fetchSpecimenType(String rawSpecimenType) added. It returns a more readable string of a specimen type, and contains code, that previously belonged to private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s).
6. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. private method void loadSpecimenInfo(DbControl dc, SpecimenTube sp) updated with new argument SnapshotManager manager, and to copy value for the "SpecimenType" sample annotation to the SpecimenTube data access object using JSON key "specimenType". The value for the "SpecimenType" annotation is passed through new private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) before being copied, in order to get a more readable string.
   b. Private method void loadRnaInfo(DbControl dc, Rna rna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Rna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   c. private method void loadDnaInfo(DbControl dc, Dna dna) updated with new argument SnapshotManager manager, and to copy values for the new extract annotations to the Dna data access object using the same JSON key, as was used for the corresponding specimen annotations. The value for the "SpecimenTypeExtract" annotation is passed through new private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) before being copied, in order to get a more readable string.
   d. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated for command "GetUnprocessedItems" to load values of annotation "OperatorDeliveryCommentExtract" for RNA and DNA extracts. Also updated in calls of methods loadRnaInfo(...) and loadDnaInfo(...) to include a SnapshotManager object argument.
   e. New private method String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) added. It obtains the value of sample annotation "SpecimenType", and calls new private method String fetchSpecimenType(String rawSpecimenType) to obtain the string to return.
   f. New private method String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) added. It obtains the value of extract annotation "SpecimenTypeExtract", and calls new private method String fetchSpecimenType(String rawSpecimenType) to obtain the string to return.
   g. New private method String fetchSpecimenType(String rawSpecimenType) added. It returns a more readable string of a specimen type.
7. JSP file case_summary.jsp in resources/reports/ updated to include rows for the new extract annotations in the DNA and RNA tables, except arrival date, since that is not shown for specimens.
8. Javascript file case_summary.js in resources/reports/ updated in function caseInfoLoaded(response) to add values for the new extract annotations in the DNA and RNA tables, except arrival date, since that is not shown for specimens.

[olle]

Functional specification update:

• MeLuDI should be updated in DNA/RNA registration/quantification wizard step 2 to allow input of lot numbers for reagents used in quality control, and to store these in annotations for the extracts, like other lot numbers. The Lab Tracking Report should be updated to display the quality control lot no.s in the header section.

Design update:

New extract annotations should be created for the quality control lot no.s:

Data	Type	Extract annotation type (new)
Kapa SYBR Fast lot. no.	String	"KapaSybrFast"
Quality Control Primers (QCP) RGT no.	String	"QualityControlPrimersQcpRgt"
QUBIT DNA High Sens lot. no.	String	"QubitDnaHighSens"
QUBIT DNA Broad Range lot. no.	String	"QubitDnaBroadRange"

1. Data access object class/file Annotationtype.java in src/net/sf/basedb/meludi/dao/ updated by adding new extract annotation types
   a. KAPA_SYBR_FAST (Type.STRING)
   b. QUALITY_CONTROL_PRIMERS_QCP_RGT (Type.STRING)
   c. QUBIT_DNA_HIGH_SENS (Type.STRING)
   d. QUBIT_DNA_BROAD_RANGE (Type.STRING)
2. Java servlet class/file InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) to include the new extract annotation types.
3. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated with support for the four new quality control annotations. Also bug fix in JSON key for Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL, where "qiaampMinEluteSpinColum" was exchanged for "qiaampMinEluteSpinColumn" (with terminal letter "n"):
   a. Private method void loadRnaInfo(DbControl dc, SnapshotManager manager, Rna rna) updated to copy values for the new extract annotations to the Rna data access object.
   b. private method void loadDnaInfo(DbControl dc, SnapshotManager manager, Dna dna) updated to copy values for the new extract annotations to the Dna data access object.
   c. Protected method void doPost(HttpServletRequest req, HttpServletResponse resp) updated for command "RegisterDnaRna" to support new annotations for RNA and DNA extracts.
4. Javascript file extraction_preparation.js in resources/reports/ updated in JSONArray exprep.REAGENTS by adding JSON keys for new extract annotations. Function lastProcessDnaLoaded(response) updated in commented-out code to use new JSON key for Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.
5. JSP file extraction_protocol2.jsp in resources/reports/ updated by adding id values for tags related to new quality control lot no.s in header section.
6. Javascript file extraction_protocol.js in resources/reports/ updated in function initializeProtocol(submitInfoJsonStr) to obtain values for the new extract annotations from the submit info JSON object, and insert them in header section of the lab tracking report form.
7. JSP file extraction_registration.jsp in resources/reports/ updated in step 2 by adding a new section for quality control lot no.s.
8. Javascript file extraction_registration.js in resources/reports/ updated:
   a. JSONArray exreg.REAGENTS by adding JSON keys for new extract annotations.
   b. Function clearReagents() updated by including new quality control lot no. fields in the ones to clear.
   c. Function lastProcessedDnaLoaded(response) updated by including new quality control lot no. values in the ones to copy to input fields.
   d. Function parseReagentFile(data) updated by including new quality control lot no. values in the ones to copy to input fields.
   e. Function createProtocol() updated by including new quality control lot no. values in the ones submitted to extraction_protocol.js.
9. JSP file extraction_formcopy.jsp in resources/reports/ updated in step 2 by adding a new section for quality control lot no.s.
10. Javascript file extraction_formcopy.js in resources/reports/ updated:
    a. JSONArray exreg.REAGENTS by adding JSON keys for new extract annotations.
    b. Function initializeStep2() updated by including new quality control lot no. fields in the ones to hide.
    c. Function sourceItemListLoaded(response) updated by including new quality control lot no. fields in the ones to disable.
    d. Function reagentLotNosFromDna(response) updated by including new quality control lot no. values in the ones to copy to input fields and show.
    e. Function createProtocol() updated by including new quality control lot no. values in the ones submitted to extraction_protocol.js.

[olle]

(In [3324]) Refs #777. MeLuDI updated in DNA/RNA registration/quantification wizard step 2 to allow input of lot numbers for reagents used in quality control, and to store these in annotations for the extracts, like other lot numbers. The Lab Tracking Report should be updated to display the quality control lot no.s in the header section.

New extract annotations should be created for the quality control lot no.s:

Data	Type	Extract annotation type (new)
Kapa SYBR Fast lot. no.	String	"KapaSybrFast"
Quality Control Primers (QCP) RGT no.	String	"QualityControlPrimersQcpRgt"
QUBIT DNA High Sens lot. no.	String	"QubitDnaHighSens"
QUBIT DNA Broad Range lot. no.	String	"QubitDnaBroadRange"

1. Data access object class/file Annotationtype.java in src/net/sf/basedb/meludi/dao/ updated by adding new extract annotation types
   a. KAPA_SYBR_FAST (Type.STRING)
   b. QUALITY_CONTROL_PRIMERS_QCP_RGT (Type.STRING)
   c. QUBIT_DNA_HIGH_SENS (Type.STRING)
   d. QUBIT_DNA_BROAD_RANGE (Type.STRING)
2. Java servlet class/file InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) to include the new extract annotation types.
3. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated with support for the four new quality control annotations. Also bug fix in JSON key for Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL, where "qiaampMinEluteSpinColum" was exchanged for "qiaampMinEluteSpinColumn" (with terminal letter "n"):
   a. Private method void loadRnaInfo(DbControl dc, SnapshotManager manager, Rna rna) updated to copy values for the new extract annotations to the Rna data access object.
   b. private method void loadDnaInfo(DbControl dc, SnapshotManager manager, Dna dna) updated to copy values for the new extract annotations to the Dna data access object.
   c. Protected method void doPost(HttpServletRequest req, HttpServletResponse resp) updated for command "RegisterDnaRna" to support new annotations for RNA and DNA extracts.
4. Javascript file extraction_preparation.js in resources/reports/ updated in JSONArray exprep.REAGENTS by adding JSON keys for new extract annotations. Function lastProcessDnaLoaded(response) updated in commented-out code to use new JSON key for Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.
5. JSP file extraction_protocol2.jsp in resources/reports/ updated by adding id values for tags related to new quality control lot no.s in header section.
6. Javascript file extraction_protocol.js in resources/reports/ updated in function initializeProtocol(submitInfoJsonStr) to obtain values for the new extract annotations from the submit info JSON object, and insert them in header section of the lab tracking report form.
7. JSP file extraction_registration.jsp in resources/reports/ updated in step 2 by adding a new section for quality control lot no.s.
8. Javascript file extraction_registration.js in resources/reports/ updated:
   a. JSONArray exreg.REAGENTS by adding JSON keys for new extract annotations.
   b. Function clearReagents() updated by including new quality control lot no. fields in the ones to clear.
   c. Function lastProcessedDnaLoaded(response) updated by including new quality control lot no. values in the ones to copy to input fields.
   d. Function parseReagentFile(data) updated by including new quality control lot no. values in the ones to copy to input fields.
   e. Function createProtocol() updated by including new quality control lot no. values in the ones submitted to extraction_protocol.js.
9. JSP file extraction_formcopy.jsp in resources/reports/ updated in step 2 by adding a new section for quality control lot no.s.
10. Javascript file extraction_formcopy.js in resources/reports/ updated:
    a. JSONArray exreg.REAGENTS by adding JSON keys for new extract annotations.
    b. Function initializeStep2() updated by including new quality control lot no. fields in the ones to hide.
    c. Function sourceItemListLoaded(response) updated by including new quality control lot no. fields in the ones to disable.
    d. Function reagentLotNosFromDna(response) updated by including new quality control lot no. values in the ones to copy to input fields and show.
    e. Function createProtocol() updated by including new quality control lot no. values in the ones submitted to extraction_protocol.js.

[olle]

(In [3326]) Refs #777. MeLuDI Lab Tracking Sheet/Report table updated by making columns for QIAcube and NanoDrop plate positions more narrow, and columns for RNA/DNA concentrations and DNA delta-Ct value wider. The update was prompted by the desire to have more space in columns, where values should be entered manually.

1. JSP file extraction_protocol2.jsp in resources/sampleproc/ updated by making columns for QIAcube and NanoDrop plate positions mor narrow, and columns for RNA/DNA concentrations and DNA delta-Ct value wider.

[olle]

(In [3328]) Refs #777. MeLuDI Lab Tracking Sheet/Report table updated by making header section title columns wider, in order for data for each quantity to fit on a single line.

1. JSP file extraction_protocol2.jsp in resources/sampleproc/ updated by making header section title columns wider.

[olle]

Functional specification update:

• MeLuDI Lab Tracking Sheet/Report should be updated by replacing the current header line with two:
  a. Header line 1 should consist of "Lab Tracking " + "Sheet" or "Report" + form version number (originally v1.0) + optional "(preview)" marker + "(MeLuDI <meludi-version-number>)".
  b. Header line 2 should consist of the protocol name.

Design update:

1. JSP file extraction_protocol2.jsp in resources/sampleproc/ updated by replacing the current header line with two.
2. Javascript file extraction_protocol.js in resources/sampleproc/ updated in function initializeProtocol(submitInfoJsonStr) to write two header lines: one consisting of "Lab Tracking " + "Sheet" or "Report" + form version number (originally v1.0) + optional "(preview)" marker + "(MeLuDI <meludi-version-number>)", the other consisting of the protocol name.

[olle]

(In [3329]) Refs #777. MeLuDI Lab Tracking Sheet/Report updated by replacing the current header line with two:
a. Header line 1 should consist of "Lab Tracking " + "Sheet" or "Report" + form version number (originally v1.0) + optional "(preview)" marker + "(MeLuDI <meludi-version-number>)".
b. Header line 2 should consist of the protocol name.

1. JSP file extraction_protocol2.jsp in resources/sampleproc/ updated by replacing the current header line with two.
2. Javascript file extraction_protocol.js in resources/sampleproc/ updated in function initializeProtocol(submitInfoJsonStr) to write two header lines: one consisting of "Lab Tracking " + "Sheet" or "Report" + form version number (originally v1.0) + optional "(preview)" marker + "(MeLuDI <meludi-version-number>)", the other consisting of the protocol name.

[olle]

(In [3331]) Refs #777. Javascript file extraction_formcopy.js in resources/sampleproc/ updated by bug fix in function exreg.reagentLotNosFromDna(response) by using new JSON key for Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL, where "qiaampMinEluteSpinColum" was exchanged for "qiaampMinEluteSpinColumn" (with terminal letter "n").

[olle]

Functional specification update:

• MeLuDI should be updated in step 2 of DNA/RNA registration/quantification and Lab tracking sheet/report copy wizards to allow download of a file with current lot numbers for future import/reference.

Design update:

1. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated with new command "DownloadReagentLotNoFile". It obtains values for start plate name, isolation date, and reagent lot numbers from the JSON input, and creates a file formatted for future import of the reagent lot no. values.
2. JSP file extraction_registration.jsp in resources/reports/ updated in step 2 by adding a new button in the "Input options" section.
3. Javascript file extraction_registration.js in resources/reports/ updated
   a. Function initPage() updated by adding new button handler for step 2, with callback function downloadReagentLotNoFile().
   b. New function downloadReagentLotNoFile() added. It calls ExtractionServlet with command "DownloadReagentLotNoFile" and suplies a JSONObject with current lot numbers.
4. JSP file extraction_formcopy.jsp in resources/reports/ updated in step 2 by adding a new button in the "Output options" section.
5. Javascript file extraction_formcopy.js in resources/reports/ updated:
   a. Function initPage() updated by adding new button handler for step 2, with callback function downloadReagentLotNoFile().
   b. New function downloadReagentLotNoFile() added. It calls ExtractionServlet with command "DownloadReagentLotNoFile" and suplies a JSONObject with current lot numbers.

[olle]

(In [3332]) Refs #777. MeLuDI updated in step 2 of DNA/RNA registration/quantification and Lab tracking sheet/report copy wizards to allow download of a file with current lot numbers for future import/reference.

1. Java servlet class/file ExtractionServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Protected method void doGet(HttpServletRequest req, HttpServletResponse resp) updated with new command "DownloadReagentLotNoFile". It obtains values for start plate name, isolation date, and reagent lot numbers from the JSON input, and creates a file formatted for future import of the reagent lot no. values.
2. JSP file extraction_registration.jsp in resources/reports/ updated in step 2 by adding a new button in the "Input options" section.
3. Javascript file extraction_registration.js in resources/reports/ updated
   a. Function initPage() updated by adding new button handler for step 2, with callback function downloadReagentLotNoFile().
   b. New function downloadReagentLotNoFile() added. It calls ExtractionServlet with command "DownloadReagentLotNoFile" and suplies a JSONObject with current lot numbers.
4. JSP file extraction_formcopy.jsp in resources/reports/ updated in step 2 by adding a new button in the "Output options" section.
5. Javascript file extraction_formcopy.js in resources/reports/ updated:
   a. Function initPage() updated by adding new button handler for step 2, with callback function downloadReagentLotNoFile().
   b. New function downloadReagentLotNoFile() added. It calls ExtractionServlet with command "DownloadReagentLotNoFile" and suplies a JSONObject with current lot numbers.

[olle]

(In [3335]) Refs #777. Bug fixed that prevented import of concentration values from a NanoDrop value file. The bug was introduced in change set ​3276 in Ticket #768 (MeLuDI v.1.2.2 bug fixes and improvements), when JSON variable item.rna.well was renamed item.rna.nanoDropWell, in order to distinguish it from the well on the storage plate. However, it was not realized, that this also prompted a change of variable name rnaOrDna.well to rnaOrDna.nanoDropWell in function exreg.parseNanoDropFile(data) in javascript file extraction_registration.js in resources/sampleproc/.

1. Javascript file extraction_registration.js in resources/sampleproc/ updated with bug fix in function exreg.parseNanoDropFile(data) by renaming variable rnaOrDna.well to rnaOrDna.nanoDropWell.

[olle]

Functional specification update:

• MeLuDI Lab Tracking Sheet/Report layout update:
  a. Lab Tracking Sheet should be renamed "Lab Tracking Protocol".
  b. The first header line (excluding version no.) should be appended by "for Allprep isolation", i.e. be either "Lab Tracking Protocol for Allprep isolation" or "Lab Tracking Report for Allprep isolation", followed by version no.
  c. Text in header section should be updated by exchanging "lot." for "lot", since "lot" is not an abbreviation.

[olle]

(In [3336]) Refs #777. MeLuDI Lab Tracking Sheet/Report layout update:
a. Lab Tracking Sheet should be renamed "Lab Tracking Protocol".
b. The first header line (excluding version no.) should be appended by "for Allprep isolation", i.e. be either "Lab Tracking Protocol for Allprep isolation" or "Lab Tracking Report for Allprep isolation", followed by version no.
c. Text in header section should be updated by exchanging "lot." for "lot", since "lot" is not an abbreviation.

1. JSP and javascript files updated in Lab Tracking Protocol header text, and in text referring to the former.

[olle]

(In [3343]) Refs #777. MeLuDI updated to report id values in error message if multiple items are found, when searching for a DNA item by name:

1. Data access object class/file Dna.java in src/net/sf/basedb/meludi/dao/ updated in public static method Dna findByName(DbControl dc, String name) to report id values in error message if multiple items are found, when searching for a DNA item by name.

[olle]

(In [3344]) Refs #777. MeLuDI updated to report id values in error message if multiple items are found, when searching for an RNA or specimen tube item by name:

1. Data access object class/file Rna.java in src/net/sf/basedb/meludi/dao/ updated in public static method Rna findByName(DbControl dc, String name) to report id values in error message if multiple items are found, when searching for an RNA item by name.
2. Data access object class/file SpecimenTube.java in src/net/sf/basedb/meludi/dao/ updated in public static method SpecimenTube findByName(DbControl dc, String name) to report id values in error message if multiple items are found, when searching for a specimen tube item by name.

[olle]

(In [3345]) Refs #777. Updates due to version number change to "1.2.4".

1. Version number change to "1.2.4":
   a. Outermost Ant XML build file build.xml in / updated.
   b. Extensions XML configuration file extensions.xml in META-INF/ updated.
   c. Javascript file meludi-2.js in resources/ updated.
   d. Javascript file samplereportgenerator.js in resources/reports/ updated.
   e. Java class/file Meludi.java in src/net/sf/basedb/meludi/ updated.

[olle]

Milestone renamed

[olle]

Ticket closed as MeLuDI version 1.2.4 has been created.