Missing sample data report

[olle]

The reggie report generator should be updated to include a report on missing data for samples. Sample type should be selected to be one of specimen, no specimen, or blood.

The report should include the current numbers for each site:

For specimen:

1. Number of specimens with missing patient name
2. Number of specimens with missing PAD reference
3. Number of specimens with missing laterality
4. Number of specimens with missing sampling date
5. Number of specimens with missing RNALater date

For no specimen:

1. Number of specimens with missing patient name
2. Number of specimens with missing sampling date

For blood:

1. Number of specimens with missing patient name
2. Number of specimens with missing blood sampling date
3. Number of specimens with missing blood freezer date

Since not all users may have permission to check patient names, if this is the case, a warning should be shown.

Note. PAD stands for the Swedish expression "Patologanatomisk Diagnostik", which corresponds to "Patho-Anatomical Diagnosis" in English.

[olle]

Ticket description updated by clarification of text.

[olle]

Ticket accepted.

[olle]

Ticket description updated by changing ticket name from "Missing specimen data report" to "Missing sample data report" and allowing sample type to be selected to be specimen, no specimen, or blood.

[olle]

Design discussion.

• All sample data of interest for this report is available as annotations of different types; ALL_FIRST_NAMES, FAMILY_NAME, PAD, LATERALITY, SAMPLING_DATETIME, RNALATER_DATETIME, BLOOD_SAMPLING_DATETIME, and BLOOD_FREEZER_DATETIME.
• A patient name is considered missing if either "all first names" or "family name" is missing.
• If a user doesn't have permission to check a patient name, a net.sf.basedb.core.PermissionDeniedException will be thrown. This exception should be caught, and if thrown, a Boolean flag should be set, and the value of the latter sent back to the JSP script, in order for the latter to show a warning message.

[olle]

Design description.

• JSP script samplereportgenerator in reggie/resources/ will have the design for the layout of the missing sample data report based on that of the first table of the overview report, as the columns do not represent time intervals.
• Servlet SampleReportServlet in reggie/src/net/sf/basedb/reggie/servlet/ will perform a database sample query for subtypes SPECIMEN, NO_SPECIMEN, or BLOOD, and then process the result to obtain values for the report. In order to decrease processing time, only the annotations relevant for the chosen sample type should be processed.
• JSP script samplereportgenerator in reggie/resources/ executes identical processing of date strings in several places. This should be refactored into use of a small number of convenience functions, e.g. addHyphensToDateString(dateStr) and dateStrToDate().

[olle]

(In [1772]) Fixes #439. First version of missing sample data report added.

[olle]

(In [1923]) Fixes #483. Refs #439. Missing sample data report updated for "no specimen" to report missing items for "PAD reference" and "Laterality":

• Servlet SampleReportServlet in reggie/src/net/sf/basedb/reggie/servlet/ updated for subtype NO_SPECIMEN to obtain data for missing items for "PAD reference" and "Laterality", and include it in the response JSON script.
• JSP script samplereportgenerator in reggie/resources/ updated to include columns for "PAD reference" and "Laterality" in the table for missing "no specimen" items.