harmonize-wq 0.3.0__tar.gz

harmonize_wq-0.3.0/LICENSE

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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+CC0 1.0 Universal
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+culture and the further production of creative, cultural and scientific
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+For these and/or other purposes and motivations, and without any
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+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.
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+1. Copyright and Related Rights. A Work made available under CC0 may be
+protected by copyright and related or neighboring rights ("Copyright and
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+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
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+ iv. rights protecting against unfair competition in regards to a Work,
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+  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
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+vii. other similar, equivalent or corresponding rights throughout the
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+2. Waiver. To the greatest extent permitted by, but not in contravention
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+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
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+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
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+person a royalty-free, non transferable, non sublicensable, non exclusive,
+irrevocable and unconditional license to exercise Affirmer's Copyright and
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+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
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+    party to this document and has no duty or obligation with respect to
+    this CC0 or use of the Work.

harmonize_wq-0.3.0/PKG-INFO

@@ -0,0 +1,245 @@
+Metadata-Version: 2.1
+Name: harmonize_wq
+Version: 0.3.0
+Summary: Package to standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats
+Author-email: Justin Bousquin <Bousquin.Justin@epa.gov>
+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. 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.
+        
+Project-URL: Homepage, https://github.com/USEPA/harmonize-wq
+Project-URL: Documentation, https://usepa.github.io/harmonize-wq/
+Project-URL: Bug Tracker, https://github.com/USEPA/harmonize-wq/issues
+Keywords: USEPA,water data,water quality
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Provides-Extra: doc
+License-File: LICENSE
+
+# 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.

harmonize_wq-0.3.0/README.md

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+# 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.

harmonize_wq-0.3.0/harmonize_wq/__init__.py

@@ -0,0 +1,11 @@
+from harmonize_wq import harmonize
+
+try:
+  from importlib.metadata import version, PackageNotFoundError
+except ImportError:
+  from importlib_metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version('harmonize_wq')
+except PackageNotFoundError:
+    __version__ = "version-unknown"