| Name | harmonize-wq JSON |
| Version |
0.3.0
JSON |
| download |
| home_page | |
| Summary | Package to standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats |
| upload_time | 2023-07-10 22:26:11 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | Creative Commons Legal Code CC0 1.0 Universal CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER. Statement of Purpose The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others. For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights. 1. Copyright and Related Rights. A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following: i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; ii. moral rights retained by the original author(s) and/or performer(s); iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work; iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below; v. rights protecting the extraction, dissemination, use and reuse of data in a Work; vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof. 2. 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Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose. 3. Public License Fallback. Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose. 4. Limitations and Disclaimers. a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document. b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law. c. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work. |
| keywords |
usepa
water data
water quality
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
pandas
geopandas
pint
dataretrieval
descartes
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# harmonize-wq
Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats
US EPA’s [Water Quality Portal (WQP)](https://www.waterqualitydata.us/) aggregates water quality, biological, and physical data provided by many organizations and has become an essential resource with tools to query and retrieval data using [python](https://github.com/USGS-python/dataretrieval) or [R](https://github.com/USGS-R/dataRetrieval). Given the variety of data and variety of data originators, using the data in analysis often requires data cleaning to ensure it meets the required quality standards and data wrangling to get it in a more analytic-ready format. Recognizing the definition of analysis-ready varies depending on the analysis, the harmonixe_wq package is intended to be a flexible water quality specific framework to help:
- Identify differences in data units (including speciation and basis)
- Identify differences in sampling or analytic methods
- Resolve data errors using transparent assumptions
- Transform data from long to wide format
Domain experts must decide what data meets their quality standards for data comparability and any thresholds for acceptance or rejection.
For more complete tutorial information, see: [demos](https://github.com/USEPA/harmonize-wq/tree/main/demos)
## Quick Start
harmonize_wq can be installed from git using pip:
```
pip install git+https://github.com/USEPA/harmonize-wq.git
```
## Example Workflow
### dataretrieval Query for a geojson
```python
import dataretrieval.wqp as wqp
from harmonize_wq import wrangle
# File for area of interest
aoi_url = r'https://github.com/USEPA/harmonize-wq/raw/master/harmonize_wq/tests/data/PPBays_NCCA.geojson'
# Build query
query = {'characteristicName': ['Temperature, water',
'Depth, Secchi disk depth',
]}
query['bBox'] = wrangle.get_bounding_box(aoi_url)
query['dataProfile'] = 'narrowResult'
# Run query
res_narrow, md_narrow = wqp.get_results(**query)
# dataframe of downloaded results
res_narrow
```
### Harmonize results
```python
from harmonize_wq import harmonize
# Harmonize all results
df_harmonized = harmonize.harmonize_all(res_narrow, errors='raise')
df_harmonized
```
### Clean results
```python
from harmonize_wq import clean
# Clean up other columns of data
df_cleaned = clean.datetime(df_harmonized) # datetime
df_cleaned = clean.harmonize_depth(df_cleaned) # Sample depth
df_cleaned
```
### Transform results from long to wide format
There are many columns in the dataframe that are characteristic specific, that is they have different values for the same sample depending on the characteristic. To ensure one result for each sample after the transformation of the data these columns must either be split, generating a new column for each characteristic with values, or moved out from the table if not being used.
```python
from harmonize_wq import wrangle
# Split QA column into multiple characteristic specific QA columns
df_full = wrangle.split_col(df_cleaned)
# Divide table into columns of interest (main_df) and characteristic specific metadata (chars_df)
main_df, chars_df = wrangle.split_table(df_full)
# Combine rows with the same sample organization, activity, location, and datetime
df_wide = wrangle.collapse_results(main_df)
```
The number of columns in the resulting table is greatly reduced
Output Column | Type | Source | Changes
--- | --- | --- | ---
MonitoringLocationIdentifier | Defines row | MonitoringLocationIdentifier | NA
Activity_datetime | Defines row | ActivityStartDate, ActivityStartTime/Time, ActivityStartTime/TimeZoneCode | Combined and UTC
ActivityIdentifier | Defines row | ActivityIdentifier | NA
OrganizationIdentifier | Defines row | OrganizationIdentifier | NA
OrganizationFormalName | Metadata| OrganizationFormalName | NA
ProviderName | Metadata | ProviderName | NA
StartDate | Metadata | ActivityStartDate | Preserves date where time NAT
Depth | Metadata | ResultDepthHeightMeasure/MeasureValue, ResultDepthHeightMeasure/MeasureUnitCode | standardized to meters
Secchi | Result | ResultMeasureValue, ResultMeasure/MeasureUnitCode | standardized to meters
QA_Secchi | QA | NA | harmonization processing quality issues
Temperature | Result | ResultMeasureValue, ResultMeasure/MeasureUnitCode | standardized to degrees Celcius
QA_Temperature | QA | NA | harmonization processing quality issues
## Issue Tracker
harmonize_wq is under development. Please report any bugs and enhancement ideas using the issue track:
https://github.com/USEPA/harmonize-wq/issues
## Disclaimer
The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.
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"description": "# harmonize-wq\r\nStandardize, clean and wrangle Water Quality Portal data into more analytic-ready formats\r\n\r\nUS EPA\u2019s [Water Quality Portal (WQP)](https://www.waterqualitydata.us/) aggregates water quality, biological, and physical data provided by many organizations and has become an essential resource with tools to query and retrieval data using [python](https://github.com/USGS-python/dataretrieval) or [R](https://github.com/USGS-R/dataRetrieval). Given the variety of data and variety of data originators, using the data in analysis often requires data cleaning to ensure it meets the required quality standards and data wrangling to get it in a more analytic-ready format. Recognizing the definition of analysis-ready varies depending on the analysis, the harmonixe_wq package is intended to be a flexible water quality specific framework to help:\r\n- Identify differences in data units (including speciation and basis)\r\n- Identify differences in sampling or analytic methods\r\n- Resolve data errors using transparent assumptions\r\n- Transform data from long to wide format\r\n\r\nDomain experts must decide what data meets their quality standards for data comparability and any thresholds for acceptance or rejection.\r\n\r\nFor more complete tutorial information, see: [demos](https://github.com/USEPA/harmonize-wq/tree/main/demos)\r\n\r\n## Quick Start\r\nharmonize_wq can be installed from git using pip:\r\n```\r\npip install git+https://github.com/USEPA/harmonize-wq.git\r\n```\r\n\r\n## Example Workflow\r\n### dataretrieval Query for a geojson\r\n\r\n```python\r\nimport dataretrieval.wqp as wqp\r\nfrom harmonize_wq import wrangle\r\n\r\n# File for area of interest\r\naoi_url = r'https://github.com/USEPA/harmonize-wq/raw/master/harmonize_wq/tests/data/PPBays_NCCA.geojson'\r\n\r\n# Build query\r\nquery = {'characteristicName': ['Temperature, water',\r\n 'Depth, Secchi disk depth',\r\n ]}\r\nquery['bBox'] = wrangle.get_bounding_box(aoi_url)\r\nquery['dataProfile'] = 'narrowResult'\r\n\r\n# Run query\r\nres_narrow, md_narrow = wqp.get_results(**query)\r\n\r\n# dataframe of downloaded results\r\nres_narrow\r\n```\r\n\r\n### Harmonize results\r\n\r\n```python\r\nfrom harmonize_wq import harmonize\r\n\r\n# Harmonize all results\r\ndf_harmonized = harmonize.harmonize_all(res_narrow, errors='raise')\r\ndf_harmonized\r\n```\r\n\r\n### Clean results\r\n\r\n```python\r\nfrom harmonize_wq import clean\r\n\r\n# Clean up other columns of data\r\ndf_cleaned = clean.datetime(df_harmonized) # datetime\r\ndf_cleaned = clean.harmonize_depth(df_cleaned) # Sample depth\r\ndf_cleaned\r\n```\r\n\r\n### Transform results from long to wide format\r\nThere are many columns in the dataframe that are characteristic specific, that is they have different values for the same sample depending on the characteristic. To ensure one result for each sample after the transformation of the data these columns must either be split, generating a new column for each characteristic with values, or moved out from the table if not being used.\r\n\r\n```python\r\nfrom harmonize_wq import wrangle\r\n\r\n# Split QA column into multiple characteristic specific QA columns\r\ndf_full = wrangle.split_col(df_cleaned)\r\n\r\n# Divide table into columns of interest (main_df) and characteristic specific metadata (chars_df)\r\nmain_df, chars_df = wrangle.split_table(df_full)\r\n\r\n# Combine rows with the same sample organization, activity, location, and datetime\r\ndf_wide = wrangle.collapse_results(main_df)\r\n\r\n```\r\n\r\nThe number of columns in the resulting table is greatly reduced\r\n\r\nOutput Column | Type | Source | Changes\r\n--- | --- | --- | ---\r\nMonitoringLocationIdentifier | Defines row | MonitoringLocationIdentifier | NA \r\nActivity_datetime | Defines row | ActivityStartDate, ActivityStartTime/Time, ActivityStartTime/TimeZoneCode | Combined and UTC\r\nActivityIdentifier | Defines row | ActivityIdentifier | NA\r\nOrganizationIdentifier | Defines row | OrganizationIdentifier | NA \r\nOrganizationFormalName | Metadata| OrganizationFormalName | NA\r\nProviderName | Metadata | ProviderName | NA\r\nStartDate | Metadata | ActivityStartDate | Preserves date where time NAT\r\nDepth | Metadata | ResultDepthHeightMeasure/MeasureValue, ResultDepthHeightMeasure/MeasureUnitCode | standardized to meters\r\nSecchi | Result | ResultMeasureValue, ResultMeasure/MeasureUnitCode | standardized to meters\r\nQA_Secchi | QA | NA | harmonization processing quality issues\r\nTemperature | Result | ResultMeasureValue, ResultMeasure/MeasureUnitCode | standardized to degrees Celcius\r\nQA_Temperature | QA | NA | harmonization processing quality issues\r\n\r\n## Issue Tracker\r\nharmonize_wq is under development. Please report any bugs and enhancement ideas using the issue track:\r\nhttps://github.com/USEPA/harmonize-wq/issues\r\n\r\n\r\n## Disclaimer\r\nThe United States Environmental Protection Agency (EPA) GitHub project code is provided on an \"as is\" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.\r\n",
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Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works (\"Commons\") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others. For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the \"Affirmer\"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights. 1. Copyright and Related Rights. A Work made available under CC0 may be protected by copyright and related or neighboring rights (\"Copyright and Related Rights\"). Copyright and Related Rights include, but are not limited to, the following: i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; ii. moral rights retained by the original author(s) and/or performer(s); iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work; iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below; v. rights protecting the extraction, dissemination, use and reuse of data in a Work; vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof. 2. Waiver. To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the \"Waiver\"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose. 3. Public License Fallback. Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the \"License\"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose. 4. Limitations and Disclaimers. a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document. b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law. c. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work. ",
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