subject:"Bug#861736\:"

Bug#861736: closed by Andreas Tille (Bug#861736: fixed in nexus 4.3.2-svn1921-5)

2017-10-16 Thread Gilles Filippini

Control: tags -1 + patch

Hi,

On Fri, 12 May 2017 08:32:28 +0200 Marc Rosanes  wrote:
> Hi,
> 
> We have found that python-nxs is still affected by problems:
> 
> The following piece of code fails on stretch + the lastest nexus from 
> unstable:
> 
> ```
> import nxs
> f = nxs.open("/tmp/foo.h5", "w5")
> f.makegroup('entry', 'NXentry')
> f.opengroup('entry')
> f.makegroup('g', 'NXcollection')
> f.opengroup('g', 'NXcollection')
> f.makedata('d', 'float64', shape=(1,))
> f.opendata('d')
> f.putdata(1.23)
> f.closedata()
> f.closegroup()
> f.flush()
> f.close()
> ```
> 
> 
> It fails with the exception:
> 
> ```
> Traceback (most recent call last):
>File "nxs_flush_bug.py", line 12, in 
>  f.flush()
>File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 397, in flush
>  raise NeXusError, "Could not flush NeXus file %s"%(self.filename)
> nxs.napi.NeXusError: Could not flush NeXus file /tmp/foo.h5
> ```
> 
> 
> The same code works correctly on a clean jessie docker.
> 
> This ticket should be reopened, till this issue is solved.
> 
> 
> 
> 
> On 05/11/2017 11:12 AM, Debian Bug Tracking System wrote:
> > This is an automatic notification regarding your Bug report
> > which was filed against the python-nxs package:
> >
> > #861736: python-nxs: Cannot save files with nxs python module
> >
> > It has been closed by Andreas Tille .
> >
> > Their explanation is attached below along with your original report.
> > If this explanation is unsatisfactory and you have not received a
> > better one in a separate message then please contact Andreas Tille 
> >  by
> > replying to this email.

New patch proposal attached. It fixes #866925 as well.

Thanks,

_g.
diff -Nru nexus-4.3.2-svn1921/debian/changelog 
nexus-4.3.2-svn1921/debian/changelog
--- nexus-4.3.2-svn1921/debian/changelog2017-05-11 09:23:17.0 
+0200
+++ nexus-4.3.2-svn1921/debian/changelog2017-10-11 19:15:12.0 
+0200
@@ -1,3 +1,12 @@
+nexus (4.3.2-svn1921-5.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * debian/control: switch B-D from libhdf4g-dev to libhdf4-dev (closes:
+#866925)
+  * Fix patch hdf5-1.10-support.patch (closes: #861736)
+
+ -- Gilles Filippini   Wed, 11 Oct 2017 19:15:12 +0200
+
 nexus (4.3.2-svn1921-5) unstable; urgency=medium
 
   * Team upload.
diff -Nru nexus-4.3.2-svn1921/debian/control nexus-4.3.2-svn1921/debian/control
--- nexus-4.3.2-svn1921/debian/control  2017-05-11 09:23:17.0 +0200
+++ nexus-4.3.2-svn1921/debian/control  2017-10-11 19:15:10.0 +0200
@@ -8,7 +8,7 @@
debhelper (>= 7),
default-jdk | java2-sdk,
dh-python,
-   libhdf4g-dev,
+   libhdf4-dev,
libhdf5-dev,
libmxml-dev,
libtool,
diff -Nru nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch 
nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch
--- nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch  2017-05-11 
09:23:17.0 +0200
+++ nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch  2017-10-11 
19:15:12.0 +0200
@@ -1,11 +1,16 @@
 Description: HDF5 1.10.x uses 64 bit handles. They're not int anymore.
 Author: Gilles Filippini 
 Bug-Debian: https://bugs.debian.org/861736
-Index: nexus-4.3.2-svn1921/src/napi5.c
+Index: nexus/src/napi5.c
 ===
 nexus-4.3.2-svn1921.orig/src/napi5.c
-+++ nexus-4.3.2-svn1921/src/napi5.c
-@@ -54,12 +54,12 @@ extern  void *NXpData;
+--- nexus.orig/src/napi5.c
 nexus/src/napi5.c
+@@ -50,16 +50,16 @@ extern  void *NXpData;
+   typedef struct __NexusFile5 {
+ struct iStack5 {
+   char irefn[1024];
+-  int iVref;
++  hid_t iVref;
hsize_t iCurrentIDX;
  } iStack5[NXMAXSTACK];
  struct iStack5 iAtt5;


signature.asc
Description: OpenPGP digital signature

Bug#861736: closed by Andreas Tille (Bug#861736: fixed in nexus 4.3.2-svn1921-5)

2017-05-11 Thread Marc Rosanes


Hi,

We have found that python-nxs is still affected by problems:

The following piece of code fails on stretch + the lastest nexus from 
unstable:


```
import nxs
f = nxs.open("/tmp/foo.h5", "w5")
f.makegroup('entry', 'NXentry')
f.opengroup('entry')
f.makegroup('g', 'NXcollection')
f.opengroup('g', 'NXcollection')
f.makedata('d', 'float64', shape=(1,))
f.opendata('d')
f.putdata(1.23)
f.closedata()
f.closegroup()
f.flush()
f.close()
```


It fails with the exception:

```
Traceback (most recent call last):
  File "nxs_flush_bug.py", line 12, in 
f.flush()
  File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 397, in flush
raise NeXusError, "Could not flush NeXus file %s"%(self.filename)
nxs.napi.NeXusError: Could not flush NeXus file /tmp/foo.h5
```


The same code works correctly on a clean jessie docker.

This ticket should be reopened, till this issue is solved.




On 05/11/2017 11:12 AM, Debian Bug Tracking System wrote:

This is an automatic notification regarding your Bug report
which was filed against the python-nxs package:

#861736: python-nxs: Cannot save files with nxs python module

It has been closed by Andreas Tille .

Their explanation is attached below along with your original report.
If this explanation is unsatisfactory and you have not received a
better one in a separate message then please contact Andreas Tille 
 by
replying to this email.




--
Marc Rosanes Siscart

Computing & Control Division
CELLS – ALBA

ALBA Synchrotron Light Facility
Carrer de la Llum 2-26
08290 Cerdanyola del Vallès, Barcelona (SPAIN)

Tel: +34 93 592 40 41 Fax: +34 93 592 43 01
web page: http://www.cells.es/

Bug#861736: Still some regression in python-nxs

2017-05-11 Thread Carlos Pascual

Hi,

while nexus 4.3.2-svn1921-5 fixes the originally reported exception, the
fix seems not to be complete [1].

In order to trigger the still-existing regression, run the following
python code (which ideally should exit without errors):

```
import nxs
f = nxs.open("/tmp/foo.h5", "w5")
f.makegroup('entry', 'NXentry')
f.opengroup('entry')
f.makegroup('g', 'NXcollection')
f.opengroup('g', 'NXcollection')
f.makedata('d', 'float64', shape=(1,))
f.opendata('d')
f.putdata(1.23)
f.closedata()
f.closegroup()
f.flush()
f.close()
```

In stretch + nexus_4.3.2-svn1921-5, it fails with the following
exception:

```
Traceback (most recent call last):
  File "nxs_flush_bug.py", line 12, in 
f.flush()
  File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 397, in flush
raise NeXusError, "Could not flush NeXus file %s"%(self.filename)
nxs.napi.NeXusError: Could not flush NeXus file /tmp/foo.h5
```

The same code works well when run on a clean jessie (I used an official
debian:stable docker) and it fails with the same exception as above when
run on sid (I used the official debian:unstable docker)

Cheers,

Carlos

[1] I am replying here because this new problem seems likely to be related
with 861736, but if you think that it may be an unrelated bug I'd be glad
to open a new bug

Bug#861736:

2017-05-11 Thread PICCA Frederic-Emmanuel

here the error message

~/Debian/nexus/bugs$ ./bug.py
Traceback (most recent call last):
  File "./bug.py", line 15, in 
f.flush()
  File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 397, in flush
raise NeXusError, "Could not flush NeXus file %s"%(self.filename)
nxs.napi.NeXusError: Could not flush NeXus file /tmp/foo.h5

Bug#861736:

2017-05-11 Thread PICCA Frederic-Emmanuel

It seems that the fix is not enought

this test failed at the flush

import nxs
f = nxs.open("/tmp/foo.h5", "w5")
f.makegroup('entry', 'NXentry')
f.opengroup('entry')
f.makegroup('g', 'NXcollection')
f.opengroup('g', 'NXcollection')
f.makedata('d', 'float64', shape=(1,))
f.opendata('d')
f.putdata(1.23)
f.closedata()
f.closegroup()
f.flush()
f.close()

Bug#861736:

2017-05-09 Thread Gilles Filippini

Control: tags -1 + patch

On Mon, 8 May 2017 14:34:31 + PICCA Frederic-Emmanuel
 wrote:
> Here after rebuilding hdf5 in debug mode
> 
> :~/Debian/nexus$ ./bug.py
> H5get_libversion(majnum=0xbf8a5b04, minnum=0xbf8a5b08, relnum=0xbf8a5b0c) = 
> SUCCEED;
> H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
> H5open() = SUCCEED;
> H5Pcreate(cls=8 (genprop class)) = 18 (genprop list);
> H5Pget_cache(plist=18 (genprop list), mdc_nelmts=0xbf8a5af8, 
> rdcc_nslots=0xbf8a5afc, rdcc_nbytes=0xbf8a5b00, rdcc_w0=0xbf8a5b10) = SUCCEED;
> H5Pset_cache(plist=18 (genprop list), mdc_nelmts=0, rdcc_nslots=521, 
> rdcc_nbytes=1024000, rdcc_w0=0.75) = SUCCEED;
> H5Pset_fclose_degree(plist=18 (genprop list), degree=H5F_CLOSE_STRONG) = 
> SUCCEED;
> H5check_version(majnum=1, minnum=10, relnum=0) = SUCCEED;
> H5open() = SUCCEED;
> H5Fcreate(filename=0x82517ef8, flags=2, fcpl=H5P_DEFAULT, fapl=18 (genprop 
> list)) = 0 (file);
> H5Pclose(plist=18 (genprop list)) = SUCCEED;
> ERROR: cannot open file: filenamenxs.h5
> Traceback (most recent call last):
>   File "./bug.py", line 5, in 
> e.save("filenamenxs.h5", 'w5')
>   File "/usr/lib/python2.7/dist-packages/nxs/tree.py", line 868, in save
> file = NeXusTree(filename, format)
>   File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 320, in __init__
> raise NeXusError, "Could not %s %s"%(op,filename)

This error and others are caused by HDF5 handles being stored as int
instead of hid_t. This type changed from int to int64_t with release
1.10.0 of HDF5.

Please find attached a patch proposal.

Thanks,

_g.
diff -Nru nexus-4.3.2-svn1921/debian/changelog 
nexus-4.3.2-svn1921/debian/changelog
--- nexus-4.3.2-svn1921/debian/changelog2016-07-22 23:05:27.0 
+0200
+++ nexus-4.3.2-svn1921/debian/changelog2017-05-09 19:49:46.0 
+0200
@@ -1,3 +1,11 @@
+nexus (4.3.2-svn1921-5) UNRELEASED; urgency=medium
+
+  * QA upload.
+  * New patch hdf5-1.10-support.patch to fix incorrect type for HDF5
+handles: should be hid_t instead of int (closes: #861736)
+
+ -- Gilles Filippini   Tue, 09 May 2017 19:49:46 +0200
+
 nexus (4.3.2-svn1921-4) unstable; urgency=medium
 
   * QA upload.
diff -Nru nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch 
nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch
--- nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch  1970-01-01 
01:00:00.0 +0100
+++ nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch  2017-05-09 
19:49:46.0 +0200
@@ -0,0 +1,111 @@
+Description: HDF5 1.10.x uses 64 bit handles. They're not int anymore.
+Author: Gilles Filippini 
+Bug-Debian: https://bugs.debian.org/861736
+Index: nexus-4.3.2-svn1921/src/napi5.c
+===
+--- nexus-4.3.2-svn1921.orig/src/napi5.c
 nexus-4.3.2-svn1921/src/napi5.c
+@@ -54,12 +54,12 @@ extern  void *NXpData;
+   hsize_t iCurrentIDX;
+ } iStack5[NXMAXSTACK];
+ struct iStack5 iAtt5;
+-int iFID;
+-int iCurrentG;
+-int iCurrentD;
+-int iCurrentS;
+-int iCurrentT;
+-int iCurrentA;
++hid_t iFID;
++hid_t iCurrentG;
++hid_t iCurrentD;
++hid_t iCurrentS;
++hid_t iCurrentT;
++hid_t iCurrentA;
+ int iNX;
+ int iNXID;
+ int iStackPtr;
+@@ -434,7 +434,7 @@ NXstatus  NX5open(CONSTCHAR *filename, N
+   NXstatus  NX5makegroup (NXhandle fid, CONSTCHAR *name, CONSTCHAR *nxclass) 
+   {
+ pNexusFile5 pFile;
+-herr_t iRet;
++hid_t iRet;
+ hid_t iVID;
+ hid_t attr1,aid1, aid2;
+ char pBuffer[1024] = "";
+@@ -487,7 +487,7 @@ NXstatus  NX5open(CONSTCHAR *filename, N
+ 
+ pNexusFile5 pFile;
+ hid_t attr1, atype;
+-herr_t iRet;
++hid_t iRet;
+ char pBuffer[1024];
+ char data[128];
+   
+@@ -654,7 +654,7 @@ static hid_t nxToHDF5Type(int datatype)
+ int compress_type, int64_t 
chunk_size[])
+   {
+   hid_t datatype1, dataspace, iNew;
+-  herr_t iRet;
++  hid_t iRet;
+   hid_t type, cparms = -1;
+   pNexusFile5 pFile;
+   char pBuffer[256];
+@@ -992,8 +992,8 @@ static hid_t nxToHDF5Type(int datatype)
+ return NX_OK;
+   }
+ /*--*/
+-static int getAttVID(pNexusFile5 pFile){
+-  int vid;
++static hid_t getAttVID(pNexusFile5 pFile){
++  hid_t vid;
+  if(pFile->iCurrentG == 0 && pFile->iCurrentD == 0){
+/* global attribute */
+vid = H5Gopen(pFile->iFID,"/", H5P_DEFAULT);
+@@ -1007,7 +1007,7 @@ static int getAttVID(pNexusFile5 pFile){
+  return vid;
+ }
+ /*---*/
+-static void killAttVID(pNexusFile5 pFile, int vid){
++static void killAttVID(pNexusFile5 pFile, hid_t vid){
+   if(pFile->iCurrentG == 0 && pFile->iCurrentD == 0){
+ H5Gclose(vid);
+   }
+@@ -1021,8 +1

Bug#861736:

2017-05-08 Thread PICCA Frederic-Emmanuel

Here after rebuilding hdf5 in debug mode

:~/Debian/nexus$ ./bug.py
H5get_libversion(majnum=0xbf8a5b04, minnum=0xbf8a5b08, relnum=0xbf8a5b0c) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5open() = SUCCEED;
H5Pcreate(cls=8 (genprop class)) = 18 (genprop list);
H5Pget_cache(plist=18 (genprop list), mdc_nelmts=0xbf8a5af8, 
rdcc_nslots=0xbf8a5afc, rdcc_nbytes=0xbf8a5b00, rdcc_w0=0xbf8a5b10) = SUCCEED;
H5Pset_cache(plist=18 (genprop list), mdc_nelmts=0, rdcc_nslots=521, 
rdcc_nbytes=1024000, rdcc_w0=0.75) = SUCCEED;
H5Pset_fclose_degree(plist=18 (genprop list), degree=H5F_CLOSE_STRONG) = 
SUCCEED;
H5check_version(majnum=1, minnum=10, relnum=0) = SUCCEED;
H5open() = SUCCEED;
H5Fcreate(filename=0x82517ef8, flags=2, fcpl=H5P_DEFAULT, fapl=18 (genprop 
list)) = 0 (file);
H5Pclose(plist=18 (genprop list)) = SUCCEED;
ERROR: cannot open file: filenamenxs.h5
Traceback (most recent call last):
  File "./bug.py", line 5, in 
e.save("filenamenxs.h5", 'w5')
  File "/usr/lib/python2.7/dist-packages/nxs/tree.py", line 868, in save
file = NeXusTree(filename, format)
  File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 320, in __init__
raise NeXusError, "Could not %s %s"%(op,filename)
nxs.napi.NeXusError: Could not create filenamenxs.h5
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a6954, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6898) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a689c, client_data=0xbf8a68a0) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6858) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a685c, client_data=0xbf8a6860) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6858) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a685c, client_data=0xbf8a6860) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6888) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a688c, client_data=0xbf8a6890) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6888) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a688c, client_data=0xbf8a6890) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6888) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a688c, client_data=0xbf8a6890) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6898) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a689c, client_data=0xbf8a68a0) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6868) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a686c, client_data=0xbf8a6870) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6868) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a686c, client_data=0xbf8a6870) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eauto_is_v2(estack=H5P_DEFAULT, is_stack=0xbf8a6868) = SUCCEED;
H5Eget_auto2(estack=H5P_DEFAULT, func=0xbf8a686c, client_data=0xbf8a6870) = 
SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;
H5Eset_auto2(estack=H5P_DEFAULT, func=NULL, client_data=NULL) = SUCCEED;

Bug#861736:

2017-05-07 Thread PICCA Frederic-Emmanuel

activating the NXError reporting we got

filenamenxs.h5 5 
ERROR: cannot open file: filenamenxs.h5
0


and looking for this errormessage,

we found it in the napi5.c file



NXstatus  NX5open(CONSTCHAR *filename, NXaccess am, 
 NXhandle* pHandle)
  {
  hid_t attr1,aid1, aid2, iVID;
  pNexusFile5 pNew = NULL;
  char pBuffer[512];
  char *time_buffer = NULL;
  char version_nr[10];
  unsigned int vers_major, vers_minor, vers_release, am1 ;
  hid_t fapl = -1; 
  int mdc_nelmts;
  size_t rdcc_nelmts;
  size_t rdcc_nbytes;
  double rdcc_w0;
  unsigned hdf5_majnum, hdf5_minnum, hdf5_relnum;

  *pHandle = NULL;

  if (H5get_libversion(&hdf5_majnum, &hdf5_minnum, &hdf5_relnum) < 0)
  {
  NXReportError("ERROR: cannot determine HDF5 library version");
  return NX_ERROR;
  }
  if (hdf5_majnum == 1 && hdf5_minnum < 8)
  {
  NXReportError("ERROR: HDF5 library 1.8.0 or higher required");
  return NX_ERROR;
  }

  /* mask of any options for now */
  am = (NXaccess)(am & NXACCMASK_REMOVEFLAGS);

  /* turn off the automatic HDF error handling */  
  H5Eset_auto(H5E_DEFAULT, NULL, NULL);  
#ifdef USE_FTIME
struct timeb timeb_struct;
#endif 


pNew = (pNexusFile5) malloc (sizeof (NexusFile5));
if (!pNew) {
  NXReportError("ERROR: not enough memory to create file structure");
  return NX_ERROR;
}
memset (pNew, 0, sizeof (NexusFile5));


/* start HDF5 interface */
if (am == NXACC_CREATE5) {  
   fapl = H5Pcreate(H5P_FILE_ACCESS);
   H5Pget_cache(fapl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0);
   rdcc_nbytes=(size_t)nx_cacheSize;
   H5Pset_cache(fapl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0);
   H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
   am1 = H5F_ACC_TRUNC;
   pNew->iFID = H5Fcreate (filename, am1, H5P_DEFAULT, fapl);
} else {
   if (am == NXACC_READ) {
  am1 = H5F_ACC_RDONLY;
} else {
  am1 = H5F_ACC_RDWR;
}
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
pNew->iFID = H5Fopen (filename, am1, fapl);
}  
if(fapl != -1) {
  H5Pclose(fapl);
}
if (pNew->iFID <= 0) {
  sprintf (pBuffer, "ERROR: cannot open file: %s", filename);
  NXReportError( pBuffer);
  free (pNew);
  return NX_ERROR;
}

Bug#861736:

2017-05-07 Thread PICCA Frederic-Emmanuel

Herethe code ofthismethod

/**/
static NXstatus   NXinternalopen(CONSTCHAR *userfilename, NXaccess am, 
   pFileStack fileStack);
/*--*/
NXstatus   NXopen(CONSTCHAR *userfilename, NXaccess am, NXhandle *gHandle){
  int status;
  pFileStack fileStack = NULL;

  *gHandle = NULL;
  fileStack = makeFileStack();
  if(fileStack == NULL){
NXReportError("ERROR: no memory to create filestack");
  return NX_ERROR;
  }
  status = NXinternalopen(userfilename,am,fileStack);
  if(status == NX_OK){
*gHandle = fileStack;
  }

  return status;


so lets's see the internalopen


static NXstatus   NXinternalopen(CONSTCHAR *userfilename, NXaccess am, 
pFileStack fileStack)
{
return LOCKED_CALL(NXinternalopenImpl(userfilename, am, fileStack));
}



/*---*/
static NXstatus   NXinternalopenImpl(CONSTCHAR *userfilename, NXaccess am, 
pFileStack fileStack)
  {
int hdf_type=0;
int iRet=0;
NXhandle hdf5_handle = NULL;
pNexusFunction fHandle = NULL;
NXstatus retstat = NX_ERROR;
char error[1024];
char *filename = NULL;
int my_am = (am & NXACCMASK_REMOVEFLAGS);

/* configure fortify 
iFortifyScope = Fortify_EnterScope();
Fortify_CheckAllMemory();
*/

/*
  allocate data
*/
fHandle = (pNexusFunction)malloc(sizeof(NexusFunction));
if (fHandle == NULL) {
  NXReportError("ERROR: no memory to create Function structure");
  return NX_ERROR;
}
memset(fHandle, 0, sizeof(NexusFunction)); /* so any functions we miss are 
NULL */
   
/*
  test the strip flag. Elimnate it for the rest of the tests to work
*/
fHandle->stripFlag = 1;
if(am & NXACC_NOSTRIP){
  fHandle->stripFlag = 0;
  am = (NXaccess)(am & ~NXACC_NOSTRIP);
}
fHandle->checkNameSyntax = 0;
if (am & NXACC_CHECKNAMESYNTAX) {
fHandle->checkNameSyntax = 1;
am = (NXaccess)(am & ~NXACC_CHECKNAMESYNTAX);
}


if (my_am==NXACC_CREATE) {
  /* HDF4 will be used ! */
  hdf_type=1;
  filename = strdup(userfilename);
} else if (my_am==NXACC_CREATE4) {
  /* HDF4 will be used ! */
  hdf_type=1;   
  filename = strdup(userfilename);
} else if (my_am==NXACC_CREATE5) {
  /* HDF5 will be used ! */
  hdf_type=2;   
  filename = strdup(userfilename);
} else if (my_am==NXACC_CREATEXML) {
  /* XML will be used ! */
  hdf_type=3;   
  filename = strdup(userfilename);
} else {
  filename = locateNexusFileInPath((char *)userfilename);
  if(filename == NULL){
NXReportError("Out of memory in NeXus-API");
free(fHandle);
return NX_ERROR;
  }
  /* check file type hdf4/hdf5/XML for reading */
  iRet = determineFileType(filename);
  if(iRet < 0) {
snprintf(error,1023,"failed to open %s for reading",
 filename);
NXReportError(error);
free(filename);
return NX_ERROR;
  }
  if(iRet == 0){
snprintf(error,1023,"failed to determine filetype for %s ",
 filename);
NXReportError(error);
free(filename);
free(fHandle);
return NX_ERROR;
  }
  hdf_type = iRet;
}
if(filename == NULL){
NXReportError("Out of memory in NeXus-API");
return NX_ERROR;
}

if (hdf_type==1) {
  /* HDF4 type */
#ifdef HDF4
NXhandle hdf4_handle = NULL;
  retstat = NX4open((const char *)filename,am,&hdf4_handle);
  if(retstat != NX_OK){
free(fHandle);
free(filename);
return retstat;
  }
  fHandle->pNexusData=hdf4_handle;
  NX4assignFunctions(fHandle);
  pushFileStack(fileStack,fHandle,filename);
#else
  NXReportError(
 "ERROR: Attempt to create HDF4 file when not linked with HDF4");
  retstat = NX_ERROR;
#endif /* HDF4 */
  free(filename);
  return retstat; 
} else if (hdf_type==2) {
  /* HDF5 type */
#ifdef HDF5
  retstat = NX5open(filename,am,&hdf5_handle);
  if(retstat != NX_OK){
free(fHandle);
free(filename);
return retstat;
  }
  fHandle->pNexusData=hdf5_handle;
  NX5assignFunctions(fHandle);
  pushFileStack(fileStack,fHandle, filename);
#else
  NXReportError(
 "ERROR: Attempt to create HDF5 file when not linked with HDF5");
  retstat = NX_ERROR;
#endif /* HDF5 */
  free(filename);
  return retstat;
} else if(hdf_type == 3){
  /*
XML type
  */
#ifdef NXXML
NXhandle xmlHandle = NULL;
  retstat = NXXopen(filename,am,&xmlHandle);
  if(retstat != NX_OK){
free(fHandle);
free(filename);
return retstat;
  }
  fHandle->pNexusData=xmlHandle;
  NXXassignFunctions(fHandle);
  pushFileStack(fileSta

Bug#861736:

2017-05-07 Thread PICCA Frederic-Emmanuel

in the napi.h files we saw this.

define CONCAT(__a,__b) __a##__b/* token concatenation */

#ifdef __VMS
#define MANGLE(__arg)   __arg
#else
#define MANGLE(__arg)   CONCAT(__arg,_)
#endif

#define NXopen  MANGLE(nxiopen)

 /**
   * Open a NeXus file.
   * NXopen honours full path file names. But it also searches
   * for files in all the paths given in the NX_LOAD_PATH environment variable.
   * NX_LOAD_PATH is supposed to hold a list of path string separated by the 
platform
   * specific path separator. For unix this is the : , for DOS the ; . Please 
note
   * that crashing on an open NeXus file will result in corrupted data. Only 
after a NXclose
   * or a NXflush will the data file be valid.
   * \param filename The name of the file to open
   * \param access_method The file access method. This can be:
   * \li NXACC__READ read access
   * \li NXACC_RDWR read write access
   * \li NXACC_CREATE, NXACC_CREATE4 create a new HDF-4 NeXus file
   * \li NXACC_CREATE5 create a new HDF-5 NeXus file
   * \li NXACC_CREATEXML create an XML NeXus file.
   * see #NXaccess_mode
   * Support for HDF-4 is deprecated.
   * \param pHandle A file handle which will be initialized upon successfull 
completeion of NXopen.
   * \return NX_OK on success, NX_ERROR in the case of an error.
   * \ingroup c_init
   */
extern  NXstatus  NXopen(CONSTCHAR * filename, NXaccess access_method, 
NXhandle* pHandle);


so we need to check in this method what is going on.

Bug#861736:

2017-05-07 Thread PICCA Frederic-Emmanuel

Let's instrument the code

print filename, mode, _ref(self.handle)
status = nxlib.nxiopen_(filename,mode,_ref(self.handle))
print status

$ python bug.py
filenamenxs.h5 5 
0

Bug#861736:

2017-05-07 Thread PICCA Frederic-Emmanuel

Hello


here the napi code which cause some trouble.

# Convert open mode from string to integer and check it is valid
if mode in _nxopen_mode: mode = _nxopen_mode[mode]
if mode not in _nxopen_mode.values():
raise ValueError, "Invalid open mode %s",str(mode)

self.filename, self.mode = filename, mode
self.handle = c_void_p(None)
self._path = []
self._indata = False
status = nxlib.nxiopen_(filename,mode,_ref(self.handle))
if status == ERROR:
if mode in [ACC_READ, ACC_RDWR]:
op = 'open'
else:
op = 'create'
raise NeXusError, "Could not %s %s"%(op,filename)


Soit seems that the nxlib.nxiopen_ method return an error

Bug#861736: python-nxs: Cannot save files with nxs python module

2017-05-05 Thread Axel Beckert

Control: tag -1 + confirmed
Control: user debian-rele...@lists.debian.org
Control: usertag -1 + bsp-2017-05-ch-zurich

Hi,

Marc Rosanes wrote:
>import nxs
>e = nxs.NXentry(name= "NXtomo")
>e.save("filenamenxs.h5", 'w5')
[...]
> /usr/lib/python2.7/dist-packages/nxs/tree.pyc in save(self,
> filename, format)
> 866 root = NXroot(NXentry(self))
> 867 if root.nxfile: root.nxfile.close()
> --> 868 file = NeXusTree(filename, format)
> 869 file.writefile(root)
> 870 file.close()
> 
> /usr/lib/python2.7/dist-packages/nxs/napi.pyc in __init__(self,
> filename, mode)
> 318 else:
> 319 op = 'create'
> --> 320 raise NeXusError, "Could not %s %s"%(op,filename)
> 321 self.isopen = True
> 322

I can reproduce this on Sid/Stretch, but not on Jessie, so this is a
regression from Jessie to Stretch.

The same happens if you don't specify the file format (as HDF5 seems
to be the default file format).

Regards, Axel
-- 
 ,''`.  |  Axel Beckert , http://people.debian.org/~abe/
: :' :  |  Debian Developer, ftp.ch.debian.org Admin
`. `'   |  4096R: 2517 B724 C5F6 CA99 5329  6E61 2FF9 CD59 6126 16B5
  `-|  1024D: F067 EA27 26B9 C3FC 1486  202E C09E 1D89 9593 0EDE

Bug#861736: Bug on NeXus library

2017-05-05 Thread Marc Rosanes


Additional information:

Storing using 'w' format (hdf4), instead of using 'w5' format (hdf5); 
the error does not appear:


import nxs
e = nxs.NXentry(name= "NXtomo")
e.save("filenamenxs.h5",*'**w**'*)

Bug#861736: python-nxs: Cannot save files with nxs python module

2017-05-03 Thread Marc Rosanes



Package: python-nxs
Version: 4.3.2-svn1921-4
Severity: grave
Justification: renders package unusable

Dear Maintainer,

   * What led up to the situation?

   Run the following python code:

   import nxs
   e = nxs.NXentry(name= "NXtomo")
   e.save("filenamenxs.h5", 'w5')


   * What was the outcome of this action?

   Got the following exception:

NeXusError
Traceback (most recent call last)
 in ()
> 1 e.save("filenamenxs.h5", 'w5')

/usr/lib/python2.7/dist-packages/nxs/tree.pyc in save(self, filename, 
format)

866 root = NXroot(NXentry(self))
867 if root.nxfile: root.nxfile.close()
--> 868 file = NeXusTree(filename, format)
869 file.writefile(root)
870 file.close()

/usr/lib/python2.7/dist-packages/nxs/napi.pyc in __init__(self, 
filename, mode)

318 else:
319 op = 'create'
--> 320 raise NeXusError, "Could not %s %s"%(op,filename)
321 self.isopen = True
322


   * What outcome did you expect instead?

An hdf5 file filenamenxs.h5 saved with no exception.

Note: Tried this with debian:stable docker and it worked correctly.


-- System Information:
Debian Release: 9.0
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64
 (x86_64)

Kernel: Linux 4.9.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Init: systemd (via /run/systemd/system)

Versions of packages python-nxs depends on:
ii  libnexus0v5  4.3.2-svn1921-4+b1
pn  python:any   

python-nxs recommends no packages.

python-nxs suggests no packages.

-- no debconf information

Bug#861736: closed by Andreas Tille (Bug#861736: fixed in nexus 4.3.2-svn1921-5)

Bug#861736: closed by Andreas Tille (Bug#861736: fixed in nexus 4.3.2-svn1921-5)

Bug#861736: Still some regression in python-nxs

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736:

Bug#861736: python-nxs: Cannot save files with nxs python module

Bug#861736: Bug on NeXus library

Bug#861736: python-nxs: Cannot save files with nxs python module

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