INI file setup

How to conifigure .ini files on Windows?

Tester 1: Shweata N. Hegde

Prerequisites

• Clone repositories: CEVOpen, dictionary, opendiagram

Open pyami.inifile (\openDiagram\physchem\python\pyami.ini)

• Make changes to the .ini file such that the HOME directs to your home directory. And in most cases, the home directory is your project directory. It should look like this:

 NOTE. All files use forward slash
; use slash (/) to separate filename components, we will convert to file-separator automatically

[DIRS]
home = C:/Users/shweata
dictionary_url = https://github.com/petermr/dictionary
project_dir = ${home}

[URLS]
petermr_url = https://github.com/petermr
petermr_raw_url = https://raw.githubusercontent.com/petermr

[PROJECTS]
cev_open = ${DIRS:project_dir}/CEVOpen
open_battery = ${DIRS:project_dir}/open-battery
pr_liion = ${open_battery}/liion
tigr2ess = ${DIRS:project_dir}/tigr2ess
tigr2ess_url = https://github.com/petermr/tigr2ess/tree/master
open_diagram = ${DIRS:project_dir}/openDiagram
open_virus = ${DIRS:project_dir}/openVirus

[PYAMIGETPAPERS]
max = 200

[DICTIONARIES]
dict_dir = ${DIRS:home}/dictionary

ov_ini = ${dict_dir}/openvirus20210120/amidict.ini
cev_ini = ${PROJECTS:cev_open}/dictionary/amidict.ini
tigr2ess_ini = ${PROJECTS:tigr2ess}/dictionaries/examples/amidict.ini
battery_ini = ${PROJECTS:open_battery}/dictionary/amidict.ini

ami3_urlini = ${URLS:petermr_raw_url}/ami3/master/src/main/resources/org/contentmine/ami/plugins/dictionary/amidict.ini

[AMISEARCH]

Note: The HOME directory is usually C:\Users\shweata(your name)

• Copy the modified pyami.ini file to HOME (i.e.,C:\Users\shweata(your name))

Run util.py from commandline or PyCharm

You've successfully configured if you get the following output:

C:\Users\shweata\anaconda3\python.exe "C:\Program Files\JetBrains\PyCharm Community Edition 2020.2.3\plugins\python-ce\helpers\pydev\pydevconsole.py" --mode=client --port=49247
import sys; print('Python %s on %s' % (sys.version, sys.platform))
sys.path.extend(['C:\\Users\\shweata', 'C:/Users/shweata'])
Python 3.8.3 (default, Jul  2 2020, 17:30:36) [MSC v.1916 64 bit (AMD64)]
Type 'copyright', 'credits' or 'license' for more information
IPython 7.16.1 -- An enhanced Interactive Python. Type '?' for help.
PyDev console: using IPython 7.16.1
Python 3.8.3 (default, Jul  2 2020, 17:30:36) [MSC v.1916 64 bit (AMD64)] on win32
In[2]: runfile('C:/Users/shweata/openDiagram/physchem/python/util.py', wdir='C:/Users/shweata/openDiagram/physchem/python')
read pyami.ini C:\Users\shweata\pyami.ini
dict key dict_dir
dict key ov_ini
dictionary ini file ov_ini C:/Users/shweata/dictionary/openvirus20210120/amidict.ini
read pyami.ini C:/Users/shweata/dictionary/openvirus20210120/amidict.ini
country entries 263 wikidata 263 
      Created from SPARQL query
disease entries 13845 wikidata 13845 
      Created from SPARQL query
no desc
organization entries 17724 wikidata 17724 
      Created from SPARQL query
no desc
dict key cev_ini
dictionary ini file cev_ini C:/Users/shweata/CEVOpen/dictionary/amidict.ini
read pyami.ini C:/Users/shweata/CEVOpen/dictionary/amidict.ini
dict_ref file does not exist C:\Users\shweata\CEVOpen\dictionary\eoActivity\eoActivity.xml
eo_analysis_method entries 117 wikidata 0 
      A dictionary of 117 entries describing instruments and methods used to [separate](https://en.wikipedia.org/wiki/Separation_process), identify, and [quantify](https://en.wikipedia.org/wiki/Quantification_(science)) matter — 105 being resolved to wikidata IDs, and 95 with short descriptions.
eo_compound entries 2114 wikidata 0 
      A dictionary of 2114 constituent chemical compounds extracted from Essential Oils converted from essoldb1.0 data
eo_extraction_method entries 89 wikidata 0 
      A dictionary of 87 terms related to Essential Oil extraction methods
dict_ref file does not exist C:\Users\shweata\CEVOpen\dictionary\eoGene\eoGene.xml
eo_plant entries 1678 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_material_history entries 81 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the **1678** entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_part entries 383 wikidata 0 
      a dictionary of 285 terms relating to plant parts used for essential oil extraction
eo_target_organism entries 307 wikidata 0 
      A dictionary of 307 target organisms resolved to wikidataIDs, including genus and species of bacteria, fungi, protist, protozoa, and other microorgnisms.
invasive_species entries 19 wikidata 0 
      Created from SPARQL query
pests entries 1032 wikidata 0 
       A dictionary of 1032 terms for two categories of insects: A) Insect vectors of human pathogens sourced from https://en.wikipedia.org/wiki/Category:Insect_vectors_of_human_pathogens, and B) Winged insects soursed from https://www.insectidentification.org/winged-insect-key.asp.
plant_genus entries 25917 wikidata 25917 
      Created from SPARQL query
dict key tigr2ess_ini
dictionary ini file tigr2ess_ini C:/Users/shweata/tigr2ess/dictionaries/examples/amidict.ini
INI file does not exist, needs creating C:/Users/shweata/tigr2ess/dictionaries/examples/amidict.ini
dict key battery_ini
dictionary ini file battery_ini C:/Users/shweata/open-battery/dictionary/amidict.ini
INI file does not exist, needs creating C:/Users/shweata/open-battery/dictionary/amidict.ini
dict key ami3_urlini
*_urlini not yet implemented
dicts None

Tester 2: Radhu Ladani

OS: Windows 10

Date: 3/10/2021

Prerequisites

• Update the already existing repositories CEVOpen, dictionary, Opendiagram using command git pull in command line.

Open pyami.inifile (\openDiagram\physchem\python\pyami.ini)

• Open pyami.ini file at specific path to my case: C:\Users\DELL\Radhu\openDiagram\physchem\python.
• Make changes to the .ini file such that the HOME directs to your home directory in my case: \Users\DELL\Radhu.

; NOTE. All files use forward slash
; use slash (/) to separate filename components, we will convert to file-separator automatically

[DIRS]
home = /Users/DELL/Radhu
dictionary_url = https://github.com/petermr/dictionary
project_dir = ${home}

[URLS]
petermr_url = https://github.com/petermr
petermr_raw_url = https://raw.githubusercontent.com/petermr

[PROJECTS]
cev_open = ${DIRS:project_dir}/CEVOpen
open_battery = ${DIRS:project_dir}/open-battery
pr_liion = ${open_battery}/liion
tigr2ess = ${DIRS:project_dir}/tigr2ess
tigr2ess_url = https://github.com/petermr/tigr2ess/tree/master
open_diagram = ${DIRS:project_dir}/openDiagram
open_virus = ${DIRS:project_dir}/openVirus

[PYAMIGETPAPERS]
max = 200

[DICTIONARIES]
dict_dir = ${DIRS:home}/dictionary

ov_ini = ${dict_dir}/openvirus20210120/amidict.ini
cev_ini = ${PROJECTS:cev_open}/dictionary/amidict.ini
tigr2ess_ini = ${PROJECTS:tigr2ess}/dictionaries/examples/amidict.ini
battery_ini = ${PROJECTS:open_battery}/dictionary/amidict.ini

ami3_urlini = ${URLS:petermr_raw_url}/ami3/master/src/main/resources/org/contentmine/ami/plugins/dictionary/amidict.ini

[AMISEARCH]

• Now copy this pyami.ini into your Home.

Run util.py in my case at path C:\Users\DELL\Radhu\openDiagram\physchem\python on commandline or PyCharm.

C:\ProgramData\Anaconda3\python.exe C:/Users/DELL/Radhu/openDiagram/physchem/python/util.py
read pyami.ini C:\Users\DELL\pyami.ini
dict key dict_dir
dict key ov_ini
dictionary ini file ov_ini /Users/DELL/Radhu/dictionary/openvirus20210120/amidict.ini
read pyami.ini /Users/DELL/Radhu/dictionary/openvirus20210120/amidict.ini
country entries 263 wikidata 263 
      Created from SPARQL query
disease entries 13845 wikidata 13845 
      Created from SPARQL query
no desc
organization entries 17724 wikidata 17724 
      Created from SPARQL query
no desc
dict key cev_ini
dictionary ini file cev_ini /Users/DELL/Radhu/CEVOpen/dictionary/amidict.ini
read pyami.ini /Users/DELL/Radhu/CEVOpen/dictionary/amidict.ini
dict_ref file does not exist \Users\DELL\Radhu\CEVOpen\dictionary\eoActivity\eoActivity.xml
eo_analysis_method entries 117 wikidata 0 
      A dictionary of 117 entries describing instruments and methods used to [separate](https://en.wikipedia.org/wiki/Separation_process), identify, and [quantify](https://en.wikipedia.org/wiki/Quantification_(science)) matter — 105 being resolved to wikidata IDs, and 95 with short descriptions.
eo_compound entries 2114 wikidata 0 
      A dictionary of 2114 constituent chemical compounds extracted from Essential Oils converted from essoldb1.0 data
eo_extraction_method entries 89 wikidata 0 
      A dictionary of 87 terms related to Essential Oil extraction methods
dict_ref file does not exist \Users\DELL\Radhu\CEVOpen\dictionary\eoGene\eoGene.xml
eo_plant entries 1678 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_material_history entries 81 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the **1678** entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_part entries 383 wikidata 0 
      a dictionary of 285 terms relating to plant parts used for essential oil extraction
eo_target_organism entries 307 wikidata 0 
      A dictionary of 307 target organisms resolved to wikidataIDs, including genus and species of bacteria, fungi, protist, protozoa, and other microorgnisms.
invasive_species entries 19 wikidata 0 
      Created from SPARQL query
pests entries 1032 wikidata 0 
       A dictionary of 1032 terms for two categories of insects: A) Insect vectors of human pathogens sourced from https://en.wikipedia.org/wiki/Category:Insect_vectors_of_human_pathogens, and B) Winged insects soursed from https://www.insectidentification.org/winged-insect-key.asp.
plant_genus entries 25917 wikidata 25917 
      Created from SPARQL query
dict key tigr2ess_ini
dictionary ini file tigr2ess_ini /Users/DELL/Radhu/tigr2ess/dictionaries/examples/amidict.ini
INI file does not exist, needs creating /Users/DELL/Radhu/tigr2ess/dictionaries/examples/amidict.ini
dict key battery_ini
dictionary ini file battery_ini /Users/DELL/Radhu/open-battery/dictionary/amidict.ini
INI file does not exist, needs creating /Users/DELL/Radhu/open-battery/dictionary/amidict.ini
dict key ami3_urlini
*_urlini not yet implemented
dicts None

Process finished with exit code 0

Tester 3: Talha Hasan

OS: Windows 10

Date: 03/11/2021

Prerequisites

• Update the following repositories CEVOpen, dictionary, Opendiagram using command git pull in command line.

Open pyami.inifile (\openDiagram\physchem\python\pyami.ini)

• Open pyami.ini file here(the name of the folder where repository is cloned)C:\Users\talha\openDiagram\physchem\python.
• Make changes to the path of .ini file to your HOME in my case: \Users\talha.

; NOTE. Use forward slash (\) in path
; use slash (/) to separate filename components, we will convert to file-separator automatically

[DIRS]
home = /Users/talha
dictionary_url = https://github.com/petermr/dictionary
project_dir = ${home}

[URLS]
petermr_url = https://github.com/petermr
petermr_raw_url = https://raw.githubusercontent.com/petermr

[PROJECTS]
cev_open = ${DIRS:project_dir}/CEVOpen
open_battery = ${DIRS:project_dir}/open-battery
pr_liion = ${open_battery}/liion
tigr2ess = ${DIRS:project_dir}/tigr2ess
tigr2ess_url = https://github.com/petermr/tigr2ess/tree/master
open_diagram = ${DIRS:project_dir}/openDiagram
open_virus = ${DIRS:project_dir}/openVirus

[PYAMIGETPAPERS]
max = 200

[DICTIONARIES]
dict_dir = ${DIRS:home}/dictionary

ov_ini = ${dict_dir}/openvirus20210120/amidict.ini
cev_ini = ${PROJECTS:cev_open}/dictionary/amidict.ini
tigr2ess_ini = ${PROJECTS:tigr2ess}/dictionaries/examples/amidict.ini
battery_ini = ${PROJECTS:open_battery}/dictionary/amidict.ini

ami3_urlini = ${URLS:petermr_raw_url}/ami3/master/src/main/resources/org/contentmine/ami/plugins/dictionary/amidict.ini

[AMISEARCH]

• copy this pyami.ini to your Home.

Run util.py in my case at path C:\Users\talha\openDiagram\physchem\python on commandline or PyCharm(I used pycharm).

C:\Users\talha\AppData\Local\Programs\Python\Python39\python.exe C:/Users/talha/openDiagram/physchem/python/util.py
read pyami.ini C:\Users\talha\pyami.ini
dict key dict_dir
dict key ov_ini
dictionary ini file ov_ini /Users/talha/dictionary/openvirus20210120/amidict.ini
read pyami.ini /Users/talha/dictionary/openvirus20210120/amidict.ini
country entries 263 wikidata 263 
      Created from SPARQL query
disease entries 13845 wikidata 13845 
      Created from SPARQL query
no desc
organization entries 17724 wikidata 17724 
      Created from SPARQL query
no desc
dict key cev_ini
dictionary ini file cev_ini /Users/talha/CEVOpen/dictionary/amidict.ini
read pyami.ini /Users/talha/CEVOpen/dictionary/amidict.ini
dict_ref file does not exist \Users\talha\CEVOpen\dictionary\eoActivity\eoActivity.xml
eo_analysis_method entries 117 wikidata 0 
      A dictionary of 117 entries describing instruments and methods used to [separate](https://en.wikipedia.org/wiki/Separation_process), identify, and [quantify](https://en.wikipedia.org/wiki/Quantification_(science)) matter — 105 being resolved to wikidata IDs, and 95 with short descriptions.
eo_compound entries 2114 wikidata 0 
      A dictionary of 2114 constituent chemical compounds extracted from Essential Oils converted from essoldb1.0 data
eo_extraction_method entries 89 wikidata 0 
      A dictionary of 87 terms related to Essential Oil extraction methods
dict_ref file does not exist \Users\talha\CEVOpen\dictionary\eoGene\eoGene.xml
eo_plant entries 1678 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_material_history entries 81 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the **1678** entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_part entries 383 wikidata 0 
      a dictionary of 285 terms relating to plant parts used for essential oil extraction
eo_target_organism entries 307 wikidata 0 
      A dictionary of 307 target organisms resolved to wikidataIDs, including genus and species of bacteria, fungi, protist, protozoa, and other microorgnisms.
invasive_species entries 19 wikidata 0 
      Created from SPARQL query
pests entries 1032 wikidata 0 
       A dictionary of 1032 terms for two categories of insects: A) Insect vectors of human pathogens sourced from https://en.wikipedia.org/wiki/Category:Insect_vectors_of_human_pathogens, and B) Winged insects soursed from https://www.insectidentification.org/winged-insect-key.asp.
plant_genus entries 25917 wikidata 25917 
      Created from SPARQL query
dict key tigr2ess_ini
dictionary ini file tigr2ess_ini /Users/talha/tigr2ess/dictionaries/examples/amidict.ini
INI file does not exist, needs creating /Users/talha/tigr2ess/dictionaries/examples/amidict.ini
dict key battery_ini
dictionary ini file battery_ini /Users/talha/open-battery/dictionary/amidict.ini
INI file does not exist, needs creating /Users/talha/open-battery/dictionary/amidict.ini
dict key ami3_urlini
*_urlini not yet implemented
dicts None

Process finished with exit code 0

Tester 4: Vasant Kumar

OS: Windows 10

Date: 03/10/2021

Prerequisites

• Update the repositries CEVOpen, dictionary, Opendiagram using command git pull in command line.

Open pyami.inifile (\openDiagram\physchem\python\pyami.ini)

• Open pyami.ini file C:\Users\vasan\openDiagram\physchem\python.
• Make changes to the path of .ini file to your HOME in my case: \Users\vasan.

 NOTE. All files use forward slash
; use slash (/) to separate filename components, we will convert to file-separator automatically

[DIRS]
home = /Users/vasan
dictionary_url = https://github.com/petermr/dictionary
project_dir = ${home}

[URLS]
petermr_url = https://github.com/petermr
petermr_raw_url = https://raw.githubusercontent.com/petermr

[PROJECTS]
cev_open = ${DIRS:project_dir}/CEVOpen
open_battery = ${DIRS:project_dir}/open-battery
pr_liion = ${open_battery}/liion
tigr2ess = ${DIRS:project_dir}/tigr2ess
tigr2ess_url = https://github.com/petermr/tigr2ess/tree/master
open_diagram = ${DIRS:project_dir}/openDiagram
open_virus = ${DIRS:project_dir}/openVirus

[PYAMIGETPAPERS]
max = 200

[DICTIONARIES]
dict_dir = ${DIRS:home}/dictionary

ov_ini = ${dict_dir}/openvirus20210120/amidict.ini
cev_ini = ${PROJECTS:cev_open}/dictionary/amidict.ini
tigr2ess_ini = ${PROJECTS:tigr2ess}/dictionaries/examples/amidict.ini
battery_ini = ${PROJECTS:open_battery}/dictionary/amidict.ini

ami3_urlini = ${URLS:petermr_raw_url}/ami3/master/src/main/resources/org/contentmine/ami/plugins/dictionary/amidict.ini

[AMISEARCH]

• copy pyami.ini to your Home.

Run util.py C:\Users\vasan\openDiagram\physchem\python PyCharm.

C:\Users\vasan\anaconda3\python.exe C:/Users/vasan/openDiagram/physchem/python/util.py
read pyami.ini C:\Users\vasan\pyami.ini
dict key dict_dir
dict key ov_ini
dictionary ini file ov_ini /Users/vasan/dictionary/openvirus20210120/amidict.ini
INI file does not exist, needs creating /Users/vasan/dictionary/openvirus20210120/amidict.ini
dict key cev_ini
dictionary ini file cev_ini /Users/vasan/CEVOpen/dictionary/amidict.ini
read pyami.ini /Users/vasan/CEVOpen/dictionary/amidict.ini
dict_ref file does not exist \Users\vasan\CEVOpen\dictionary\eoActivity\eoActivity.xml
eo_analysis_method entries 117 wikidata 0 
      A dictionary of 117 entries describing instruments and methods used to [separate](https://en.wikipedia.org/wiki/Separation_process), identify, and [quantify](https://en.wikipedia.org/wiki/Quantification_(science)) matter — 105 being resolved to wikidata IDs, and 95 with short descriptions.
eo_compound entries 2114 wikidata 0 
      A dictionary of 2114 constituent chemical compounds extracted from Essential Oils converted from essoldb1.0 data
eo_extraction_method entries 89 wikidata 0 
      A dictionary of 87 terms related to Essential Oil extraction methods
dict_ref file does not exist \Users\vasan\CEVOpen\dictionary\eoGene\eoGene.xml
eo_plant entries 1678 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_material_history entries 81 wikidata 0 
      A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the **1678** entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs
eo_plant_part entries 383 wikidata 0 
      a dictionary of 285 terms relating to plant parts used for essential oil extraction
eo_target_organism entries 307 wikidata 0 
      A dictionary of 307 target organisms resolved to wikidataIDs, including genus and species of bacteria, fungi, protist, protozoa, and other microorgnisms.
invasive_species entries 19 wikidata 0 
      Created from SPARQL query
pests entries 1032 wikidata 0 
       A dictionary of 1032 terms for two categories of insects: A) Insect vectors of human pathogens sourced from https://en.wikipedia.org/wiki/Category:Insect_vectors_of_human_pathogens, and B) Winged insects soursed from https://www.insectidentification.org/winged-insect-key.asp.
plant_genus entries 25917 wikidata 25917 
      Created from SPARQL query
dict key tigr2ess_ini
dictionary ini file tigr2ess_ini /Users/vasan/tigr2ess/dictionaries/examples/amidict.ini
INI file does not exist, needs creating /Users/vasan/tigr2ess/dictionaries/examples/amidict.ini
dict key battery_ini
dictionary ini file battery_ini /Users/vasan/open-battery/dictionary/amidict.ini
INI file does not exist, needs creating /Users/vasan/open-battery/dictionary/amidict.ini
dict key ami3_urlini
*_urlini not yet implemented
dicts None
Process finished with exit code 0