issue in sql database

[harperrc]

not sure if i have done something wrong or not. i pip install xraydb but when i try to run it an error occurs because there is no column in the elements table with the name 'name'.

2 solutions (1) is the obvious simple one

1. replace self.__atomic_name = [e.name..... with self.__atomic_name = [e.element......

2. dump xraydb.sqlite and fix the sqlite commands to add a name key (this is what i did because i wanted to learn more about sqlite), i have put my code in http://github.com/harperrc/xraydb-addName-to-xraydb if you want to look at it

thanks for providing this tool

[newville]

@harperrc Please say what you are trying to do. And post actual, runnable code, and the results you get including complete error messages.

Your link does not exist. But, I sort of doubt that we are going alter the column names in the database.

This should work:

import xraydb
print(xraydb.atomic_symbol(30), xraydb.atomic_name(30))

Maybe you want something like

import xraydb
xdb = xraydb.XrayDB()
print([(el.atomic_number, el.name) for el in xdb.get_cache('elements')])

or maybe

~> sqlite3 xraydb.sqlite
sqlite> select name from elements;

but those are guesses.

[harperrc]

i am a retired systems analyst and just like to goof around. i am implementing a x-ray transport code and have be messing around with various methods to compute some of needed data (e.g. barns & lighthill, XCOM, mucal......) i went down a rabbit hole on computing the mean free path and was interested in how you handled compound elements here is the correct path to my little script to update the sql file https://github.com/harperrc/addName-to-xraydb.sqlite this is the simple code i was running that caused the error ------------------------------------------------------- #!/usr/bin/python3 import math import numpy as np import sys import xraydb from xraydb import material_mu ene = np.linspace(1000.,5000.,10) # keV e0 = 1.0 e1 = 100.0 # eV e0 = e0 * 1000.0 e1 = e1 * 1000.0 ene = np.logspace(math.log10(e0),math.log10(e1),512) mu = material_mu('air',ene) fo = open('out.mu','w') for (i,e) in enumerate(ene): fo.write('%11.4e %11.4e\n' % (e / 1000.0,mu[i])) fo.close() ------------------------------------------------------- here is what i get when i use the supplied xraydb.sqlite Traceback (most recent call last): File "/home/harper/.local/lib/python3.12/site-packages/sqlalchemy/engine/result.py", line 199, in _key_not_found self._key_fallback(key, None) File "/home/harper/.local/lib/python3.12/site-packages/sqlalchemy/engine/cursor.py", line 825, in _key_fallback raise exc.NoSuchColumnError( sqlalchemy.exc.NoSuchColumnError: Could not locate column in row for column 'name' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/harper/nuclear/XRay/XrayDB/tst.py", line 20, in <module> mu = material_mu('air',ene) ^^^^^^^^^^^^^^^^^^^^^^ File "/home/harper/.local/lib/python3.12/site-packages/xraydb/materials.py", line 122, in material_mu mass = frac * atomic_mass(elem) ^^^^^^^^^^^^^^^^^ File "/home/harper/.local/lib/python3.12/site-packages/xraydb/xray.py", line 407, in atomic_mass return xdb._elem_data(element).mass ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/harper/.local/lib/python3.12/site-packages/xraydb/xraydb.py", line 425, in _elem_data row.element.title(), row.name, ^^^^^^^^ File "lib/sqlalchemy/cyextension/resultproxy.pyx", line 66, in sqlalchemy.cyextension.resultproxy.BaseRow.__getattr__ File "lib/sqlalchemy/cyextension/resultproxy.pyx", line 63, in sqlalchemy.cyextension.resultproxy.BaseRow._get_by_key_impl File "/home/harper/.local/lib/python3.12/site-packages/sqlalchemy/engine/result.py", line 201, in _key_not_found raise AttributeError(ke.args[0]) from ke AttributeError: Could not locate column in row for column 'name' ------------------------------------------------------------------------- when i swap out with my updated db i get no errors and the code produces the table of data thanks for responding. i am a very low priority user so if this has not impacted any other folks then i would close it out. On Monday 20 October 2025 10:14:31 PM (-05:00), Matt Newville wrote: [Unlabeled Image] newville left a comment (xraypy/XrayDB#39) <#39 (comment)> @harperrc <https://github.com/harperrc> Please say what you are trying to do. And post actual, runnable code, and the results you get including complete error messages. Your link does not exist. But, I sort of doubt that we are going alter the column names in the database. This should work: import xraydb print(xraydb.atomic_symbol(30), xraydb.atomic_name(30)) Maybe you want something like import xraydb xdb = xraydb.XrayDB() print([(el.atomic_number, el.name) for el in xdb.get_cache('elements')]) or maybe ~> sqlite3 xraydb.sqlite sqlite> select name from elements; but those are guesses. — Reply to this email directly, view it on GitHub <#39 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGFHUYO3BHLIOF37GQ65PND3YWQJPAVCNFSM6AAAAACJXOL7TKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIMRUGUYDOMRUGI> . You are receiving this because you were mentioned.

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-- Robert Harper 2932 Green Mountain Rd SE Huntsville, Al 35803

[newville]

@harperrc Hm, this works for me:

import numpy as np
import math
from xraydb import material_mu

e0 =   1000.
e1 = 100000.

ene = np.logspace(math.log10(e0),math.log10(e1),512)

mu  = material_mu('air',ene)

It does seem like something must be wrong with that "xraydb.sqlite" database file.

If you do

import xraydb
xdb = xraydb.XrayDB()
print(xdb.dbname)

do you get something like "..../.local/lib/python3.12/site-packages/xraydb/xraydb.sqlite"?
For me, that file is 10305536 bytes. Is that the database file you are altering?

[harperrc]

file had that length. i removed my old version and installed new when i try the import..... if errors off with the e.name issue thanks again for the response. On Tuesday 21 October 2025 07:15:27 AM (-05:00), Matt Newville wrote: [Unlabeled Image] newville left a comment (xraypy/XrayDB#39) <#39 (comment)> @harperrc <https://github.com/harperrc> Hm, this works for me: import numpy as np import math from xraydb import material_mu e0 = 1000. e1 = 100000. ene = np.logspace(math.log10(e0),math.log10(e1),512) mu = material_mu('air',ene) It does seem like something must be wrong with that "xraydb.sqlite" database file. If you do import xraydb xdb = xraydb.XrayDB() print(xdb.dbname) do you get something like "..../.local/lib/python3.12/site-packages/xraydb/xraydb.sqlite"? For me, that file is 10305536 bytes. Is that the database file you are altering? — Reply to this email directly, view it on GitHub <#39 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGFHUYP2AOS4WSM53OA5IX33YYPV7AVCNFSM6AAAAACJXOL7TKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIMRWGI4TOOBQGU> . You are receiving this because you were mentioned.

…

-- Robert Harper 2932 Green Mountain Rd SE Huntsville, Al 35803