Open hermands opened 9 years ago
I just ran ./flowanal.py -vvv make_ML_HDF5 --tubes "Hodgkin"
Running into a problem with db.query? Any suggestions?
Error message below:
INFO query_database 39 Querying...
Traceback (most recent call last):
File "./flowanal.py", line 7, in
I'll take a peak tomorrow
I am missing the point. What is the goal of this script?
How is it different from the make_ML_input I made on Friday/Saturday?
Issue with query is probably that getCaseAnnotations is not a listed function. This is a remnant of our previous model in which the case annotations came from the db. I have not written the function that exports annotation from db. make_ML_input is just built to take the text files.
use 1) dev/test_run.sh 2) direct call to make features. 3) dev/test_run_custom.sh
Sorry, I didn't notice make_ML_input and make_ML_HDF5 were similar files. Your comment on Issue 46 suggested this was not yet done (as it was assigned to me) so I probably duplicated this work.
On Thu, Jan 15, 2015 at 7:43 AM, Daniel Herman notifications@github.com wrote:
Issue with query is probably that getCaseAnnotations is not a listed function. This is a remnant of our previous model in which the case annotations came from the db. I have not written the function that exports annotation from db. make_ML_input is just built to take the text files.
use 1) dev/test_run.sh 2) direct call to make features. 3) dev/test_run_custom.sh
— Reply to this email directly or view it on GitHub https://github.com/davidpng/FCS_Database/issues/46#issuecomment-70104943 .
I had assigned to you because I was done and handing it off to you to work with / try out. I should have commented as such. Sorry.
-Dan
On Jan 15, 2015, at 7:54 AM, David Ng notifications@github.com wrote:
Sorry, I didn't notice make_ML_input and make_ML_HDF5 were similar files. Your comment on Issue 46 suggested this was not yet done (as it was assigned to me) so I probably duplicated this work.
On Thu, Jan 15, 2015 at 7:43 AM, Daniel Herman notifications@github.com wrote:
Issue with query is probably that getCaseAnnotations is not a listed function. This is a remnant of our previous model in which the case annotations came from the db. I have not written the function that exports annotation from db. make_ML_input is just built to take the text files.
use 1) dev/test_run.sh 2) direct call to make features. 3) dev/test_run_custom.sh
— Reply to this email directly or view it on GitHub https://github.com/davidpng/FCS_Database/issues/46#issuecomment-70104943 .
— Reply to this email directly or view it on GitHub.
I should have been more careful with names. I spent a lot of time to get it to work...sorry if you did also. We walked through this script together on Friday.
-Dan
On Jan 15, 2015, at 7:54 AM, David Ng notifications@github.com wrote:
Sorry, I didn't notice make_ML_input and make_ML_HDF5 were similar files. Your comment on Issue 46 suggested this was not yet done (as it was assigned to me) so I probably duplicated this work.
On Thu, Jan 15, 2015 at 7:43 AM, Daniel Herman notifications@github.com wrote:
Issue with query is probably that getCaseAnnotations is not a listed function. This is a remnant of our previous model in which the case annotations came from the db. I have not written the function that exports annotation from db. make_ML_input is just built to take the text files.
use 1) dev/test_run.sh 2) direct call to make features. 3) dev/test_run_custom.sh
— Reply to this email directly or view it on GitHub https://github.com/davidpng/FCS_Database/issues/46#issuecomment-70104943 .
— Reply to this email directly or view it on GitHub.
No, its my fault, I should have remembered we walked through it. Its actually a good thing I went through it because I had to modify some of the HDF5_IO functions to handle panda series objects and incorporate the passage of bin descriptions and other meta data from Feature_IO to MLInput_IO hdf5 files.
On Thu, Jan 15, 2015 at 8:08 AM, Daniel Herman notifications@github.com wrote:
I should have been more careful with names. I spent a lot of time to get it to work...sorry if you did also. We walked through this script together on Friday.
-Dan
On Jan 15, 2015, at 7:54 AM, David Ng notifications@github.com wrote:
Sorry, I didn't notice make_ML_input and make_ML_HDF5 were similar files. Your comment on Issue 46 suggested this was not yet done (as it was assigned to me) so I probably duplicated this work.
On Thu, Jan 15, 2015 at 7:43 AM, Daniel Herman notifications@github.com
wrote:
Issue with query is probably that getCaseAnnotations is not a listed function. This is a remnant of our previous model in which the case annotations came from the db. I have not written the function that exports annotation from db. make_ML_input is just built to take the text files.
use 1) dev/test_run.sh 2) direct call to make features. 3) dev/test_run_custom.sh
— Reply to this email directly or view it on GitHub < https://github.com/davidpng/FCS_Database/issues/46#issuecomment-70104943> .
— Reply to this email directly or view it on GitHub.
— Reply to this email directly or view it on GitHub https://github.com/davidpng/FCS_Database/issues/46#issuecomment-70109596 .
Needs some QC/QI.
Subcommand:
Class: ML_DATA_HDF5_IO