Friday, April 17 2009
- Changed Affymetrix Order, removing quality control and changing options for requestedServices.
- Added 280/230 ratio to Affymetrix Order and AffymetrixSample.
- Only view Bioanalyzer run and sampleId when the user does not request a Bioanalyzer run.
- Removed option to upload sample information because everyone gets it wrong.
- Sort billing options for Confocal orders.
Wednesday, February 11 2009
- Cosmetic modifications to Confocal billing.
- Changed service options for HTS orders adding number of cycles to the choosable options.
- Added NUMBER_OF_CYCLES to the HTS_ORDER database table.
- Changed the current experiment types to the reflect changes in the experiment type naming convention (e.g. from 'single_read' to 'single_read_36').
- Recalculate HTS order cost when marking "completed" to insure the price per lane is correct. Some runs have 8 lanes of samples and others have 7 lanes of samples plus a lane standard. So the price per lane varies depending on the number of lanes used.
Tuesday, February 3 2009
- Loosened permissions on Rolemanager.getProject so that users can view more project information.
- Updated Genotype order cost computation.
Friday, January 16 2009
- Allow central lab personnel to edit and cancel pending orders.
- Added Confocal orders. Confocal information is entered by Central Lab personnel.
Monday, January 5 2009
- Upper-case all billing ids and activity codes upon creation to comply with OSU Banner specification.
- Do not allow billing ids starting with 'ARF' per Rosa's request.
Tuesday, December 16 2008
- Removed activity code from billing ids in ACCOUNT table so that activity codes would not be duplicated.
- Changed action mapping for order update and view for all order types. This allows for variable view options between order types.
Friday, November 14 2008
- Replaced SequenceOrderView3 with OrderView3 in processManageComplete method for all order types to remove dependency on a SequenceOrderView object by all order types.
- If the experiment name for an Affymetrix order is not given, display the experiment as "(not named)" when billing.
Wednesday, November 5 2008
- Added activityCode to accounts to prepare for bulk entries of monthly billing information into Data Warehouse.
- Changed HTS orders so that you can order 8 samples instead of 7.
- Changed "Delete Account" to work similarly to "Deactivate Account".
- Implemented 2-color ordering form for Nimblegen orders.
Friday, October 19 2008
- Added ability to bill Nimblegen orders.
- Implemented QC cost in Affymetrix monthly billing.
- Implemented ability to view user(s) that can access Genesifter.
- Fix bug in downloading Affymetrix orders. This bug limited the ability to download older data.
Friday, August 8 2008
- Added Nimblegen order.
- Removed Label Custom Array order.
- Renamed "experimentType" to "serviceType" for HTS orders and include serviceType in monthly billing statements.
Friday, June 6 2008
- Quietly replace spaces in data download file name with underscores. This will fix problem that a filename is not resolved because people enter a space in the file name without prepending an escape charater.
- Since the amount of a sample required depends on the labeling method, we implemented a labeling method-dependent check for the amount of each sample.
- Display more order-dependent parameters when viewing a project.
Monday, June 2 2008
- Added button in Manage Profile to allow Central Lab Members to add an access code to a user profile. The access code is randomly picked from a list of codes in a database table. Once a code has been chosen it is marked as inUse so that it will not be used by a second user. Principal investigators and lab managers can view access codes of lab members.
Monday, May 19 2008
- Changed behavior such that once the billingStatus is "billed" it cannot be changed. This is because sometimes core lab personnel want to correct an order after it has been billed. However, editing a previously billed order would mark it as "reviewed".
Friday, April 18 2008
- Added experimentType to HTS project.
- Entered pipelineConfig and pipelineCommand data into HTS_PROJECT.
Wednesday, April 16 2008
- For genotype order, changed allowed values for sampleType, filterSet, standardType, dyes, and outputType per Alex request.
- Added pipelineConfig and pipelineCommand to HTS Project.
Monday, April 14 2008
- Added view HTS project.
- Added experimentType to HTS order and project to discriminate between single read runs and the new paired-end run.
Thursday, April 10 2008
- fixed bug that caused the second genome in HTS order to be overwritten if the order was later edited.
- added Affymetrix output file to Affymetrix project so now it's written to both the project and the order. It would probably be better to write to only one of either the project or the order but we could not decide.
- can enter a comma-delimited list of Affymetrix output files to download for a given project.
- added "unassigned" as an option for contaminate genomes.
- Changed the upper limit for 260/280 ratio for Affymetrix orders from 2.25 to ???
- Created a new icon for "information"
- Added AppliedBiosystems.iso to download directory and renamed the "Forms" link to "Resources".
Wednesday, December 20 2007
- Added validation to project parameter values for Affymetrix projects.
- Set default values for different status types for Affymetrix projects.
Wednesday, December 5 2007
- Add DATE_SCHEDULED to HTS orders.
- Stubbed methods to manage HTS orders and create an HTS project.
Friday, September 14 2007
- Made many changes to Affymetrix and HTS projects and orders ... too many to enumerate. We decided that researchers should send us their genome library required for analysis before they can submit an HTS order. That decision impacts the ordering system in that one cannot submit an HTS order if they do not choose among a list of predefined genomes.
Wednesday, November 28 2007
- Added LANES_CHARGED column to HTS orders so that we can charge a different number of lanes than the number ordered.
Friday, November 15 2007
- Converted old Affy orders to new one adding the following fields: orderId, bioanalyzerId, bioanalyzerSampleId, qcVisualPass, bioanalyzerRin, rnaLabelingAmount, labelingQcPass, labeler, hyber, scanner, qcCost, dateCompleted, dateLabeled, dateScanned, scanNotes.
- Used the following mysql commands to transfer data from AFFYMETRIX_ORDER tabel to AFFYMETRIX_PROJECT:
mysql> insert into AFFYMETRIX_PROJECT (ID,TITLE,ORDER_TYPE, LOGIN_NAME,PHONE,EMAIL,AFFILIATION,PI_ID,LAB_ID,DATE_CREATED,DATE_UPDATED,DATE_COMPLETED,STATUS,CHIP_TYPE,COMMENTS,LAB_COMMENTS,NUMBER_SAMPLES,PROJECT_TYPE,LABEL_METHOD) select AFFYMETRIX_ORDER.PROJECT_ID, AFFYMETRIX_ORDER.EXPERIMENT_NAME,AFFYMETRIX_ORDER.ORDER_TYPE, AFFYMETRIX_ORDER.LOGIN_NAME, AFFYMETRIX_ORDER.PHONE, AFFYMETRIX_ORDER.EMAIL ,AFFYMETRIX_ORDER.AFFILIATION,AFFYMETRIX_ORDER.PI_ID,AFFYMETRIX_ORDER.LAB_ID,AFFYMETRIX_ORDER.DATE_CREATED,AFFYMETRIX_ORDER.DATE_UPDATED,AFFYMETRIX_ORDER.DATE_COMPLETED,AFFYMETRIX_ORDER.STATUS,AFFYMETRIX_ORDER.CHIP_TYPE,AFFYMETRIX_ORDER.COMMENTS,AFFYMETRIX_ORDER.LAB_COMMENTS,AFFYMETRIX_ORDER.NUMBER_SAMPLES,'Affymetrix',AFFYMETRIX_ORDER.LABEL_METHOD from AFFYMETRIX_ORDER;
Query OK, 106 rows affected (0.01 sec)
Records: 106 Duplicates: 0 Warnings: 0
mysql> update AFFYMETRIX_PROJECT set PARAMETER_NAMES='undefined';
Query OK, 106 rows affected (0.01 sec)
Rows matched: 106 Changed: 106 Warnings: 0
mysql> update AFFYMETRIX_PROJECT set PARAMETER_VALUES='undefined';
Query OK, 106 rows affected (0.02 sec)
Rows matched: 106 Changed: 106 Warnings: 0
mysql> update AFFYMETRIX_PROJECT set PROJECT_MANAGER='girarda';
Query OK, 106 rows affected (0.04 sec)
Rows matched: 106 Changed: 106 Warnings: 0
- Replaced values in "replicateGroup" with new attribute "nameOnTube".
- Created Affymetrix projects for each order. Each project is named as"project_{orderId}. This will satisfy the requirement that each order must be affiliated with a project.
Friday, August 31 2007
- Changed DNA Sequence monthly billing to also check affiliation (besides piId and department).
- Fixed the affiliation for some old orders to be consistent with the account affiliation. Sometimes, the PI enters the wrong account affiliation which we fix but the original order retains the incorrect affiliation.
- Added runID and flowcell to Bill.java for HTS orders.
Wednesday, August 22 2007
- Added feature to download csv files for HTS orders.
- Added feature to view summary and ivc plots for HTS orders.
Thursday, June 21 2007
- Added ability to download sample information for Affymetrix orders.
Wednesday, June 20 2007
- I pulled individual order definitions from sqlmap/Order.xml to better compartmentalize the application.
- Added HTS order type.
- Merged the previous version of Affymetrix orders with a new one. The new version tracks a project identifier for each order.
Thursday, June 7 2007
- On May 26 2007, I started running the web application using Java 1.5.0_11.
- On June 1 2007, I started running the web application using Tomcat 6 and the mod_jk connector. Using the connector allows us to forward requests through port 80 on apache so as to hide the port number in URLs.
- I just noticed in the log files that an error appeared first in the June 1 log:
2007-06-01 10:38:46 StandardWrapperValve[jsp]: Servlet.service() for servlet jsp threw exception
javax.servlet.jsp.JspException: Error - tag.getAsString : component context is not defined. Check tag syntax
at org.apache.struts.taglib.tiles.GetAttributeTag.doEndTag(GetAttributeTag.java:198)
at org.apache.jsp.APP_005flayout_005f2_jsp._jspx_meth_tiles_getAsString_0(APP_005flayout_005f2_jsp.java:280)
at org.apache.jsp.APP_005flayout_005f2_jsp._jspService(APP_005flayout_005f2_jsp.java:99)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:133)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:856)
at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:311)
The line for this error in file created by the server is:
if (_jspx_th_tiles_getAsString_0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE)
The line for this error in the APP_layout_2.jsp source file is:
<title><tiles:getAsString name="title"/></title>
I compared an old version of APP_layout_2.jsp with the current one and there are no changes so the problem is a configuration one, not within this file. I'm trying to figure out what causes this error. It does not look serious but it bugs me.
Friday, May 11 2007
- Added a feedback form so users can email suggestions/complaints.
Thursday, May 10 2007
- For DNA Sequence data, added ability to download text data as a single file that is the result of the chosen text files appended together.
Tuesday, May 8 2007
- Separated "struts-config.xml" into several files based on order type. These new config files are listed in "web.xml".
Friday, May 4 2007
- Updated Javadoc documentation and removed dead code.
- Moved some classes from the "view" package to the "bo" package. Removed the deprecated "sql" package.
Tuesday, April 24 2007
Friday, March 2 2007
- For DNA Sequence orders, added parameters for DGTP and hardwired addDMSO to "yes" in jsp pages.
Friday, February 23 2007
- Enabled central lab members to deactivate billing accounts.
- Added AffymetrixSamplesWriter to produce text output for Affymetrix orders (similar to Bioanalyzer orders).
Tuesday, February 20 2007
- Added shipping charge to Store orders.
- Removed $30 premium from Affymetrix chip price and added a $35 shipping charge.
Friday, February 2 2007
- Changed the sample names created for DNA Sequence orders to include the order id number. This is to guarantee that sample names will be unique. To maintain backwards compatibility, there is a test for the order id number at which this change occurred in SequenceSampleParser: prepareDownload().
- Added View Data for Sequence data which uses a Java applet to view the data.
- Added Nitrosomonas europaea as an Affymetrix chip type.
Friday, January 12 2007
- Minor changes to LabelCustomArray orders.
- Added some fields to AffymetrixSample to be able to identify a cost for each service of each sample.
- Wrote AffymetrixTranslator to change the shape of all AffymetrixSample objects contained in the AffymetrixOrder objects.
- backed up database on web.cgrb.oregonstate.edu, translated Affymetrix orders, repopulated database with new Affymetrix table.
Friday, November 17 2006
- Exported all orderType tables to text (.sql) files, removed prefix (for example, "SO_") for each field and reimported data. This makes field names more similar so that we can reduce the number of SQL commands that are located in the sqlmap Order.xml file.
- Added a view for monthly billing (in ) to facilitate a department-level billing comparison between our records and Rosa's accounting records. One can also drill down an view orders for each department in that month.
Friday, October 27 2006
- Changed the MySQL driver connection class from 3.0.7-stable to 3.1.14. This also required adding "zeroDateTimeBehavior=convertToNull" to the connection URLto satisfy SQL compliance.
Friday, October 20 2006
- Changed getCredentials(emailAddress) to allow for more than one account to be associated with one email address. Now, when someone fills in the "forgot my password action, an email containing account information will be emailed to that address for each account.
- Split the package count from the chip description in application.properties key "this.affymetrix.onlineStore". This enables using just the chip description when ordering a hyb/scan.
- Added sample information to Bill so that we can display sample specific information in monthly billing, especially for Affymetrix billing.
Friday, October 13 2006
Today's changes are:
- Cleaned up billing for genotyping, store orders and service orders.
- Changed account edit so that central lab personnel can mark an account as
either external or internal.
Wednesday, July 26 2006
Today's changes are:
- In "dao/DaoConfig.java" get location of "dao.xml" file from ApplicationService rather than hardcoded.
- Cleaned up directory locations of view files.
Monday July 10, 2006
Today's changes are:
- disabled zip code validation because different countries have different rules.
- Added DatastoreException code to catch errors associated with the database being inaccessible.
Tuesday June 27, 2006
Today's changes are:
- enabled changing price for labelCustomArray orders.
- fixed discount pricing for genotyping orders.
- changed values for Affymetrix chips to reflect Tier 2 pricing.
Monday May 29, 2006
Today's changes are:
- implemented discount computation for genotyping orders.
- replaced instances of "CSL" with "Core Labs" in html (jps) files.
Tuesday January 31, 2006
Changes implemented on live site are:
- added an online store. You can buy one type of item at a time. This guarantees the billing for a given order will not be split between internal service groups (such as CustomArrays, Sequencing, etc.) .
- removed ability to buy affy chips through the affy order option and moved it to the online store.
- removed ability to buy non-service related items from service order option (such as alien RNA and BioRobot tips) and moved them to the online store.
- implemented a different sorting order for monthly billing and for viewing previous bills by adding a new group of select statements in "Order.xml".
- changed references of "Fragment Analysis" to "Genotyping" per Alex's request.
- added volume discount to Genotyping billing.
- edited "welcome.jsp" to fine tune options available to a centralLabHelper.
- changed format of Bioanalyzer Excel files to match new Bioanalyzer format rules (deleted some commas).
Tuesday November 8, 2005
Today's changes are:
- added ability to mark "reviewed" orders as billed for all order types registered in monthly billing.
Friday September 30, 2005
Today's changes are:
- added monthly billing summary information for DNA Sequence, Fragment
Analysis, Bioanalyzer, and Service orders.
Thursday September 15, 2005
Today's changes are:
- implemented a mask for sequence primer name to disallow any character not matching the characters [0-9a-zA-Z_-].
- include billing totals in monthly billing output for sequence data.
Thursday September 1, 2005
Today's changes are:
- changed validation for the primer name in sequence orders such that the
primer name is required only when the primer source is "CSL".
- increased the permitted size of address fields when adding a new user or lab.
- change the charge for fragment analysis orders to 2 bucks a sample, regardless of affiliation.
- added Genetix 384-well plate to "Big Dye & cleanup". I plan to create
a new row for these miscellaneous items.
Thursday June 30, 2005
Today's changes are:
- added csv format for Bioanalyzer sample data output.
Monday, June 27, 2005
Today's changes are:
- added "affiliation" to all order types to guarantee uniqueness of the triad of billingId, department, and affiliation.
- changed edit orders so that CSL members can edit other users orders without changing the fields that defined who initially submitted the order.
Monday, June 20, 2005
Changes copied to the live server include:
- changed "order" services so that CSL members can order for a PI. I've
started but not completed work on this for updating orders.
- fixed a bug in the date validation for data download.
- fixed a bug for managing completed Fragment Analysis orders where the
billingStatus was marked "reviewed" only for one order instead of all orders
in the list.
- display billing account balance in dollars rather than integer money.
- changed links for forward and backward arrows in javascript date function
to correct image locations.
- added this log to the application. It is viewable by clicking Status on
the main menu and then the "Development Log" link.
Wednesday, June 15, 2005
I've been working on getting pages to render consistently for as
many browsers as possible. Pages should all render better on IE,
Netscape, and Safari and slightly worse on Firefox. I've copied the
pages over to the development web server and will update the live web server tonight.
For Netscape, a reported bug was that sample data did not render when
entering a DNA sequence order. This bug appears to be fixed. Let me
know if you see any other rendering problems.
Wednesday, June 8, 2005
I copied the following changes to the web server last night:
- added "billingStatus" to View and Manage pages.
- added "affiliation", "billingType", and "comment" fields to billing accounts. The comment can be used to add a descriptive comment about the billing index if there is something confusing about it.
- increased the size of the billingIndex from 20 characters to 60 characters to allow for long ids that include call numbers (like for the EPA).
- changed the Update Accounts page to edit accounts one at a time which enables validation.
- "department" and "affiliation" select lists for accounts are now derived from the accounts themselves rather than the lab list.
Thursday, June 2, 2005
- when viewing sequence order billing, the "Printout" column now shows an "*" when this charge applies.
- added blank option in menu for billing so that central lab members can see billing for all users of a given service.
- added "Monthly Billing" link to homepage for central lab personnel. This link is similar to the billing link on the main menu but formats the output in the paper format used for billing.
Monday, May 23, 2005
I copied the following changes to the jcclab server for testing. I created a
(temporary) test account that can be used for testing.
- added a "centralLabHelper" role for students working in the CSL. This role allows one to manage orders, view all data, view all billing as well as add/update/view/cancel orders.
- added shading to every other Sequence order for View and Manage to more easily discriminate order boundaries. Economy and full bulk colors take precedence over alternating shading in Manage.
Friday, May 20, 2005
Today's changes are:
- Email lookup for "Forgot my password" link on the login page is now case- independent
- Can now see sample data file for Frag data in View and Manager links
- Added validation so duplicate billingId/department combination cannot be added under Add Account
- Bug fix to download sample data files that have duplicate sample names (but unique file names).
- Create spreadsheet containing Bioanalyzer sample data. Access
this data by choosing "Manage" and then "Bioanalyzer". The order
number is now a link - click it to access a page that contains an
order summary with a link to the spreadsheet. This will not work on
the development web server until I add some info to the web server config file.
- I'll likely perform some database maintenance this weekend to delete a couple of users and labs that do not want accounts.
Thursday, May 19, 2005
- re-implemented validation for Fragment Analysis input file name. I took this out at some point for some reason that I forgot.
- changed charges from integer to dollar amount (!) when completing an order for all order types.
- implemented validation when orders are complete. The validation part is done but I'm not done regenerating the form with a validation error. So, for now, you need to click the "Back" button if you get a validation error when submitting form for order completion that is not valid.
- reversed order that bills are displayed.
- implemented downloading hqx format Fragment Analysis files.
Friday, May 13, 2005
Here are today's changes, barely tested. I've updated the development
web server if you want to test them out on that machine. You won't be
able to test the date download stuff because I haven't copied data
from the live web server. I'll update the live web server over the
weekend.
- changed Account View so that CSL members can view accounts for other labs
- added data download methods to CustomArray data
- added "otherDepartment" to Add Account so users can input a department that is not in the list
- alphabetically ordered department list
- allow update of department name when specifying otherDepartment in Lab Edit
- reorder list of orders when viewing and managing orders
Thursday, May 12, 2005
No changes to the application itself today but I did set up
Bioanalyzer, Affymetrix, and Custom Array data so that, when you
put the data into /data/csl/download/{directory} on cgrb-svr it will:
- automatically copy the data to /data/csl/backup/{directory}
- transfer the file to /home/web/webapps/csl/data2/{directory}/zip on the web server
When you enter this file name into the database, user's will be able to download the archived file.
Wednesday, May 11, 2005
Today's changes include:
Bioanalyzer:
- implemented ability to download Bioanalyzer data
Sequence:
- color fill full bulk orders in manage menu
- print both sample comment and order comment when marking orders
"inProgress"
- update sequence order now has a dropdown menu for primerSource
- removed test for primerName having a particular range of values when filling in samples
I have not updated the development web server with these changes yet. I'll do that tomorrow.
Tuesday, May 10, 2005
Last night, I copied up changes to:
- set the sequence primer name validation to allow someone to define a primer name not in the dropdown list even if it provided by the CSL.
- allow users to download Frag files in zip format (but not hqx yet).
- automatically email users account information when a new account is created for them.
Monday, May 2, 2005
Closed down the old ordering site so all users must now order through
the new site. Much still needs to be done to "complete" the
application and this log file will document application changes since
initial release (version 0.1 beta!).