Re: addfiles from thredds vs. looping through files

Hi Sam-

The URL with dodsC in it is an OPeNDAP URL and needs to point to a
specific file. You also can't use ls to list files on a remote server
via http.

You could request the catalog as XML (use .xml instead of .html) and
then parse that in NCL, but that would be pretty complicated.

Don

On 6/5/14 11:24 AM, Sam McClatchie (NOAA Federal) wrote:
> Colleagues
>
> I would like to subset some model output from a remote server that is
> not setup for opendap selection across files
> <http://oceanmodeling.pmc.ucsc.edu:8080/thredds/catalog/wc12.0_ccsra31_01/posterior/catalog.html>.
> I could just loop through each file in turn, but addfiles() would be a
> nicer way to access the whole directory of netcdf files, and concatenate
> a redimensioned subset. I have no problem accessing a single file in the
> directory using this code:
>
> filename =
> "http://oceanmodeling.pmc.ucsc.edu:8080/thredds/dodsC/wc12.0_coamps_woa_gls_v563_01/posterior/20140526_20140601_posterior_his.nc"
>
> exists = isfilepresent(filename)
> if(.not.exists) then
> print("OPeNDAP isfilepresent test unsuccessful.")
> print("Either file doesn't exist, or NCL does not have OPeNDAP
> capabilities on this system")
> else
> print("OPeNDAP isfilepresent test successful.")
> f = addfile(filename,"r")
> vars = getfilevarnames(f)
> print(vars) ; should be (in any order): "l","j","i","cross","aloan",
> ; "shot","order","bears"
> end if
>
> ;--------------------------------------
> ;;; output follows
> ---------------------------------------
>
> Copyright (C) 1995-2014 - All Rights Reserved
> University Corporation for Atmospheric Research
> NCAR Command Language Version 6.2.0
> The use of this software is governed by a License Agreement.
> See http://www.ncl.ucar.edu/ for more details.
> (0) OPeNDAP isfilepresent test successful.
>
>
> Variable: vars
> Type: string
> Total Size: 1008 bytes
> 126 values
> Number of Dimensions: 1
> Dimensions and sizes: [126]
> Coordinates:
> (0) ntimes
> (1) ndtfast
> (2) dt
> (3) dtfast
> (4) dstart
> (5) nHIS
> (6) ndefHIS
> (7) nRST
> (8) nADJ
> (9) ndefADJ
> (10) nTLM
> (11) ndefTLM
> (12) Nouter
> (13) Ninner
> (14) Falpha
> (15) Fbeta
> (16) Fgamma
> (17) nl_tnu2
> (18) ad_tnu2
> (19) tl_tnu2
> (20) nl_visc2
> (21) ad_visc2
> (22) tl_visc2
> (23) Akt_bak
> (24) Akv_bak
> (25) Akk_bak
> (26) Akp_bak
> (27) ad_Akt_fac
> (28) tl_Akt_fac
> (29) ad_Akv_fac
> (30) tl_Akv_fac
> (31) rdrg
> (32) rdrg2
> (33) Zob
> (34) Zos
> (35) gls_p
> (36) gls_m
> (37) gls_n
> (38) gls_cmu0
> (39) gls_c1
> (40) gls_c2
> (41) gls_c3m
> (42) gls_c3p
> (43) gls_sigk
> (44) gls_sigp
> (45) gls_Kmin
> (46) gls_Pmin
> (47) Charnok_alpha
> (48) Zos_hsig_alpha
> (49) sz_alpha
> (50) CrgBan_cw
> (51) Znudg
> (52) M2nudg
> (53) M3nudg
> (54) Tnudg
> (55) rho0
> (56) R0
> (57) Tcoef
> (58) Scoef
> (59) gamma2
> (60) LhessianEV
> (61) Lprecond
> (62) Lritz
> (63) GradErr
> (64) HevecErr
> (65) Nmethod
> (66) Rscheme
> (67) Nrandom
> (68) Hgamma
> (69) Vgamma
> (70) Hdecay
> (71) Vdecay
> (72) spherical
> (73) xl
> (74) el
> (75) Vtransform
> (76) Vstretching
> (77) theta_s
> (78) theta_b
> (79) Tcline
> (80) hc
> (81) s_rho
> (82) s_w
> (83) Cs_r
> (84) Cs_w
> (85) user
> (86) h
> (87) f
> (88) pm
> (89) pn
> (90) lon_rho
> (91) lat_rho
> (92) lon_u
> (93) lat_u
> (94) lon_v
> (95) lat_v
> (96) lon_psi
> (97) lat_psi
> (98) angle
> (99) mask_rho
> (100) mask_u
> (101) mask_v
> (102) mask_psi
> (103) ocean_time
> (104) zeta
> (105) ubar
> (106) DU_avg1
> (107) DU_avg2
> (108) vbar
> (109) DV_avg1
> (110) DV_avg2
> (111) u
> (112) v
> (113) w
> (114) temp
> (115) salt
> (116) AKv
> (117) AKt
> (118) AKs
> (119) shflux
> (120) ssflux
> (121) EminusP
> (122) sustr
> (123) svstr
> (124) bustr
> (125) bvstr
> [Finished in 0.6s]
> ;---------------------------------------------------------------------
> but when I try to access multiple files I have a problem:
> ;----------------------------------------------------------------------
> diri =
> "http://oceanmodeling.pmc.ucsc.edu:8080/thredds/dodsC/wc12.0_coamps_woa_gls_v563_01/posterior/"
> st = "ls " + diri + "*.*"
> fils = systemfunc(st)
> print(diri)
> print(st)
> print(fils)
> exit()
>
> ;--------------------------
> ;;; output follows:
> ;--------------------------
> ls: cannot access
> http://oceanmodeling.pmc.ucsc.edu:8080/thredds/dodsC/wc12.0_coamps_woa_gls_v563_01/posterior/*.*:
> No such file or directory
>
> Variable: diri
> Type: string
> Total Size: 8 bytes
> 1 values
> Number of Dimensions: 1
> Dimensions and sizes: [1]
> Coordinates:
> (0)
> http://oceanmodeling.pmc.ucsc.edu:8080/thredds/dodsC/wc12.0_coamps_woa_gls_v563_01/posterior/
>
>
> Variable: st
> Type: string
> Total Size: 8 bytes
> 1 values
> Number of Dimensions: 1
> Dimensions and sizes: [1]
> Coordinates:
> (0) ls
> http://oceanmodeling.pmc.ucsc.edu:8080/thredds/dodsC/wc12.0_coamps_woa_gls_v563_01/posterior/*.*
>
>
> Variable: fils
> Type: string
> Total Size: 8 bytes
> 1 values
> Number of Dimensions: 1
> Dimensions and sizes: [1]
> Coordinates:
> Number Of Attributes: 1
> _FillValue : missing
> (0) missing
> [Finished in 0.2s]
>
> ;-----------------------------------------------------------------
> I can easily list files in a local directory so I must be doing
> something silly when accessing the remote server?
>
> Thanks for any help,
> Sam
> --
> email signature Sam McClatchie,
> Supervisory oceanographer,
> Fisheries oceanography, Ichthyoplankton, Ship Operations
> Southwest Fisheries Science Center, NOAA,
> 8901 La Jolla Shores Dr.
> La Jolla, CA 92037-1509, U.S.A.
> email <Sam.McClatchie@noaa.gov>
> Office: 858 546 7083, Cellular: 858 752 8495
> Research home page <www.fishocean.info>
>
>
>
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>

--
Don Murray
NOAA/ESRL/PSD and CU-CIRES
303-497-3596
http://www.esrl.noaa.gov/psd/people/don.murray/
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Received on Thu Jun 05 05:48:44 2014