I'm relatively inexperienced in coding, so right now I'm just familiarizing myself with the basics of how to use SE, which I'll need to use in the near future.
At the moment I'm trying to get it to analyze a FITS file on my computer (which is a Mac). I'm sure this is something obvious, but I haven't been able to get it do that. Following the instructions in Chapters 6 and 7 of Source Extractor for Dummies (linked below), I input the following:
sex MedSpiral_20deg_Serl2_.45_.fits.fits -c configuration_file.txt
And got the following error message:
WARNING: configuration_file.txt not found, using internal defaults
----- SExtractor 2.19.5 started on 2020-02-05 at 17:10:59 with 1 thread
Setting catalog parameters
ERROR: can't read default.param
I then tried entering parameters manually:
sex MedSpiral_20deg_Ser12_.45_.fits.fits -c configuration_file.txt -DETECT_TYPE CCD -MAG_ZEROPOINT 2.5 -PIXEL_SCALE 0 -SATUR_LEVEL 1 -SEEING_FWHM 1
And got the same error message. I tried referencing default.sex directly:
sex MedSpiral_20deg_Ser12_.45_.fits.fits -c default.sex
And got the same error message again, substituting "configuration_file.txt not found" with "default.sex not found" (I checked that default.sex was on my computer, it is). The same thing happened when I tried to use default.param.
Here's the link to SE for Dummies (Chapter 6 begins on page 19):
http://astroa.physics.metu.edu.tr/MANUALS/sextractor/Guide2source_extractor.pdf
If you run the command "sex MedSpiral_20deg_Ser12_.45_fits.fits -c default.sex" within the config folder (within the sextractor folder), you will be able to run it.
However, I wonder how I can possibly run sextractor command from any folder in my computer?
Related
I had a Windows 10 machine working great with bq/gloud and gsutils all working great. Had to move to new machine and setting all of this back up. I cannot seem to get bq to recognize the entries in my .bigqueryrc file which was copied from my working machine. On my working machine, I am not using BIGQUERYRC environmental file, but just HOME, ie ~/.bigqueryrc
I say it does not seem to recognize is because if I introduce a random character I get an error about my .bigqueryrc file.
Let me first show that bq seems to be operating, overall, as expected
C:\Users\boyer>bq ls --project_id=broad-tapestry-sbx-boyer-14
datasetId
---------------
Broad_DataGov
Broad_EDW
Broad_Kitchen
Broad_Lake
Broad_Tableau
Broad_Utils
SHELL> bq ls brings nothing. The contents of my .biqqueryrc file is as thus:
credential_file = C:\Users\boyer\AppData\Roaming\gcloud\legacy_credentials\boyer#broadinstitute.org\singlestore_bq.json
project_id = broad-tapestry-sbx-boyer-14
[query]
--use_legacy_sql=false
Here is showing where my .bigqueryrc file is:
:\Users\boyer>ls -ls ~/.bigqueryrc
1 -rwx------+ 1 CHARLES+boyer CHARLES+boyer 198 Dec 22 12:48 /cygdrive/c/Users/boyer/.bigqueryrc
So, I try this and nothing happens either:
C:\Users\boyer>bq ls --bigqueryrc=c:/users/boyer/.bigqueryrc
C:\Users\boyer>bq ls --bigqueryrc=c:\users\boyer\.bigqueryrc
C:\Users\boyer>
But here is the error I purposefully introduced to see if it is actually looking at the file and it seems it is finding it.
C:\Users\boyer>bq ls --bigqueryrc=c:\users\boyer\.bigqueryrc
Unknown flag x found in bigqueryrc file in section global
The error above was introduced by adding a random 'x' character to the top of the file:
x
credential_file = C:\Users\boyer\AppData\Roaming\gcloud\legacy_credentials\boyer#broadinstitute.org\singlestore_bq.json
project_id = broad-tapestry-sbx-boyer-14
[query]
--use_legacy_sql=false
Background:
using postgres 11 on RDS, interface is psql on a Centos 7 box; objective is to show the source of certain stored procs / functions so that I can work with them
Problem description : When I attempt to list / show the source of a given stored function using the \df+ command which I understand to be correct for this use based on [official docs here](https://www.postgresql.org/docs/current/app-psql.html], an error is given as shown:
psql=> \df+ schema_foo.proc_bar;
ERROR: column p.proisagg does not exist
LINE 6: WHEN p.proisagg THEN 'agg'
I have no clue how to interpret this; the function in question does not contain the snippet of logic shown in the error, nor the column referenced there p.proisagg. I have verified this by opening the function in vim with \ef.
My guess based on several unrelated github issues that mention this same error for example is that it is in reference to some schema code internal to postgres.
Summary: in short, I can view the source of the functions using \ef, so my work is not impaired from a practical standpoint, however I wish to understand this error and why I'm encountering it with \df+.
I had the same issue and ran these 2 commands to fix it
sed -i "s/NOT pp.proisagg/pp.prokind='f'/g" /usr/share/phpPgAdmin/classes/database/Postgres.php
sed -i "s/NOT p.proisagg/p.prokind='f'/g" /usr/share/phpPgAdmin/classes/database/Postgres.php
I am currently working on making a CICD script to deploy a complex environment into another environment. We have multiple technology involved and I currently want to optimize this script because it's taking too much time to fetch information on each environment.
In the OpenShift 3.6 section, I need to get the last successful deployment for each application for a specific project. I try to find a quick way to do so, but right now I only found this solution :
oc rollout history dc -n <Project_name>
This will give me the following output
deploymentconfigs "<Application_name>"
REVISION STATUS CAUSE
1 Complete config change
2 Complete config change
3 Failed manual change
4 Running config change
deploymentconfigs "<Application_name2>"
REVISION STATUS CAUSE
18 Complete config change
19 Complete config change
20 Complete manual change
21 Failed config change
....
I then take this output and parse each line to know which is the latest revision that have the status "Complete".
In the above example, I would get this list :
<Application_name> : 2
<Application_name2> : 20
Then for each application and each revision I do :
oc rollout history dc/<Application_name> -n <Project_name> --revision=<Latest_Revision>
In the above example the Latest_Revision for Application_name is 2 which is the latest complete revision not building and not failed.
This will give me the output with the information I need which is the version of the ear and the version of the configuration that was used in the creation of the image use for this successful deployment.
But since I have multiple application, this process can take up to 2 minutes per environment.
Would anybody have a better way of fetching the information I required?
Unless I am mistaken, it looks like there are no "one liner" with the possibility to get the information on the currently running and accessible application.
Thanks
Assuming that the currently active deployment is the latest successful one, you may try the following:
oc get dc -a --no-headers | awk '{print "oc rollout history dc "$1" --revision="$2}' | . /dev/stdin
It gets a list of deployments, feeds it to awk to extract the name $1 and revision $2, then compiles your command to extract the details, finally sends it to standard input to execute. It may be frowned upon for not using xargs or the like, but I found it easier for debugging (just drop the last part and see the commands printed out).
UPDATE:
On second thoughts, you might actually like this one better:
oc get dc -a -o jsonpath='{range .items[*]}{.metadata.name}{"\n\t"}{.spec.template.spec.containers[0].env}{"\n\t"}{.spec.template.spec.containers[0].image}{"\n-------\n"}{end}'
The example output:
daily-checks
[map[name:SQL_QUERIES_DIR value:daily-checks/]]
docker-registry.default.svc:5000/ptrk-testing/daily-checks#sha256:b299434622b5f9e9958ae753b7211f1928318e57848e992bbf33a6e9ee0f6d94
-------
jboss-webserver31-tomcat
registry.access.redhat.com/jboss-webserver-3/webserver31-tomcat7-openshift#sha256:b5fac47d43939b82ce1e7ef864a7c2ee79db7920df5764b631f2783c4b73f044
-------
jtask
172.30.31.183:5000/ptrk-testing/app-txeq:build
-------
lifebicycle
docker-registry.default.svc:5000/ptrk-testing/lifebicycle#sha256:a93cfaf9efd9b806b0d4d3f0c087b369a9963ea05404c2c7445cc01f07344a35
You get the idea, with expressions like .spec.template.spec.containers[0].env you can reach for specific variables, labels, etc. Unfortunately the jsonpath output is not available with oc rollout history.
UPDATE 2:
You could also use post-deployment hooks to collect the data, if you can set up a listener for the hooks. Hopefully the information you need is inherited by the PODs. More info here: https://docs.openshift.com/container-platform/3.10/dev_guide/deployments/deployment_strategies.html#lifecycle-hooks
I'm doing some optimization using a model whose number of constraints and variables exceeds the cap for the student version of, say, AMPL, so I've found a webpage [http://www.neos-server.org/neos/solvers/milp:Gurobi/AMPL.html] which can solve my type of model.
I've found however that when using a solver where you can provide a commandfile (which I assume is the same as a .run file) the documentation of NEOS server tells that you should see the documentation of the input file. I'm using AMPL input which according to [http://www.neos-guide.org/content/FAQ#ampl_variables] should be able to print the decision variables using a command file with the appearance:
solve;
display _varname, _var;
The problem is that NEOS claim that you cannot add the:
data datafile;
model modelfile;
commands into the .run file, resulting in that the compiler cannot find the variables.
Does anyone know of a way to work around this?
Thanks in advance!
EDIT: If anyone else has this problem (which I believe many people have based on my Internet search). Try to remove any eventual reset; command from the .run file!
You don't need to specify model or data commands in the script file submitted to NEOS. It loads the model and data files automatically, solves the problem, and then executes the script (command file) you provide. For example submitting diet1.mod model diet1.dat data and this trivial command file
display _varname, _var;
produces the output which includes
: _varname _var :=
1 "Buy['Quarter Pounder w/ Cheese']" 0
2 "Buy['McLean Deluxe w/ Cheese']" 0
3 "Buy['Big Mac']" 0
4 "Buy['Filet-O-Fish']" 0
5 "Buy['McGrilled Chicken']" 0
6 "Buy['Fries, small']" 0
7 "Buy['Sausage McMuffin']" 0
8 "Buy['1% Lowfat Milk']" 0
9 "Buy['Orange Juice']" 0
;
As you can see this is the output from the display command.
I am posting here after asking the question at the openslice dds forum, and not receiving any reply.I am trying to use opensplice dds on a ubuntu machine. I am not sure if it serves as a proof of proper installation, but I have pasted my release.com file below. Now, I was able to run the ping pong example just fine. But when I ran the executable sac_helloworld_pub ( HelloWorld example in the C programming language), I got the following error
vishal#expmach:~/HDE/x86.linux2.6/examples/dcps/HelloWorld/c/standalone$ ./sac_helloworld_pub
Error in DDS_DomainParticipantFactory_create_participant: Creation failed: invalid handle
I did some searching, and it looks like I need to be running the ospl start command from the terminal. But when I do so, I get a No command ospl found message. Below is the release.comfile's contents
echo "<<< OpenSplice HDE Release V6.3.130716OSS For x86.linux2.6, Date 2013-07-30 >>>"
if [ "${SPLICE_ORB:=}" = "" ]
then
SPLICE_ORB=DDS_OpenFusion_1_6_1
export SPLICE_ORB
fi
if [ "${SPLICE_JDK:=}" = "" ]
then
SPLICE_JDK=jdk
export SPLICE_JDK
fi
OSPL_HOME="/home/vishal/HDE/x86.linux2.6"
OSPL_TARGET=x86.linux2.6
PATH=$OSPL_HOME/bin:$PATH
LD_LIBRARY_PATH=$OSPL_HOME/lib${LD_LIBRARY_PATH:+:}$LD_LIBRARY_PATH
CPATH=$OSPL_HOME/include:$OSPL_HOME/include/sys:${CPATH:=}
OSPL_URI=file://$OSPL_HOME/etc/config/ospl.xml
OSPL_TMPL_PATH=$OSPL_HOME/etc/idlpp
. $OSPL_HOME/etc/java/defs.$SPLICE_JDK
export OSPL_HOME OSPL_TARGET PATH LD_LIBRARY_PATH CPATH OSPL_TMPL_PATH OSPL_URI
$#
release.com (END)
Sorry for the holidays-driven lack of 'reactivity' on the OpenSplice forum .. I've answered your question there though ..
Here's that same answer for completeness:
*For the 6.3 community-edition, the deployment-model changed from shared-memory (v5.x) to the so-called single-process standalone deployment mode where the middleware is simply linked (as libraries) with the application so you don't need to start any daemons first (as was the case for the federated 'shared-memory' mode that was the default in V5).
So its OK that you get the error when trying to call 'ospl' as thats not used anymore so isn't in the distribution.
Now to your issue, your release.com looks OK to me, but perhaps you didn't actually 'source' it in your environment i.e. calling it with a '.' in front of it:
promtp> . release.com
you can verify that by doing an 'echo $OSPL_HOME' in your shell and see if it actually shows the value of the env. variable as set by the release.com.
Hope that helps,
-Hans*