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Sshade-csv2xml.ipynb
View file @ a2af762c
......@@ -2,12 +2,12 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import sys\n",
"sys.path.append(\"/mntdirect/_users/letard/Jupyter/Scripts/Sshade\")\n",
"sys.path.append(\"/home/kieffer/Isabelle/local/sshade/sshade\")\n",
"import csv2xml\n",
"csv2xml?\n",
"#csv2xml.experiments_file_writer?"
......@@ -15,11 +15,12 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"my_directory = \"/users/letard/Jupyter/Sshade/DataTestemale/Cu2005_v7\""
"my_directory = \"/home/kieffer/Isabelle/DataSshade/Bissardon_Se2015\"\n",
"#my_directory = \"/home/kieffer/Isabelle/local/sshade/Data/Testemale_Cu2005\""
]
},
{
......@@ -28,7 +29,8 @@
"metadata": {},
"outputs": [],
"source": [
"csv2xml.ods_converter(my_directory,\"20190417_Cu_v7.ods\")"
"csv2xml.ods_converter(my_directory,\"Bissardon_Se_2019_v7.ods\")\n",
"#csv2xml.ods_converter(my_directory,\"20190417_Cu_v7.ods\")"
]
},
{
......@@ -37,7 +39,7 @@
"metadata": {},
"outputs": [],
"source": [
"csv2xml.multiple_file_writer(my_directory,\"frozen_solution\")"
"csv2xml.multiple_file_writer(my_directory,\"experimentalist\")"
]
},
{
......@@ -87,17 +89,17 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"FILE experiments_spectra_DT_20050706_001.xml ALREADY EXISTS\n",
"FILE experiments_spectra_CB_20190408_001.xml ALREADY EXISTS\n",
"Do you want to overwrite it? y\n",
"\n",
"=== The file experiments_spectra_DT_20050706_001.xml has been written in /mntdirect/_users/letard/Jupyter/Sshade/DataTestemale/Cu2005_v7. ===\n"
"=== The file experiments_spectra_CB_20190408_001.xml has been written in /home/kieffer/Isabelle/DataSshade/Bissardon_Se2015. ===\n"
]
}
],
......@@ -138,7 +140,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.1"
}
},
"nbformat": 4,
......
Templates/experimentalist.xml
View file @ a2af762c
<?xml version="1.0" encoding="UTF-8"?>
<import type="experimentalist" ssdm_version="0.8.4">
<experimentalist>
<import_mode>first import</import_mode>
<uid>EXPER_$$$</uid> <!-- Ex: EXPER_Denis_Testemale -->
<manager_databases>
<database_uid>DB_FAME</database_uid>
</manager_databases>
<first_name>$$$</first_name>
<family_name>$$$</family_name>
<acronym>$$$</acronym> <!-- Ex: DT -->
<orcid_identifier>$$$</orcid_identifier> <!-- Ex: 0000-0003-2204-5464 ou NULL -->
<!-- EXPERIMENTALIST LABORATORIES -->
<laboratories>
<laboratory state="current">
<uid>LAB_$$$</uid>
<status>$$$</status>
<date_begin>$$$</date_begin>
<date_end>$$$</date_end>
</laboratory>
</laboratories>
<email>$$$</email>
</experimentalist>
<import type="experimentalist" ssdm_version="0.9.0">
<experimentalist>
<import_mode>first import</import_mode>
<uid>EXPER_$$$</uid> <!-- Ex: EXPER_Denis_Testemale -->
<manager_databases>
<database_uid>DB_FAME</database_uid>
</manager_databases>
<first_name>$$$</first_name>
<family_name>$$$</family_name>
<acronym>$$$</acronym> <!-- Ex: DT -->
<orcid_identifier>$$$</orcid_identifier> <!-- Ex: 0000-0003-2204-5464 ou NULL -->
<!-- EXPERIMENTALIST LABORATORIES -->
<laboratories>
<laboratory state="current">
<uid>LAB_$$$</uid>
<status>$$$</status>
<date_begin>$$$</date_begin>
<date_end>$$$</date_end>
</laboratory>
</laboratories>
<email>$$$</email>
</experimentalist>
</import>
\ No newline at end of file
Templates/experiments_spectra.xml
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Templates/laboratory.xml
View file @ a2af762c
<?xml version="1.0" encoding="UTF-8"?>
<import type="laboratory" ssdm_version="0.9.0">
<!-- All the $$$ should be replaced -->
<import type="laboratory" ssdm_version="0.8.3">
<laboratory>
<import_mode>first import</import_mode>
<uid>LAB_$$$</uid> <!-- Ex: LAB_SYMMES -->
......
Templates/manip_test_vide.ods 100755 → 100644
View file @ a2af762c
No preview for this file type
Templates/sample_HPHT_solution.xml
View file @ a2af762c
<?xml version="1.0" encoding="UTF-8"?>
<import type="sample" ssdm_version="0.8.3">
<sample><!-- multiple -->
<import_mode>$$$</import_mode> <!-- sample import_mode -->
<uid>SAMPLE_DT_20161207_001</uid> <!-- sample uid - Ex: SAMPLE_OP_20180717_001 -->
<owner_databases>
<database_uid>DB_FAME</database_uid>
</owner_databases>
<provider><![CDATA[]]></provider> <!-- sample provider -->
<experimentalists> <!-- Ex: EXPER_Olivier_Proux -->
<experimentalist_uid>$$$</experimentalist_uid>
</experimentalists>
<name>$$$</name> <!-- sample name -->
<date>$$$</date> <!-- Ex: 2006-09-02 -->
<is_generic>no</is_generic>
<surface_roughness>NULL</surface_roughness>
<size_unit>mm</size_unit>
<volume>$$$</volume> <!-- in mm3 -->
<substrate_material>NULL</substrate_material>
<parameters_environment>
<time_unit>min</time_unit>
<temperature>
<unit>C</unit>
<value>20</value>
<error>5</error>
<time>10000</time>
<max>20</max>
</temperature>
<pressure>
<unit>bar</unit>
<value>1</value>
<time>10000</time>
<max>1</max>
</pressure>
<fluid>
<type>ambient air</type>
<temperature>20</temperature>
</fluid>
</parameters_environment>
<publications>
<publication_uid>$$$</publication_uid>
</publications>
<layers>
<layer>
<import_mode>$$$</import_mode> <!-- layer import_mode -->
<name>$$$</name> <!-- layer name -->
<order>1</order>
<type>fluid</type>
<thickness>4</thickness>
<thickness_error>0.1</thickness_error>
<texture>liquid</texture>
<porosity_type>other</porosity_type>
<compacity>1</compacity>
<density>$$$</density> <!-- Density of the layer [Float] (g/cm3) -->
<formation_mode>NULL</formation_mode>
<formation_temperature>NULL</formation_temperature>
<formation_pressure>NULL</formation_pressure>
<materials_mixing>single material</materials_mixing>
<materials>
<material>
<import_mode>first import</import_mode> <!-- material import_mode -->
<uid>$$$</uid> <!-- material uid - Ex: MATERIAL_OP_20180717_001 -->
<mass_fraction>1</mass_fraction>
<mass_fraction_error>NULL</mass_fraction_error>
<name>$$$</name> <!-- material name -->
<origin>laboratory</origin> <!-- Enum: {natural terrestrial, extraterrestrial, laboratory, commercial, simulated} -->
<constituents_mixing>single phase</constituents_mixing>
<constituents>
<constituent>
<import_mode>first import</import_mode> <!-- constituent import_mode -->
<uid>$$$</uid> <!-- constituent uid - Ex: CONST_OP_20180717_001 -->
<arrangement>single phase</arrangement>
<mass_fraction>1</mass_fraction>
<mass_fraction_error>NULL</mass_fraction_error>
<name>$$$></name> <!-- constituent name -->
<family>liquid solution</family>
<class>hydrogen bonded molecular liquid</class>
<compound_type>liquid solution</compound_type>
<isotope_mixture_type>terrestrial abundance</isotope_mixture_type>
<phase_type>liquid</phase_type>
<texture>liquid</texture>
<species>
<specie>
<family>$$$</family>
<uid>$$$</uid>
<state>$$$</state>
<relevance>$$$</relevance>
<mass>$$$</mass>
<mass_error>$$$</mass_error>
<mole>$$$</mole>
<mole_error>$$$</mole_error>
<comments><![CDATA[$$$]]></comments>
</specie>
</species>
</constituent>
</constituents>
</material>
</materials>
</layer>
</layers>
</sample>
</import>
<import type="sample" ssdm_version="0.9.0">
<sample><!-- multiple -->
<import_mode>$$$</import_mode> <!-- sample import_mode -->
<uid>SAMPLE_DT_20161207_001</uid> <!-- sample uid - Ex: SAMPLE_OP_20180717_001 -->
<owner_databases>
<database_uid>DB_FAME</database_uid>
</owner_databases>
<provider><![CDATA[]]></provider> <!-- sample provider -->
<experimentalists> <!-- Ex: EXPER_Olivier_Proux -->
<experimentalist_uid>$$$</experimentalist_uid>
</experimentalists>
<name>$$$</name> <!-- sample name -->
<date>$$$</date> <!-- Ex: 2006-09-02 -->
<is_generic>no</is_generic>
<surface_roughness>NULL</surface_roughness>
<size_unit>mm</size_unit>
<volume>$$$</volume> <!-- in mm3 -->
<substrate_material>NULL</substrate_material>
<parameters_environment>
<time_unit>min</time_unit>
<temperature>
<unit>C</unit>
<value>20</value>
<error>5</error>
<max>20</max>
</temperature>
<fluid>
<type>ambient air</type>
<temperature>20</temperature>
<pressure_unit>bar</pressure_unit>
<pressure>1</pressure>
</fluid>
</parameters_environment>
<publications>
<publication_uid>$$$</publication_uid>
</publications>
<layers>
<layer>
<import_mode>$$$</import_mode> <!-- layer import_mode -->
<name>$$$</name> <!-- layer name -->
<order>1</order>
<type>fluid</type>
<thickness>4</thickness>
<thickness_error>0.1</thickness_error>
<texture>liquid</texture>
<porosity_type>other</porosity_type>
<compacity>1</compacity>
<density>$$$</density> <!-- Density of the layer [Float] (g/cm3) -->
<formation_mode>NULL</formation_mode>
<formation_temperature>NULL</formation_temperature>
<formation_pressure>NULL</formation_pressure>
<materials_mixing>single material</materials_mixing>
<materials>
<material>
<import_mode>first import</import_mode> <!-- material import_mode -->
<uid>$$$</uid> <!-- material uid - Ex: MATERIAL_OP_20180717_001 -->
<relevance>main - major</relevance>
<mass_fraction>1</mass_fraction>
<mass_fraction_error>NULL</mass_fraction_error>
<name>$$$</name> <!-- material name -->
<family>fluid</family> <!-- Enum: {solid, mineral, carbonaceous, extraterrestrial, fluid, mixed, other, unknown} -->
<origin>laboratory</origin> <!-- Enum: {natural terrestrial, extraterrestrial, laboratory, commercial, simulated} -->
<constituents_mixing>single phase</constituents_mixing>
<constituents>
<constituent>
<import_mode>first import</import_mode> <!-- constituent import_mode -->
<uid>$$$</uid> <!-- constituent uid - Ex: CONST_OP_20180717_001 -->
<relevance>main - major</relevance>
<arrangement>single phase</arrangement>
<mass_fraction>1</mass_fraction>
<mass_fraction_error>NULL</mass_fraction_error>
<name>$$$></name> <!-- constituent name -->
<family>liquid solution</family>
<class>hydrogen bonded molecular liquid</class>
<compound_type>liquid solution</compound_type>
<isotope_mixture_type>terrestrial abundance</isotope_mixture_type>
<phase_type>liquid</phase_type>
<texture>liquid</texture>
<species>
<specie>
<family>$$$</family>
<uid>$$$</uid>
<state>$$$</state>
<relevance>$$$</relevance>
<mass>$$$</mass>
<mass_error>$$$</mass_error>
<mole>$$$</mole>
<mole_error>$$$</mole_error>
<comments><![CDATA[$$$]]></comments>
</specie>
</species>
</constituent>
</constituents>
</material>
</materials>
</layer>
</layers>
</sample>
</import>
Templates/sample_frozen_solution.xml
View file @ a2af762c
<?xml version="1.0" encoding="UTF-8"?>
<!-- All the $$$ should be replaced -->
<!-- All the @@@ should be replaced by the sample name -->
<import type="sample" ssdm_version="0.8.4">
<sample><!-- multiple -->
<import_mode>first import</import_mode> <!-- sample import_mode -->
<uid>SAMPLE_$$$</uid> <!-- sample uid - Ex: SAMPLE_OP_20180717_001 -->
<owner_databases>
<database_uid>DB_FAME</database_uid>
</owner_databases>
<provider><![CDATA[]]></provider> <!-- sample provider -->
<experimentalists> <!-- Ex: EXPER_Olivier_Proux -->
<experimentalist_uid>$$$</experimentalist_uid>
</experimentalists>
<!-- SAMPLE NAME and REFERENCES -->
<name>Frozen solution of @@@</name> <!-- sample name -->
<date>$$$</date> <!-- Ex: 2006-09-02 -->
<is_generic>no</is_generic>
<surface_roughness>NULL</surface_roughness>
<size_unit>mm</size_unit>
<substrate_material>NULL</substrate_material>
<parameters_environment>
<time_unit>min</time_unit>
<temperature>
<unit>K</unit>
<value>77</value>
<error>5</error>
<time>5</time>
<max>77</max>
</temperature>
<pressure>
<unit>bar</unit>
<value>1</value>
<time>5</time>
<max>1</max>
</pressure>
<fluid>
<type>molecular liquid</type>
<temperature>77</temperature>
<composition_species>
<composition_specie>
<uid>MOLEC_N2</uid>
<mole_fraction>1</mole_fraction>
</composition_specie>
</composition_species>
<comments><![CDATA[Stored in liquid nitrogen]]></comments> <!-- parameters_environment comments -->
</fluid>
</parameters_environment>
<layers>
<layer>
<import_mode>first import</import_mode> <!-- layer import_mode -->
<name>Frozen solution of @@@</name> <!-- layer name -->
<order>1</order>
<type>compact</type>
<thickness>2</thickness>
<thickness_error>0.2</thickness_error>
<texture>compact glassy</texture>
<porosity_type>without pores</porosity_type>
<compacity>1</compacity>
<density>1</density>
<formation_mode>freezing of a liquid solution</formation_mode>
<formation_temperature>77</formation_temperature>
<formation_pressure>1</formation_pressure>
<formation_comments><![CDATA[Liquid drop frozen over a liquid nitrogen bath and stored in it]]></formation_comments>
<materials_mixing>single material</materials_mixing>
<materials>
<material>
<import_mode>first import</import_mode> <!-- material import_mode -->
<uid>MATERIAL_$$$</uid> <!-- material uid - Ex: MATERIAL_OP_20180717_001 -->
<mass_fraction>1</mass_fraction> <!-- material mass fraction -->
<mass_fraction_error>NULL</mass_fraction_error> <!-- material mass fraction error -->
<name>Frozen solution of @@@</name> <!-- material name -->
<origin>$$$</origin> <!-- Enum: {natural terrestrial, extraterrestrial, laboratory, commercial, simulated} -->
<bulk_density>1</bulk_density>
<comments><![CDATA[$$$]]></comments> <!-- material comments - Ex: prepared in glove box -->
<publications>
<publication_uid>PUBLI_$$$</publication_uid>
</publications>
<constituents_mixing>single phase</constituents_mixing>
<constituents>
<constituent>
<import_mode>first import</import_mode> <!-- constituent import_mode -->
<uid>CONST_$$$</uid> <!-- constituent uid - Ex: CONST_OP_20180717_001 -->
<name>Frozen solution of @@@</name> <!-- constituent name -->
<arrangement>single phase</arrangement>
<mass_fraction>1</mass_fraction>
<mass_fraction_error>NULL</mass_fraction_error>
<family>molecular solid</family>
<class>hydrogen bonded molecular solid</class>
<relevance>main - major</relevance>
<compound_type>molecular solid solution</compound_type>
<isotope_mixture_type>terrestrial abundance</isotope_mixture_type>
<phase_type>amorphous</phase_type>
<texture>amorphous</texture>
<!-- SPECIES -->
<species>
<specie>
<family>$$$</family>
<uid>$$$</uid>
<state>$$$</state>
<relevance>$$$</relevance>
<mass>$$$</mass>
<mass_error>$$$</mass_error>
<mole>$$$</mole>
<mole_error>$$$</mole_error>
<comments><![CDATA[$$$]]></comments>
</specie>
</species>
</constituent>
</constituents>
</material>
</materials>
</layer>
</layers>
</sample>
</import>
<import type="sample" ssdm_version="0.9.0">
<sample><!-- multiple -->
<import_mode>first import</import_mode> <!-- sample import_mode -->
<uid>SAMPLE_$$$</uid> <!-- sample uid - Ex: SAMPLE_OP_20180717_001 -->
<owner_databases>
<database_uid>DB_FAME</database_uid>
</owner_databases>
<provider><![CDATA[]]></provider> <!-- sample provider -->
<experimentalists> <!-- Ex: EXPER_Olivier_Proux -->
<experimentalist_uid>$$$</experimentalist_uid>
</experimentalists>
<!-- SAMPLE NAME and REFERENCES -->
<name>Frozen solution of @@@</name> <!-- sample name -->
<date>$$$</date> <!-- Ex: 2006-09-02 -->
<is_generic>no</is_generic>
<surface_roughness>NULL</surface_roughness>
<size_unit>mm</size_unit>
<substrate_material>NULL</substrate_material>
<parameters_environment>
<time_unit>min</time_unit>
<temperature>
<unit>K</unit>
<value>77</value>
</temperature>
<fluid>
<type>molecular liquid</type>
<temperature>77</temperature>
<pressure_unit>bar</pressure_unit>
<pressure>1</pressure>
<composition_species>
<composition_specie>
<uid>MOLEC_N2</uid>
<mole_fraction>1</mole_fraction>
</composition_specie>
</composition_species>
<comments><![CDATA[Stored in liquid nitrogen]]></comments> <!-- parameters_environment comments -->
</fluid>
</parameters_environment>
<layers>
<layer>
<import_mode>first import</import_mode> <!-- layer import_mode -->
<name>Frozen solution of @@@</name> <!-- layer name -->
<order>1</order>
<type>compact</type>
<thickness>2</thickness>
<thickness_error>0.2</thickness_error>
<texture>compact glassy</texture>
<porosity_type>without pores</porosity_type>
<compacity>1</compacity>
<density>1</density>
<formation_mode>freezing of a liquid solution</formation_mode>
<formation_temperature>77</formation_temperature>
<formation_pressure>1</formation_pressure>
<formation_comments><![CDATA[Liquid drop frozen over a liquid nitrogen bath and stored in it]]></formation_comments>
<materials_mixing>single material</materials_mixing>
<materials>
<material>
<import_mode>first import</import_mode> <!-- material import_mode -->
<uid>MATERIAL_$$$</uid> <!-- material uid - Ex: MATERIAL_OP_20180717_001 -->
<relevance>main - major</relevance>
<mass_fraction>1</mass_fraction> <!-- material mass fraction -->
<mass_fraction_error>NULL</mass_fraction_error> <!-- material mass fraction error -->
<name>Frozen solution of @@@</name> <!-- material name -->
<origin>$$$</origin> <!-- Enum: {natural terrestrial, extraterrestrial, laboratory, commercial, simulated} -->
<family>solid</family> <!-- Enum: {solid, mineral, carbonaceous, extraterrestrial, fluid, mixed, other, unknown} -->
<bulk_density>1</bulk_density>
<comments><![CDATA[$$$]]></comments> <!-- material comments - Ex: prepared in glove box -->
<publications>
<publication_uid>PUBLI_$$$</publication_uid>
</publications>
<constituents_mixing>single phase</constituents_mixing>
<constituents>
<constituent>
<import_mode>first import</import_mode> <!-- constituent import_mode -->
<uid>CONST_$$$</uid> <!-- constituent uid - Ex: CONST_OP_20180717_001 -->
<name>Frozen solution of @@@</name> <!-- constituent name -->
<relevance>main - major</relevance>
<arrangement>single phase</arrangement>
<mass_fraction>1</mass_fraction>
<mass_fraction_error>NULL</mass_fraction_error>
<family>molecular solid</family>
<class>hydrogen bonded molecular solid</class>
<compound_type>molecular solid solution</compound_type>
<isotope_mixture_type>terrestrial abundance</isotope_mixture_type>
<phase_type>amorphous</phase_type>
<texture>amorphous</texture>
<!-- SPECIES -->
<species>
<specie>
<family>$$$</family>
<uid>$$$</uid>
<state>$$$</state>
<relevance>$$$</relevance>
<mass>$$$</mass>
<mass_error>$$$</mass_error>
<mole>$$$</mole>
<mole_error>$$$</mole_error>
<comments><![CDATA[$$$]]></comments>
</specie>
</species>
</constituent>
</constituents>
</material>
</materials>
</layer>
</layers>
</sample>
</import>
Templates/sample_pellet.xml
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sshade/csv2xml.py
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