Importing ESRI shapefile to Spatialite via Python script

[Justyna Dębicka]

Hi,

I am a student and now writing MA thesis. I need to import shapefile to Spatialite via Python script. I am not an expert at programming. I have read some forums and found some options to do this task. However, none of this works for me. I prefer the fastest solution (I supose that using virtual table is slower in further spatial analysis since you cannot create spatial indexes?).

I would be gratefull if you could show me where I make mistake or provide better solution.

I have installed: (my system is 64-bit but with these files I've manager to load Spatialite extension)

• Python 2.7.10 (win32)
• mod_spatialite-4.3.0a-win-x86 http://www.gaia-gis.it/gaia-sins/windows-bin-x86/
• spatialite_gui-4.3.0a-win-x86 http://www.gaia-gis.it/gaia-sins/windows-bin-x86/
• sqlite-dll-win32-x86-3220000 https://www.sqlite.org/download.html
• sqlite-tools-win32-x86-3220000 https://www.sqlite.org/download.html

I have replaced default Python file sqlite3.dll with file from sqlite-dll-win32-x86-3220000.

I set environment path to C:\sqlite folder (shared via my gogle drive): https://drive.google.com/file/d/1YwlRsjAb5dv35ZdBgeo33o-00mGUTFnQ/view?usp=sharing

• test-2.3.sqlite - this is the database where I want import shapefile
• shape_towns - this is the shapefile
• sql_statements - folder with used in script sql statements

Python script:

I am loading Spatialite extension:

import os

import subprocess

import sqlite3

with sqlite3.connect('test-2.3.sqlite') as conn:

    conn.enable_load_extension(True)

    c = conn.cursor()

    c.execute("SELECT load_extension('mod_spatialite')") # https://www.gaia-gis.it/fossil/libspatialite/wiki?name=mod_spatialite

    c.execute("SELECT InitSpatialMetaData(1)")

    os.putenv("SPATIALITE", "relaxed") # set SPATIALITE_SECURITY=relaxed

    # testing if Spatialite works well

    for row in c.execute("SELECT ST_AsText(MakePoint(11.5,42.5,4326))"):

        print row

    # checking Spatialite version

    for vs in c.execute("SELECT spatialite_version()"):

        print 'Version Spatialite: ',vs[0] 

This works well - I get answers:

     (u'POINT(11.5 42.5)',)

    Version Spatialite: 4.3.0

And now I have difficulties in loading shapefiles. I've tried 3 options:

    VERSION 1 Using ImportSHP:

    filename = 'shape_towns'

    table = 'NewTowns2'

    charset = 'CP1252'

    srid = 32632

    c.execute("SELECT ImportSHP(filename,table,charset,srid);")

     ERROR MESSAGE: 

     Traceback (most recent call last):

     File "C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\sqliteIGI.py", line 63, in <module>

     c.execute("SELECT ImportSHP(filename,table,charset,srid);")

     OperationalError: near "table": syntax error

    VERSION 2:

    os.system('spatialite.exe test-2.3.sqlite < C:\sqlite\sql_statements\file*.sql')

    *files content:

• importSHP.sql: "SELECT ImportSHP('shape_towns','NewTowns2','CP1252',32632);"
• VT.sql: "CREATE VIRTUAL TABLE NewTowns2 USING VirtualShape(C:/sqlite/shape_towns, CP1252, 32632);"
• loadshp.sql: ".loadshp "C:\sqlite\shape_towns" NewTowns2 CP1252 32632 geom"

      ERROR MESSAGE:

      Error: incomplete SQL: ... (content)

     VERSION 3:

       subprocess.call(["spatialite_gui", "-e", "-shp", "shape_towns", "-d", "test-2.3.sqlite", "-t", "NewTowns2", "-g", "Geometry", "-c", "CP1252", "--type", "POINT"])

     

      ERROR MESSAGE (window from spatialite_gui):

      Failure while connecting to DB unable to open database file -e

After each version I add:

     conn.commit()

Thank you for helping,

Justyna

[mj10777]

On Tuesday, 3 April 2018 15:12:48 UTC+2, Justyna Dębicka wrote:

Hi,

I am a student and now writing MA thesis. I need to import shapefile to Spatialite via Python script. I am not an expert at programming. I have read some forums and found some options to do this task. However, none of this works for me. I prefer the fastest solution (I supose that using virtual table is slower in further spatial analysis since you cannot create spatial indexes?).

Correct, ImportSHP (when used correctly)  will import the Data and store it in a SpatialTable

- a SpatialIndex can then be created for that SpatialTable

--> the Shape-file is then no longer needed

CREATE VIRTUAL TABLE NewTowns2 USING VirtualShape

- would only create a reference (full path to the ShapeFile), so the origianl ShapeFile must remain available

A SpatialIndex can be made (which is then contained in the Database)

So the difference is only if you if you want to store the Shapefile Data in the Database permanently

- if you are going to read the data very often: then yes

- if not (maybe reading it only once):  then no

I would be gratefull if you could show me where I make mistake or provide better solution.

I have installed: (my system is 64-bit but with these files I've manager to load Spatialite extension)

• Python 2.7.10 (win32)
• mod_spatialite-4.3.0a-win-x86 http://www.gaia-gis.it/gaia-sins/windows-bin-x86/
• spatialite_gui-4.3.0a-win-x86 http://www.gaia-gis.it/gaia-sins/windows-bin-x86/
• sqlite-dll-win32-x86-3220000 https://www.sqlite.org/download.html
• sqlite-tools-win32-x86-3220000 https://www.sqlite.org/download.html

I have replaced default Python file sqlite3.dll with file from sqlite-dll-win32-x86-3220000.

I set environment path to C:\sqlite folder (shared via my gogle drive): https://drive.google.com/file/d/1YwlRsjAb5dv35ZdBgeo33o-00mGUTFnQ/view?usp=sharing

• test-2.3.sqlite - this is the database where I want import shapefile

Good gracious! Why are you using a test Database that was created to test Spatialite Version 2.3 ???  

- jut create a new, empty Database using Spatialite 4.3.0

• shape_towns - this is the shapefile
• sql_statements - folder with used in script sql statements

Python script:

I am loading Spatialite extension:

import os

import subprocess

import sqlite3

with sqlite3.connect('test-2.3.sqlite') as conn:

    conn.enable_load_extension(True)

    c = conn.cursor()

    c.execute("SELECT load_extension('mod_spatialite')") # https://www.gaia-gis.it/fossil/libspatialite/wiki?name=mod_spatialite

    c.execute("SELECT InitSpatialMetaData(1)")

    os.putenv("SPATIALITE", "relaxed") # set SPATIALITE_SECURITY=relaxed

If you give an non-existing Database, then a new Database will be created (using the present version).

    # testing if Spatialite works well

    for row in c.execute("SELECT ST_AsText(MakePoint(11.5,42.5,4326))"):

        print row

    # checking Spatialite version

    for vs in c.execute("SELECT spatialite_version()"):

        print 'Version Spatialite: ',vs[0] 

This works well - I get answers:

     (u'POINT(11.5 42.5)',)

    Version Spatialite: 4.3.0

And now I have difficulties in loading shapefiles. I've tried 3 options:

    VERSION 1 Using ImportSHP:

    filename = 'shape_towns'

    table = 'NewTowns2'

    charset = 'CP1252'

    srid = 32632

    c.execute("SELECT ImportSHP(filename,table,charset,srid);")

     ERROR MESSAGE: 

     Traceback (most recent call last):

     File "C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\sqliteIGI.py", line 63, in <module>

     c.execute("SELECT ImportSHP(filename,table,charset,srid);")

Here you are not formatting your Sql-string correctly.

You are telling ImportSHP:

- the file to be loaded is 'filename' (not value contained in the variable filename 'shape_towns')

- same for table,charset,srid

Read the Python documentation how to build a string from variables (filename,table,charset,srid)

     OperationalError: near "table": syntax error

 "table" is a reserved word in sql ; you must format the string so that value of the variable of  table is to be used

    VERSION 2:

    os.system('spatialite.exe test-2.3.sqlite < C:\sqlite\sql_statements\file*.sql')

    *files content:

• importSHP.sql: "SELECT ImportSHP('shape_towns','NewTowns2','CP1252',32632);"
• VT.sql: "CREATE VIRTUAL TABLE NewTowns2 USING VirtualShape(C:/sqlite/shape_towns, CP1252, 32632);"
• loadshp.sql: ".loadshp "C:\sqlite\shape_towns" NewTowns2 CP1252 32632 geom"

Is 'shape_towns.shp' inside the  C:\sqlite\ directory ?

      ERROR MESSAGE:

      Error: incomplete SQL: ... (content)

     VERSION 3:

       subprocess.call(["spatialite_gui", "-e", "-shp", "shape_towns", "-d", "test-2.3.sqlite", "-t", "NewTowns2", "-g", "Geometry", "-c", "CP1252", "--type", "POINT"])

     

      ERROR MESSAGE (window from spatialite_gui):

      Failure while connecting to DB unable to open database file -e

After each version I add:

     conn.commit()

Thank you for helping,

Hope this helps

Mark 

Justyna

[Justyna Dębicka]

Thank you Mark :)

So if I only need the shapefile to make a buffer out of it I should use ImportSHP?

Now my script looks as below:

import os

import sqlite3

## LOADING EXTENSION SPATIALITE

with sqlite3.connect('test4.sqlite') as conn:

    conn.enable_load_extension(True)

    c = conn.cursor()

    c.execute("SELECT load_extension('mod_spatialite')")

    c.execute("SELECT InitSpatialMetaData(1)")

    os.putenv("SPATIALITE", "relaxed")

## LOADING SHAPEFILE

    filename = 'shape_towns'

    table = 'NewTowns2'

    charset = 'CP1252'

    srid = 32632

    c.execute("SELECT ImportSHP(" + filename + "," + table + "," + charset + "," + str(srid) + ");")

    conn.commit()

After running script I get such a message:

Traceback (most recent call last):

File "C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\sqlite5.py", line 20, in <module>

c.execute("SELECT ImportSHP(" + filename + "," + table + "," + charset + "," + str(srid) + ");")

OperationalError: no such column: shape_towns

shape_towns is my shapefile I do not understand the message no such column

Justyna

[mj10777]

On Tuesday, 3 April 2018 17:15:40 UTC+2, Justyna Dębicka wrote:

Thank you Mark :)

So if I only need the shapefile to make a buffer out of it I should use ImportSHP?

If you are going to read the data only once : no 

Now my script looks as below:

import os

import sqlite3

## LOADING EXTENSION SPATIALITE

with sqlite3.connect('test4.sqlite') as conn:

    conn.enable_load_extension(True)

    c = conn.cursor()

    c.execute("SELECT load_extension('mod_spatialite')")

    c.execute("SELECT InitSpatialMetaData(1)")

    os.putenv("SPATIALITE", "relaxed")

## LOADING SHAPEFILE

    filename = 'shape_towns'

    table = 'NewTowns2'

    charset = 'CP1252'

    srid = 32632

    c.execute("SELECT ImportSHP(" + filename + "," + table + "," + charset + "," + str(srid) + ");")

    conn.commit()

After running script I get such a message:

Traceback (most recent call last):

File "C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\sqlite5.py", line 20, in <module>

c.execute("SELECT ImportSHP(" + filename + "," + table + "," + charset + "," + str(srid) + ");")

OperationalError: no such column: shape_towns

You must read the command syntax more carefully:

http://www.gaia-gis.it/gaia-sins/spatialite-sql-latest.html#advanced 

ImportSHP( filename Text , table Text , charset Text [ , srid Integer [ , geom_column Text [ , pk_column Text [ , geometry_type Text [ , coerce2D Integer [ , compressed Integer [ , spatial_index Integer [ , text_dates Integer ] ] ] ] ] ] ] ] )

- filename,table,charset are of type Text

- srid is of Type Integer

SELECT ImportSHP("shape_towns","NewTowns2","CP1252",32632);

- note the Text fields have " before and behind the text, whereas an Integer does not

"SELECT ImportSHP(" + filename + "," + table + "," + charset + "," + str(srid) + ");"

results in :

SELECT ImportSHP(shape_towns,NewTowns2,CP1252,32632);

which is not correct.

[Kyle Felipe Vieira Roberto]

Good morning...
Try this

c.execute("SELECT ImportSHP({filename}, {table}, {charset}, {srid});".format(filename=filename, table=table, charset=charset, srid=srid))

Remember: if your script is not placed in the same folder with shapefile you have to use full path to the file (C:....)

[mj10777]

On Wednesday, 4 April 2018 14:39:58 UTC+2, Kyle Felipe Vieira Roberto wrote:

Good morning...
Try this

c.execute("SELECT ImportSHP({filename}, {table}, {charset}, {srid});".format(filename=filename, table=table, charset=charset, srid=srid))

Will this insure that there are quotes around the strings (filename,table,charset) ?

- I am not a python person, but this is one of the problems

Remember: if your script is not placed in the same folder with shapefile you have to use full path to the file (C:....)

- correct, thus the question that was not answered

[Kyle Felipe Vieira Roberto]

So sory... 

Try this..... i wrote a script some time ago and run very well...

c.execute("""SELECT ImportSHP('{filename}', '{table}', '{charset}', {srid});"""".format(filename=filename, table=table, charset=charset, srid=srid))

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Skype: kyle.felipe

[Justyna Dębicka]

Thanks :) I've tried the code (delete one extra "), but I get such a message:

Traceback (most recent call last):

File "C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\sqlite5.py", line 20, in <module>

c.execute("""SELECT ImportSHP('{filename}', '{table}', '{charset}', {srid});""".format(filename=filename, table=table, charset=charset, srid=srid))

OperationalError: no such function: ImportSHP

InitSpatiaMetaData() error:"table spatial_ref_sys already exists"

[mj10777]

On Friday, 6 April 2018 12:58:45 UTC+2, Justyna Dębicka wrote:

Thanks :) I've tried the code (delete one extra "), but I get such a message:

Traceback (most recent call last):

File "C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\sqlite5.py", line 20, in <module>

c.execute("""SELECT ImportSHP('{filename}', '{table}', '{charset}', {srid});""".format(filename=filename, table=table, charset=charset, srid=srid))

OperationalError: no such function: ImportSHP

InitSpatiaMetaData() error:"table spatial_ref_sys already exists"

This is a sign that the spatialite interface is active and working

- this command should only be used for a new spatialite database, but is not an error

I would advise you to place the sql-statement in an extra variable 'sql_statement'

- then print the variable out to the terminal and with copy and past try it in spatialite_gui to make sure that the syntax and values are correct.

OperationalError: no such function: ImportSHP

- this may be a python error, since InitSpatiaMetaData() worked correctly [if  InitSpatiaMetaData a known function, then ImportSHP should also be known]

You problem here is that you are using 2 different system and it is not clear which one is causing the error.

So print out the sql-statements, checking in spatialite_gui that it is correct (using a full path to the shape-file)

- any other error must then be a python problem

Mark

[a.fu...@lqt.it]

On Fri, 6 Apr 2018 03:58:45 -0700 (PDT), Justyna Dębicka wrote:
> OperationalError: NO SUCH FUNCTION: IMPORTSHP
>

Hi Justyna,

ImportSHP() could potentially open a security breach,
because it will directly access external files on the
filesystem.
a maliciously crafted SQL script could then possibly
attempt to exploit ImportSHP() for silently steal
your data.

so, you necessarily have to set the following environment
variable in order to explicitly authorize ImportSHP()
(and other potentially dangerous SQL functions) to be
really enabled:

SPATIALITE_SECURITY=relaxed

if the above variable is not set while opening the
connection SpatiaLite will completely ignore all
security-sensible functions, and you'll then get
a "NO SUCH FUNCTION" error when attempting to call
anyone of them.

bye Sandro

[a.fu...@lqt.it]

On Fri, 6 Apr 2018 04:38:49 -0700 (PDT), Justyna Dębicka wrote:
> Hi Sandro,
> I have such a line in my code:

> os.putenv("SPATIALITE", "relaxed")

> is it not correct?
>

Justyna,

I'm sorry but I'm not a Python programmer.

the name of the variable you are using is wrong;
it's not "SPATIALITE", it should correctly be
"SPATIALITE_SECURITY"

accordingly to the documentation you can check
if the variable has effectively been set by
calling an instruction like:

print os.envirom("SPATIALITE_SECURITY");

bye Sandro

[mj10777]

On Friday, 6 April 2018 13:38:50 UTC+2, Justyna Dębicka wrote:

Hi Sandro,

I have such a line in my code:

os.putenv("SPATIALITE", "relaxed")

is it not correct?

Sorry, I overlooked that compleatly from the original post:

os.putenv("SPATIALITE", "relaxed") # set SPATIALITE_SECURITY=relaxed 

 

should be done BEFORE the connection:

os.putenv("SPATIALITE_SECURITY", "relaxed") # set SPATIALITE_SECURITY=relaxed 

Mark

[Justyna Dębicka]

Thank you Mark, Sandro for helping :)

I have printed the statement - it looks ok:

>>> print sql_statement

SELECT ImportSHP('shape_towns', 'NewTowns2', 'CP1252', 32632);

And after pasting into gui I get the correct result.

I have to add that Buffer function works via Python script.

As to SPATIALITE_SECURITY this does not work also:

os.putenv("SPATIALITE_SECURITY", "relaxed")

I have also tried using cmd:

SET SPATIALITE_SECURITY=relaxed

python scrypt_name.py

and I got the same error message.

If I manage to find what is the problem I'll put here the answer :)

Justyna

[mj10777]

On Friday, 6 April 2018 14:06:40 UTC+2, Justyna Dębicka wrote:

Thank you Mark, Sandro for helping :)

I have printed the statement - it looks ok:

>>> print sql_statement

SELECT ImportSHP('shape_towns', 'NewTowns2', 'CP1252', 32632);

And after pasting into gui I get the correct result.

I have to add that Buffer function works via Python script.

As to SPATIALITE_SECURITY this does not work also:

os.putenv("SPATIALITE_SECURITY", "relaxed")

I have also tried using cmd:

SET SPATIALITE_SECURITY=relaxed

python scrypt_name.py

and I got the same error message.

Did you do this before the connection was opened? 

os.putenv("SPATIALITE_SECURITY", "relaxed")

with sqlite3.connect('test-2.3.sqlite') as conn:

[Justyna Dębicka]

Yes. This is the problem with setting this Spatialsecurity:

>>>print os.environ.get("SPATIALITE_SECURITY")

None

[Justyna Dębicka]

I've changed the code:

os.environ['SPATIALITE_SECURITY']='relaxed'

with sqlite3.connect('test.sqlite') as conn: ........

and printed in terminal:

>>> print os.environ["SPATIALITE_SECURITY"]

relaxed

but still the same error message

[a.fu...@lqt.it]

On Fri, 6 Apr 2018 06:03:51 -0700 (PDT), Justyna Dębicka wrote:
> I've changed the code:
> os.environ['SPATIALITE_SECURITY']='relaxed'
>
> with sqlite3.connect('test.sqlite') as conn: ........
>
> and printed in terminal:
>
>>>> print os.environ["SPATIALITE_SECURITY"]
>
> relaxed
>
> but still the same error message
>

ustyna,

accordingly to the code you've attached to your
first post it seems that you set the environment
_AFTER_ executing "select load_extension(..)".

that is wrong: the environment must necessarily
be set _BEFORE_ loading the extension.

bye Sandro

[mj10777]

On Friday, 6 April 2018 15:03:51 UTC+2, Justyna Dębicka wrote:

I've changed the code:

os.environ['SPATIALITE_SECURITY']='relaxed'

This should be: 

os.putenv("SPATIALITE_SECURITY", "relaxed") 

-------> with 'put' <----------

[mj10777]

On Friday, 6 April 2018 15:20:07 UTC+2, mj10777 wrote:

On Friday, 6 April 2018 15:03:51 UTC+2, Justyna Dębicka wrote:

I've changed the code:

os.environ['SPATIALITE_SECURITY']='relaxed'

This should be: 

os.putenv("SPATIALITE_SECURITY", "relaxed") 

-------> with 'put' <----------

For a better understanding:

When 'mod_spatialite' is called:

   c.execute("SELECT load_extension('mod_spatialite')") 

all Spatialite specific functions are loaded.

- it is then that 'SPATIALITE_SECURITY' is checked

--> only when 'relaxed' is set, will certain functions be loaded

---> it is then never checked again.

Look in:

http://www.gaia-gis.it/gaia-sins/spatialite-sql-latest.html

searching for 'SPATIALITE_SECURITY=relaxed' will list about 17 functions where this is needed.

Mark

[Justyna Dębicka]

I think putenv does not work:

>>> import os

>>> os.putenv("SPATIALITE_SECURITY", "relaxed")

>>> print os.environ.get("SPATIALITE_SECURITY")

None

But setting as below:

>>> import os 

>>> os.environ['SPATIALITE_SECURITY']='relaxed'

>>> print os.environ.get("SPATIALITE_SECURITY")

relaxed

This is mu current code:

import os

import sqlite3

## LOADING EXTENSION SPATIALITE

os.environ['SPATIALITE_SECURITY']='relaxed'

with sqlite3.connect("testing.sqlite") as conn:

    conn.enable_load_extension(True)

    c = conn.cursor()

    c.execute("SELECT load_extension('mod_spatialite')")

    c.execute("SELECT InitSpatialMetaData(1)")

## LOADING SHAPEFILE

    filename = r'C:\Users\justa\Documents\Magisterka2018\SkryptyPython\testy\shape'

    table = 'NewTowns2'

    charset = 'CP1252'

    srid = 32632

    sql_statement="""SELECT ImportSHP('{filename}', '{table}', '{charset}', {srid});""".format(filename=filename, table=table, charset=charset, srid=srid)

    c.execute(sql_statement)

    conn.commit()

[Kyle Felipe Vieira Roberto]

just a question, why r you using python 2.7?? why not 3.6....

I make this script here to help you, i tested here and works well on python 2.7

https://gist.github.com/kylefelipe/67e3329b8a1d268f385af9fed7461baf

[Justyna Dębicka]

Thank you. Still the same error. I am using 2.7 because somebody wrote on the internet that this enable me to load Spatialite on Windows 64-bit. I had some difficulties to do that.

I have installed:

• Python 2.7.10 (win32)
• mod_spatialite-4.3.0a-win-x86 http://www.gaia-gis.it/gaia-sins/windows-bin-x86/
• spatialite_gui-4.3.0a-win-x86 http://www.gaia-gis.it/gaia-sins/windows-bin-x86/
• sqlite-dll-win32-x86-3220000 https://www.sqlite.org/download.html
• sqlite-tools-win32-x86-3220000 https://www.sqlite.org/download.html

However I prefer Python 3 and Windows 64-bit files. Maybe I do not installed something?

I have this files on my computer:

 https://plus.google.com/u/0/photos/photo/107743842596466306842/6542426919605935762?authkey=CNujqMC68oHfGQ

[Kyle Felipe Vieira Roberto]

Have you  installed QGIs on your desktop???
It have all dependencies installed.

I give up windows about 1 year ago....

[Justyna Dębicka]

Yes, I have QGIS. Apparently  I want to compare some spatial analysis time in QGIS, ArcGIS, Spatialite and PostGIS. I suppose you use UNIX? :)  Ok, I'll try to use QGIS Python.

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Pozdrawiam,

Justyna Dębicka

-../--..-./.-/.../-/.-//

[Kyle Felipe Vieira Roberto]

Use "OSGEO4W Shell" you can find python there....

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[Justyna Dębicka]

It does not work. I give up and make analisys on earlier build spatial database in Spatialite_GUI

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[Majid Hojati]

Does it work with 3.6?

[Kyle Felipe Vieira Roberto]

Yes....

[Majid Hojati]

thanks very much